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The rising incidence of cancer underscores the imperative for innovative diagnostic and prognostic methodologies. This study delves into the potential of RNA-Seq gene expression data to enhance cancer classification accuracy. Introducing a pioneering approach, we model gene expression data as point clouds, capitalizing on the data's intrinsic properties to bolster classification performance. Utilizing PointNet, a typical technique for processing point cloud data, as our framework's cornerstone, we incorporate inductive biases pertinent to gene expression and pathways. This integration markedly elevates model efficacy, culminating in developing an end-to-end deep learning classifier with an accuracy rate surpassing 99%. Our findings not only illuminate the capabilities of AI-driven models in the realm of oncology but also highlight the criticality of acknowledging biological dataset nuances in model design. This research provides insights into application of deep learning in medical science, setting the stage for further innovation in cancer classification through sophisticated biological data analysis. The source code for our study is accessible at: https://github.com/cialab/GPNet. [ABSTRACT FROM AUTHOR]

BACKGROUND: Alicyclobacillus acidoterrestris is a common microorganism in fruit juice. It can produce off‐odor metabolites and has been considered to be an important factor in juice contamination. Thus, the development of new strategy for the control of A. acidoterrestris has important practical significance. The primary objective of this work was to assess the antibacterial performance of ε‐polylysine‐functionalized magnetic composites (Fe3O4@MoS2@PAA‐EPL) in apple juice and its effect on juice quality. Moreover, the molecular mechanism of Fe3O4@MoS2@PAA‐EPL against A. acidoterrestris was explored by RNA sequencing (RNA‐Seq). RESULTS: Experimental results indicated that the synthesized composites possessed the ability to inhibit the viability of A. acidoterrestris vegetative cells and spores. Besides, investigation on the quality of apple juice incubated with Fe3O4@MoS2@PAA‐EPL implied that the fabricated composites displayed negligible adverse effects on juice quality. In addition, the results of RNA‐Seq demonstrated that 833 differentially expressed genes (DEGs) were identified in Fe3O4@MoS2@PAA‐EPL‐treated A. acidoterrestris, which were associated with translation, energy metabolism, amino acid metabolism, membrane transport and cell integrity. CONCLUSION: These results suggested that the treatment of Fe3O4@MoS2@PAA‐EPL disrupted energy metabolism, repressed cell wall synthesis and caused membrane transport disorder of bacterial cells. This work provides novel insights into the molecular antibacterial mechanism for ε‐polylysine‐functionalized magnetic composites against A. acidoterrestris. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Background: With the improvement of living standards, the quality of chicken has become a significant concern. Chinese Dagu Chicken (dual-purpose type) and Arbor Acres plus broiler (AA+ broiler) (meat-type) were selected as the research subjects in this study, the meat quality of the breast and leg muscles were measured. However, the molecular mechanism(s) underlying regulation of muscle development are not yet fully elucidated. Therefore, finding molecular markers or major genes that regulate muscle quality has become a crucial breakthrough in chicken breeding. Unraveling the molecular mechanism behind meat traits in chicken and other domestic fowl is facilitated by identifying the key genes associated with these developmental events. Here, a comparative transcriptomic analysis of chicken meat was conducted on breast muscles (BM) and leg muscles (LM) in AA+ broilers (AA) and Dagu chicken (DG) to explore the differences in their meat traits employing RNA-seq. Results: Twelve cDNA libraries of BM and LM from AA and DG were constructed from four experimental groups, yielding 14,464 genes. Among them, Dagu chicken breast muscles (DGB) vs AA+ broilers breast muscles (AAB) showed 415 upregulated genes and 449 downregulated genes, Dagu chicken leg muscles (DGL) vs AA+ broilers leg muscles (AAL) exhibited 237 upregulated genes and 278 downregulated genes, DGL vs DGB demonstrated 391 upregulated genes and 594 downregulated genes, and AAL vs AAB displayed 122 upregulated genes and 154 downregulated genes. 13 genes, including nine upregulated genes (COX5A, COX7C, NDUFV1, UQCRFS1, UQCR11, BRT-1, FGF14, TMOD1, MYOZ2) and four downregulated genes (MYBPC3, MYO7B, MTMR7, and TNNC1), were found to be associated with the oxidative phosphorylation signaling pathway. Further analysis revealed that the differentially expressed genes (DEGs) from muscle were enriched in various pathways, such as metabolic pathways, oxidative phosphorylation, carbon metabolism, glycolysis, extracellular matrix-receptor interaction, biosynthesis of amino acids, focal adhesion, vascular smooth muscle contraction, and cardiac muscle contraction, all of which are involved in muscle development and metabolism. This study also measured the meat quality of the breast and leg muscles from the two breeds, which demonstrated superior overall meat quality in Chinese Dagu Chicken compared to the AA+ broiler. Conclusions: Our findings show that the meat quality of dual-purpose breeds (Chinese Dagu chicken) is higher than meat-type (AA+ broiler), which may be related to the DEGs regulating muscle development and metabolism. Our findings also provide transcriptomic insights for a comparative analysis of molecular mechanisms underlying muscle development between the two breeds, and have practical implications for the improvement of chicken breeding practices. [ABSTRACT FROM AUTHOR]

Overflow metabolism is a well-known phenomenon that describes the seemingly wasteful and incomplete substrate oxidation by aerobic cells, such as yeasts, bacteria, and mammalian cells, even when conditions allow for total combustion via respiration. This cellular response, triggered by an excess of C-source, has not yet been investigated in archaea. In this study, we conducted chemostat cultivations to compare the metabolic and physiological states of the thermoacidophilic archaeon Sulfolobus acidocaldarius under three conditions, each with gradually increasing nutrient stress. Our results show that S. acidocaldarius has different capacities for the uptake of the two C-sources, monosodium glutamate and glucose. A saturated tricarboxylic acid cycle at elevated nutrient concentrations affects the cell's ability to deplete its intermediates. This includes deploying additional cataplerotic pathways and the secretion of amino acids, notably valine, glycine, and alanine, while glucose is increasingly metabolized via glycogenesis. We did not observe the secretion of common fermentation products, like organic acids. Transcriptomic analysis indicated an upregulation of genes involved in fatty acid metabolism, suggesting the intracellular conservation of energy. Adapting respiratory enzymes under nutrient stress indicated high metabolic flexibility and robust regulatory mechanisms in this archaeon. This study enhances our fundamental understanding of the metabolism of S. acidocaldarius. [ABSTRACT FROM AUTHOR]

Maternal nutrition significantly influences fetal development and postnatal outcomes. This study investigates the impact of maternal overfeeding during mid to late pregnancy on gene expression in the round and sirloin muscles of Hanwoo neonatal calves. Eight cows were assigned to either a control group receiving standard nutrition (100%) or a treated group receiving overnutrition (150%). After birth, tissue samples from the round and sirloin muscles of neonatal calves were collected and subjected to RNA sequencing to assess differentially expressed genes (DEGs). RNA sequencing identified 43 DEGs in round muscle and 15 in sirloin muscle, involving genes related to myogenesis, adipogenesis, and energy regulation. Key genes, including PPARGC1A, THBS1, CD44, JUND, CNN1, ENAH, and RUNX1, were predominantly downregulated. Gene ontology (GO) enrichment analyses revealed terms associated with muscle development, such as "biological regulation," "cellular process," and "response to stimulus." Protein-protein interaction networks highlighted complex interactions among DEGs. Random Forest analysis identified ARC, SLC1A5, and GNPTAB as influential genes for distinguishing between control and treated groups. Overall, maternal overnutrition during mid-to-late pregnancy results in the downregulation of genes involved in muscle development and energy metabolism in neonatal Hanwoo calves. These findings provide insights into the molecular effects of maternal nutrition on muscle development. [ABSTRACT FROM AUTHOR]

Prostate cancer, the most common malignancy in men, has a relatively favourable prognosis. However, when it spreads to the bone, the survival rate drops dramatically. The development of bone metastases leaves patients with aggressive prostate cancer, the leading cause of death in men. Moreover, bone metastases are incurable and very painful. Hepatocyte growth factor receptor (MET) and fusion of genes encoding E26 transformation‐specific (ETS) transcription factors are both involved in the progression of the disease. ETS gene fusions, in particular, have the ability to induce the migratory and invasive properties of prostate cancer cells, whereas MET receptor, through its signalling cascades, is able to activate transcription factor expression. MET signalling and ETS gene fusions are intimately linked to high‐grade prostate cancer. However, the collaboration of these factors in prostate cancer progression has not yet been investigated. Here, we show, using cell models of advanced prostate cancer, that ETS translocation variant 1 (ETV1) and transcriptional regulator ERG (ERG) transcription factors (members of the ETS family) promote tumour properties, and that activation of MET signalling enhances these effects. By using a specific MET tyrosine kinase inhibitor in a humanised hepatocyte growth factor (HGF) mouse model, we also establish that MET activity is required for ETV1/ERG‐mediated tumour growth. Finally, by performing a comparative transcriptomic analysis, we identify target genes that could play a relevant role in these cellular processes. Thus, our results demonstrate for the first time in prostate cancer models a functional interaction between ETS transcription factors (ETV1 and ERG) and MET signalling that confers more aggressive properties and highlight a molecular signature characteristic of this combined action. [ABSTRACT FROM AUTHOR]

Bioconversion of abundant lactose-replete whey permeate to value-added chemicals holds promise for valorization of this expanding food processing waste. Efficient conversion of whey permeate-borne lactose requires adroit microbial engineering to direct carbon to the desired chemical. An engineered strain of Clostridium beijerinckii NCIMB 8052 (C. beijerinckii_mgsA+mgR) that produces 87% more butanol on lactose than the control strain was assessed for global transcriptomic changes. The results revealed broadly contrasting gene expression patterns in C. beijerinckii_mgsA+mgR relative to the control strain. These were characterized by widespread decreases in the abundance of mRNAs of Fe-S proteins in C. beijerinckii_ mgsA+mgR, coupled with increased differential expression of lactose uptake and catabolic genes, iron uptake genes, two-component signal transduction and motility genes, and genes involved in the biosynthesis of vitamins B5 and B12, aromatic amino acids (particularly tryptophan), arginine, and pyrimidines. Conversely, the mRNA patterns suggest that the L-aspartate-dependent de novo biosynthesis of NAD as well as biosynthesis of lysine and asparagine and metabolism of glycine and threonine were likely down-regulated. Furthermore, genes involved in cysteine and methionine biosynthesis and metabolism, including cysteine desulfurase--a central player in Fe-S cluster biosynthesis--equally showed reductions in mRNA abundance. Genes involved in biosynthesis of capsular polysaccharides and stress response also showed reduced mRNA abundance in C. beijerinckii_mgsA+mgR. The results suggest that remodeling of cellular and metabolic networks in C. beijerinckii_mgsA+mgR to counter anticipated effects of methylglyoxal production from heterologous expression of methylglyoxal synthase led to enhanced growth and butanol production in C. beijerinckii_mgsA+mgR. IMPORTANCE Biological production of commodity chemicals from abundant waste streams such as whey permeate represents an opportunity for decarbonizing chemical production. Whey permeate remains a vastly underutilized feedstock for bioproduction purposes. Thus, enhanced understanding of the cellular and metabolic repertoires of lactose-mediated production of chemicals such as butanol promises to identify new targets that can be fine tuned in recombinant and native microbial strains to engender stronger coupling of whey permeate-borne lactose to value-added chemicals. Our results highlight new genetic targets for future engineering of C. beijerinckii for improved butanol production on lactose and ultimately in whey permeate. [ABSTRACT FROM AUTHOR]

BACKGROUND: Garlic is a promising source of antimicrobial peptide separation, and chemical modification is an effective method for activity improvement. The present study aimed to improve the antifungal activity of a peptide extracted from garlic. Chemical modifications were conducted, and the structure–activity relationship and antifungal mechanism were investigated. RESULTS: The results indicated that the cationic charge induced by Lys residue at the N‐terminal was important for the antimicrobial activity, and the modified sequence exhibited significant antifungal activity with low mammalian toxicity and a low tendency of drug resistance (p < 0.05). The structure–activity relationship analysis revealed that the modified active peptide had a predominant α‐helical structure and an inner cyclic correlation. Transcriptomic analysis showed that peptide KMLKKLFR (Lys‐Met‐Leu‐Lys‐Lyse‐Leu‐Phe‐Arg) affected the rRNA processing and carbon metabolism process of Candida albicans. In addition, the membrane potential study indicated a non‐membrane destruction mechanism, and molecular docking analysis and a DNA interaction assay suggested promising inner targets. CONCLUSION: The results of the present study indicate that chemical modification by amino acid substitution was effective for antimicrobial activity improvement. The present study would benefit future antimicrobial peptide development and suggests that garlic is a great source of antibacterial peptides and peptide template separations for coping with antibiotic resistance. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Sodium hypochlorite (NaClO) has been widely utilized since the initial outbreak of coronavirus disease (COVID-19). The widespread use of NaClO means that it can directly enter aquatic ecosystems through wastewater discharge. In this study, we analyzed the expression of PPAR-γ, FAS, and ACC1, which significantly increased in larval zebrafish following exposure to 300 μg/L NaClO for 7 days. Additionally, we examined the effects of high concentrations of NaClO on zebrafish through non-targeted lipidomics and transcriptomics. A total of 44 characteristic lipid molecules were identified using non-targeted lipidomics; an absolute quantitative analysis revealed that the contents of these subclasses of lipids decreased significantly following exposure to 300 μg/L NaClO for 7 days. The levels of triglyceride (TG), phosphatidylethanolamines (PE), and diglyceride (DG) were particularly affected. Transcriptomic analysis revealed that exposure to 300 μg/L NaClO could significantly disrupt global gene transcription in larval zebrafish. Interestingly, more than 700 differentially expressed genes (DEGs) were identified, primarily associated with lipid metabolism and glycometabolism pathways. Overall, our study provided new insights into the toxicological effects of chlorine-containing disinfectants in aquatic organisms. [ABSTRACT FROM AUTHOR]

Drought stress, as one of the most common environmental factors, seriously affects seed- ling establishment as well as plant growth and productivity. The growth of Toona ciliata is constrained by soil moisture deficit, and drought stress can reduce its productivity and limit its suitable growing environment. To explore the molecular mechanism of Toona ciliata responding to drought stress, leaves of two-year-old Toona ciliata seedlings were used as experimental materials for transcriptome sequencing and physiological index measurements. Under drought stress, the contents of Chl, MDA, POD, SP, SS, and RWC all change differently. We performed transcriptome sequencing, obtaining 4830 differential genes. The enrichment analysis indicates that the primary effects on the leaves of Toona ciliata under drought stress are related to photosynthesis and responses to plant hormone signal transduction. Transcription factor families associated with drought resistance include the NAC, WRKY, bZIP, bHLH, AP2-EREBP, C3H, GRAS, and FRAI transcription factor families. A weighted gene co-expression network analysis (WGCNA) analysis successfully identified 10 hub genes in response to drought stress in Toona ciliata leaves. Real-time quantitative PCR (RT-qPCR) validated the reliability of the transcriptomic data, and the analysis of its results showed a close correlation with the data obtained from RNA-seq. This study clarifies the transcriptional response of Toona ciliata to drought stress, contributing to the revelation of the molecular mechanisms of drought adaptation. [ABSTRACT FROM AUTHOR]

Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species. Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing germplasm innovation and ensuring sustainable development of the industry. Though numerous candidate genes have been identified, their functional validation remains challenging. Fortunately, the dwarf surf clam (Mulinia lateralis) serves as a promising model organism for investigating genetic mechanisms underlying growth regulation in bivalves. The GWAS study in the Yesso scallop (Patinopecten yessoensis) has pinpointed the E2F3 gene as a key regulator of growth-related traits. However, the specific role of E2F3 in bivalve growth remains unclear. This study aimed to further confirm the regulatory function of the E2F3 gene in the dwarf surf clam through RNA interference experiments. Our results revealed several genes are associated with individual growth and development, including CTS7, HSP70B2, and PGLYRP3, as well as genes involved in lipid metabolism such as FABP2 and FASN. Functional enrichment analysis indicated that E2F3 primarily modulates critical processes like amino acid and lipid metabolism. These findings suggest that E2F3 likely regulates growth in the dwarf surf clam by influencing amino acid and lipid metabolism. Overall, this study advances our understanding on the function of E2F3 gene in growth regulation in bivalves, providing valuable insights for future research in this field. [ABSTRACT FROM AUTHOR]

Drought is the primary abiotic stress limiting wheat growth and yield. Transcriptomic analysis can unravel innovative mechanisms of drought tolerance and putative tolerance genes. The current study employed meta-analysis and supervised machine learning approaches, including attribute weighting algorithms (AWAs) and models of decision trees, to identify the most informative genes associated with drought tolerance and assess their expression patterns in drought-sensitive and drought-tolerant cultivars. First, a meta-analysis of microarray data was performed separately for drought-tolerant and drought-sensitive cultivars to identify differentially expressed probe sets in drought-tolerant and drought-sensitive cultivars under stress conditions. Subsequently, 10 AWAs were implemented on the meta-analysis results to specify probe sets that differentiate between drought-tolerant and drought-sensitive cultivars. We identified 261 and 300 probe sets by at least four AWAs in control and drought stress conditions, respectively, as the probe sets associated with tolerance. For validation, the expression profiles of two candidate genes, DAD1, and MYB80, were evaluated by real-time PCR. According to the expression analysis results, DAD1 and MYB80 exhibited opposing expression trends in drought-sensitive and drought-tolerant cultivars, thus indicating their functions in wheat drought tolerance. The identification of key genes associated with drought tolerance in wheat cultivars, which has been achieved through our study, has important implications for breeding drought-resistant wheat cultivars and potential applications in agricultural practices. These genes can be specifically targeted in future breeding efforts. Altogether, the integrated approach could provide great potential to identify key genes in drought tolerance responses and predict drought resistance and sensitivity in various wheat cultivars. [ABSTRACT FROM AUTHOR]

Background: Nocardia, a rare but potentially fatal pathogen, can induce systemic infections with diverse manifestations. This study aimed to investigate the tissue and organ damage caused by Nocardia farcinica (N. farcinica) in mice via different infection routes, evaluate the resulting host immune responses, and assess its invasiveness in brain tissue. Methods: BALB/c mice were infected with N. farcinica through intranasal, intraperitoneal, and intravenous routes (doses: 1 × 10^8, 1 × 10^7, 1 × 10^7 CFU in 50 µl PBS). Over a 7-day period, body temperature, weight, and mortality were monitored, and samples were collected for histopathological analysis and bacterial load assessment. Serum was isolated for cytokine detection via ELISA. For RNA-seq analysis, mice were infected with 1 × 107 CFU through three infection routes, after which brain tissue was harvested. Results: Intraperitoneal and intravenous N. farcinica infections caused significant clinical symptoms, mortality, and neural disruption in mice, resulting in severe systemic infection. Conversely, intranasal infection primarily affected the lungs without causing significant damage to other organs. Intraperitoneal and intravenous infections significantly increased serum cytokines, particularly TNF-α and IFN-γ. RNA-seq analysis of brains from intravenously infected mice revealed significant differential gene expression, whereas the intranasal and intraperitoneal routes showed limited differences (only three genes). The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the intravenous group were primarily related to immune processes. Conclusion: The study demonstrated that intravenous N. farcinica infection induces significant clinical symptoms, triggers an inflammatory response, damages multiple organs, and leads to systemic infections. [ABSTRACT FROM AUTHOR]

Neurological disorders such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and schizophrenia are associated with altered neuronal excitability, resulting from dysfunctions in the molecular architecture and physiological regulation of ion channels and synaptic transmission. Ion channels and synapses are regarded as suitable therapeutic targets in modern pharmacology. Cannabinoids have received great attention as an original therapeutic approach for their effects on human health due to their ability to modulate the neurotransmitter release through interaction with the endocannabinoid system. In our study, we explored the effect of cannabinol (CBN) through next-generation sequencing analysis of NSC-34 cell physiology. Our findings revealed that CBN strongly influences the ontologies related to ion channels and synapse activity at all doses tested. Specifically, the genes coding for calcium and potassium voltage-gated channel subunits, and the glutamatergic and GABAergic receptors (Cacna1b, Cacna1h, Cacng8, Kcnc3, Kcnd1, Kcnd2, Kcnj4, Grik5, Grik1, Slc17a7, Gabra5), were up-regulated. Conversely, the genes involved into serotoninergic and cholinergic pathways (Htr3a, Htr3b, Htr1b, Chrna3, Chrnb2, Chrnb4), were down-regulated. These findings highlight the influence of CBN in the expression of genes involved into ion influx and synaptic transmission. [ABSTRACT FROM AUTHOR]

Background: Systemic Lupus Erythematosus (SLE) is acknowledged for its significant influence on systemic health. This study sought to explore potential crosstalk genes, pathways, and immune cells in the relationship between SLE and moyamoya disease (MMD). Methods: We obtained data on SLE and MMD from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify common genes. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on these shared genes. Hub genes were further selected through the least absolute shrinkage and selection operator (LASSO) regression, and a receiver operating characteristic (ROC) curve was generated based on the results of this selection. Finally, singlesample Gene Set Enrichment Analysis (ssGSEA) was utilized to assess the infiltration levels of 28 immune cells in the expression profile and their association with the identified hub genes. Results: By intersecting the important module genes from WGCNA with the DEGs, the study highlighted CAMP, CFD, MYO1F, CTSS, DEFA3, NLRP12, MAN2B1, NMI, QPCT, KCNJ2, JAML, MPZL3, NDC80, FRAT2, THEMIS2, CCL4, FCER1A, EVI2B, CD74, HLA-DRB5, TOR4A, GAPT, CXCR1, LAG3, CD68, NCKAP1L, TMEM33, and S100P as key crosstalk genes linking SLE and MMD. GO analysis indicated that these shared genes were predominantly enriched in immune system process and immune response. LASSO analysis identified MPZL3 as the optimal shared diagnostic biomarkers for both SLE and MMD. Additionally, the analysis of immune cell infiltration revealed the significant involvement of activation of T and monocytes cells in the pathogenesis of SLE and MMD. Conclusion: This study is pioneering in its use of bioinformatics tools to explore the close genetic relationship between MMD and SLE. The genes CAMP, CFD, MYO1F, CTSS, DEFA3, NLRP12, MAN2B1, NMI, QPCT, KCNJ2, JAML, MPZL3, NDC80, FRAT2, THEMIS2, CCL4, FCER1A, EVI2B, CD74, HLA-DRB5, TOR4A, GAPT, CXCR1, LAG3, CD68, NCKAP1L, TMEM33, and S100P have been identified as key crosstalk genes that connect MMD and SLE. Activation of T and monocytes cells-mediated immune responses are proposed to play a significant role in the association between MMD and SLE. [ABSTRACT FROM AUTHOR]

Legumes enhance pasture health and soil productivity by fixing atmospheric nitrogen and boosting soil microbiota. We investigated the effects of tropical pasture legumes, including butterfly pea (Clitoria ternatea), seca stylo (Stylosanthes scabra), desmanthus (Desmanthus virgatus), lablab (Lablab purpureus), and Wynn cassia (Chamaecrista rotundifolia), on the soil microbial community and buffel grass (Cenchrus ciliaris) gene expression. Additionally, we explored the impact of a phytogenic bioactive product (PHY) in the coculture system. A pot trial using soil enriched with cow paunch compost included four treatments: monoculture of buffel grass and five legume species with and without PHY supplementation and coculture of buffel grass with each legume species with and without PHY supplementation. Actinobacteriota and Firmicutes were the dominant bacterial phyla. Regardless of PHY application, the coculture of buffel grass with legumes positively influenced microbial composition and diversity. Transcriptomic analysis revealed significant gene expression changes in buffel grass shoots and roots, with each legume uniquely affecting nitrogen metabolism. Lablab and Wynn cassia exhibited similarities in modulating metabolic processes, butterfly pea contributed to mycotoxin detoxification, and desmanthus balanced cell death and growth. Seca stylo enhanced root cell growth and regeneration. These findings offer insights for optimizing legume–grass coculture systems, enhancing soil activity and promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

To explore the molecular mechanisms of the Litopenaeus vannamei response to infection by Photobacterium damselae, reveal its immune response and energetic metabolic effect, and provide a valuable genetic data source for the scientific prevention and control of Vibrio infection, transcriptomic analysis, RT-qPCR, and physiological and biochemical tests were conducted. The results showed that the expression of key genes involved in lipid and carbohydrate transport, such as apolipoprotein and TPS, was upregulated after pathogenic infection, which brought the accumulation of triacylglycerol and trehalose into the hemolymph. Additionally, the pathogenic infection selectively triggered an immune response in infected L. vannamei, activating certain immune pathways, such as the serpins and MAPK pathways. The pathogenic infection suppressed the activity of phenoloxidase (PO), and the prophenoloxidase (PPO) cascade responses were suppressed by the invasive bacteria. This paper will help us understand the energetic metabolism, immune response, and activation of the immune recognition response after pathogenic infection by P. damselae, and it lays a theoretical foundation for the biological prevention and control of P. damselae infection. [ABSTRACT FROM AUTHOR]

With the coming of the post‐antibiotic era, there is an increasingly urgent need for safe and efficient antibacterial vaccines. Bacterial outer membrane vesicles (OMVs) have received increased attention recently as a potential subunit vaccine. OMVs are non‐replicative and contain the principle immunogenic bacterial antigen, which circumvents the safety concerns of live‐attenuated vaccines. Here, we developed a novel nano‐vaccine by coating OMVs onto PEGylated nano‐Rehmannia glutinosa polysaccharide (pRL) in a structure consisting of concentric circles, resulting in a more stable vaccine with improved immunogenicity. The immunological function of the pRL‐OMV formulation was evaluated in vivo and in vitro, and the underlying mechanism was studied though transcriptomic analysis. The pRL‐OMV formulation significantly increased dendritic cell (DC) proliferation and cytokine secretion. Efficient phagocytosis of the formulation by DCs was accompanied by DC maturation. Further, the formulation demonstrated superior lymph node targeting, contributing to a potent mixed cellular response and bacterial‐specific antibody response against Bordetella bronchiseptica infection. Specifically, transcriptomic analysis revealed that the immune protection function correlated with T‐cell receptor signalling and Th1/Th2/Th17 differentiation, among other markers of enhanced immunological activity. These findings have implications for the future application of OMV‐coated nano‐carriers in antimicrobial immunotherapy. [ABSTRACT FROM AUTHOR]

With the growing dependence on lithium-ion batteries, there is an urgent need to understand the potential developmental toxicity of LiPF6, a key component of these batteries. Although lithium's toxicity is well-established, the biological toxicity of LiPF6 has been minimally explored. This study leverages the zebrafish model to investigate the developmental impact of LiPF6 exposure. We observed morphological abnormalities, reduced spontaneous movement, and decreased hatching and swim bladder inflation rates in zebrafish embryos, effects that intensified with higher LiPF6 concentrations. Whole-mount in situ hybridization demonstrated that the specific expression of the swim bladder outer mesothelium marker anxa5b was suppressed in the swim bladder region under LiPF6 exposure. Transcriptomic analysis disclosed an upregulation of apoptosis-related gene sets. Acridine orange staining further supported significant induction of apoptosis. These findings underscore the environmental and health risks of LiPF6 exposure and highlight the necessity for improved waste management strategies for lithium-ion batteries. [ABSTRACT FROM AUTHOR]

Understanding the brain's mechanisms in individuals with obesity is important for managing body weight. Prior neuroimaging studies extensively investigated alterations in brain structure and function related to body mass index (BMI). However, how the network communication among the large‐scale brain networks differs across BMI is underinvestigated. This study used diffusion magnetic resonance imaging of 290 young adults to identify links between BMI and brain network mechanisms. Navigation efficiency, a measure of network routing, was calculated from the structural connectivity computed using diffusion tractography. The sensory and frontoparietal networks indicated positive associations between navigation efficiency and BMI. The neurotransmitter association analysis identified that serotonergic and dopaminergic receptors, as well as opioid and norepinephrine systems, were related to BMI‐related alterations in navigation efficiency. The transcriptomic analysis found that genes associated with network routing across BMI overlapped with genes enriched in excitatory and inhibitory neurons, specifically, gene enrichments related to synaptic transmission and neuron projection. Our findings suggest a valuable insight into understanding BMI‐related alterations in brain network routing mechanisms and the potential underlying cellular biology, which might be used as a foundation for BMI‐based weight management. [ABSTRACT FROM AUTHOR]

Key message: Cd induces photosynthetic inhibition and oxidative stress damage in H. citrina, which mobilizes the antioxidant system and regulates the expression of corresponding genes to adapt to Cd and Pb stress. Cd and Pb are heavy metals that cause severe pollution and are highly hazardous to organisms. Physiological measurements and transcriptomic analysis were combined to investigate the effect of 5 mM Cd or Pb on Hemerocallis citrina Baroni. Cd significantly inhibited H. citrina growth, while Pb had a minimal impact. Both Cd and Pb suppressed the expression levels of key chlorophyll synthesis genes, resulting in decreased chlorophyll content. At the same time, Cd accelerated chlorophyll degradation. It reduced the maximum photochemical efficiency of photosystem (PS) II, damaging the oxygen-evolving complex and leading to thylakoid dissociation. In contrast, no such phenomena were observed under Pb stress. Cd also inhibited the Calvin cycle by down-regulating the expression of Rubisco and SBPase genes, ultimately disrupting the photosynthetic process. Cd impacted the light reaction processes by damaging the antenna proteins, PS II and PS I activities, and electron transfer rate, while the impact of Pb was weaker. Cd significantly increased reactive oxygen species and malondialdehyde accumulation, and inhibited the activities of antioxidant enzymes and the expression levels of the corresponding genes. However, H. citrina adapted to Pb stress by the recruitment of antioxidant enzymes and the up-regulation of their corresponding genes. In summary, Cd and Pb inhibited chlorophyll synthesis and hindered the light capture and electron transfer processes, with Cd exerting great toxicity than Pb. These results elucidate the physiological and molecular mechanisms by which H. citrina responds to Cd and Pb stress and provide a solid basis for the potential utilization of H. citrina in the greening of heavy metal-polluted lands. [ABSTRACT FROM AUTHOR]

Fish skin acts as the first immune barrier against pathogens from external environments. Recently, fish skin immunity research has gradually become a hot topic in aquaculture disease control. Interestingly, the skin can do air-breathing in some bimodal respiration fish. However, there is no comprehensive understanding of these two functions. In this study, the skin regeneration of loach (Paramisgurnus dabryanus) was investigated through morphological and histological observations. Then, original skins (OS) and the regenerated skins (RS) when their capillaries were the most abundant during healing, were collected for transcriptomic analysis. 285,899,386 clean reads with a total length of 42.34 Gb were obtained. A total of 1282 differentially expressed genes (DEGs) were detected, including 1030 DEGs up-regulated and 252 DEGs down-regulated in the comparison of RS vs. OS. Fc gamma R-mediated phagocytosis (containing gelsolin (Gsn)), chemokine signaling pathway (containing C--C motif chemokine ligand 28 (Ccl28)), and B cell receptor signaling pathway (containing CD80 molecule (Cd81)) were closely related to skin immune response of the loach. PI3K-Akt signaling pathway [containing fibronectin 1 (Fn1) and lysyl oxidase-like 2b (Loxl2b)], TGF-beta signaling pathway [containing thrombospondin 1 (Thbs1)], ECM-receptor interaction [containing integrin alpha 7 (Itga7), Itgb8, Itgb10 and Itgb5], and dilated cardiomyopathy [containing laminin subunit alpha1 (Lama1)] were closely associated with skin air-breathing of the loach. This study is conducive to explore the molecular mechanisms of skin immune response during its regeneration and air-breathing of bimodal respiration fish. This study will benefit for the aquaculture of P. dabryanus and its related species. [ABSTRACT FROM AUTHOR]

Research on bioactive compounds has grown recently due to their health benefits and limited adverse effects, particularly in reducing the risk of chronic diseases, including neurodegenerative conditions. According to these observations, this study investigates the activity of sulforaphane (RS-GRA) on an in vitro model of differentiated NSC-34 cells. We performed a transcriptomic analysis at various time points (24 h, 48 h, and 72 h) and RS-GRA concentrations (1 µM, 5 µM, and 10 µM) to identify molecular pathways influenced by this compound and the effects of dosage and prolonged exposure. We found 39 differentially expressed genes consistently up- or downregulated across all conditions. Notably, Nfe2l2, Slc1a5, Slc7a11, Slc6a9, Slc6a5, Sod1, and Sod2 genes were consistently upregulated, while Ripk1, Glul, Ripk3, and Mlkl genes were downregulated. Pathway perturbation analysis showed that the overall dysregulation of these genes results in a significant increase in redox pathway activity (adjusted p-value 1.11 × 10−3) and a significant inhibition of the necroptosis pathway (adjusted p-value 4.64 × 10−3). These findings suggest RS-GRA's potential as an adjuvant in neurodegenerative disease treatment, as both increased redox activity and necroptosis inhibition may be beneficial in this context. Furthermore, our data suggest two possible administration strategies, namely an acute approach with higher dosages and a chronic approach with lower dosages. [ABSTRACT FROM AUTHOR]

Acute myeloid leukaemia (AML) is a highly heterogeneous disease, which lead to various findings in transcriptomic research. This study addresses these challenges by integrating 34 datasets, including 26 control groups, 6 prognostic datasets and 2 single‐cell RNA sequencing (scRNA‐seq) datasets to identify 10,000 AML‐related genes (ARGs). We focused on genes with low variability and high consistency and successfully discovered 191 AML signatures (ASs). Leveraging machine learning techniques, specifically the XGBoost model and our custom framework, we classified AML subtypes with both scRNA‐seq and bulk RNA‐seq data, complementing the ELN2022 classification approach. Our research also identified promising treatments for AML through drug repurposing, with solasonine showing potential efficacy for high‐risk AML patients, supported by molecular docking and transcriptomic analyses. To enhance reproducibility and customizability, we developed CSAMLdb, a user‐friendly database platform. It facilitates the reuse and personalized analysis of nearly all results obtained in this research, including single‐gene prognostics, multi‐gene scoring, enrichment analysis, machine learning risk assessment, drug repositioning analysis and literature abstract named entity recognition. CSAMLdb is available at http://www.csamldb.com. [ABSTRACT FROM AUTHOR]

Abstract Background With the improvement of living standards, the quality of chicken has become a significant concern. Chinese Dagu Chicken (dual-purpose type) and Arbor Acres plus broiler (AA+ broiler) (meat-type) were selected as the research subjects in this study, the meat quality of the breast and leg muscles were measured. However, the molecular mechanism(s) underlying regulation of muscle development are not yet fully elucidated. Therefore, finding molecular markers or major genes that regulate muscle quality has become a crucial breakthrough in chicken breeding. Unraveling the molecular mechanism behind meat traits in chicken and other domestic fowl is facilitated by identifying the key genes associated with these developmental events. Here, a comparative transcriptomic analysis of chicken meat was conducted on breast muscles (BM) and leg muscles (LM) in AA+ broilers (AA) and Dagu chicken (DG) to explore the differences in their meat traits employing RNA-seq. Results Twelve cDNA libraries of BM and LM from AA and DG were constructed from four experimental groups, yielding 14,464 genes. Among them, Dagu chicken breast muscles (DGB) vs AA+ broilers breast muscles (AAB) showed 415 upregulated genes and 449 downregulated genes, Dagu chicken leg muscles (DGL) vs AA+ broilers leg muscles (AAL) exhibited 237 upregulated genes and 278 downregulated genes, DGL vs DGB demonstrated 391 upregulated genes and 594 downregulated genes, and AAL vs AAB displayed 122 upregulated genes and 154 downregulated genes. 13 genes, including nine upregulated genes (COX5A, COX7C, NDUFV1, UQCRFS1, UQCR11, BRT-1, FGF14, TMOD1, MYOZ2) and four downregulated genes (MYBPC3, MYO7B, MTMR7, and TNNC1), were found to be associated with the oxidative phosphorylation signaling pathway. Further analysis revealed that the differentially expressed genes (DEGs) from muscle were enriched in various pathways, such as metabolic pathways, oxidative phosphorylation, carbon metabolism, glycolysis, extracellular matrix-receptor interaction, biosynthesis of amino acids, focal adhesion, vascular smooth muscle contraction, and cardiac muscle contraction, all of which are involved in muscle development and metabolism. This study also measured the meat quality of the breast and leg muscles from the two breeds, which demonstrated superior overall meat quality in Chinese Dagu Chicken compared to the AA+ broiler. Conclusions Our findings show that the meat quality of dual-purpose breeds (Chinese Dagu chicken) is higher than meat-type (AA+ broiler), which may be related to the DEGs regulating muscle development and metabolism. Our findings also provide transcriptomic insights for a comparative analysis of molecular mechanisms underlying muscle development between the two breeds, and have practical implications for the improvement of chicken breeding practices.

Abstract Immune checkpoint inhibitors (ICIs) have transformed cancer treatment, providing significant benefit to patients across various tumour types, including melanoma. However, around 40% of melanoma patients do not benefit from ICI treatment, and accurately predicting ICI response remains challenging. We now describe a novel and simple approach that integrates immune-associated transcriptome signatures and tumour volume burden to better predict ICI response in melanoma patients. RNA sequencing was performed on pre-treatment (PRE) tumour specimens derived from 32 patients with advanced melanoma treated with combination PD1 and CTLA4 inhibitors. Of these 32 patients, 11 also had early during treatment (EDT, 5–15 days after treatment start) tumour samples. Tumour volume was assessed at PRE for all 32 patients, and at first computed tomography (CT) imaging for the 11 patients with EDT samples. Analysis of the Hallmark IFNγ gene set revealed no association with ICI response at PRE (AUC ROC curve = 0.6404, p = 0.24, 63% sensitivity, 71% specificity). When IFNg activity was evaluated with tumour volume (ratio of gene set expression to tumour volume) using logistic regression to predict ICI response, we observed high discriminative power in separating ICI responders from non-responders (AUC = 0.7760, p = 0.02, 88% sensitivity, 67% specificity); this approach was reproduced with other immune-associated transcriptomic gene sets. These findings were further replicated in an independent cohort of 23 melanoma patients treated with PD1 inhibitor. Hence, integrating tumour volume with immune-associated transcriptomic signatures improves the prediction of ICI response, and suggest that higher levels of immune activation relative to tumour burden are required for durable ICI response.

Abstract Maternal nutrition significantly influences fetal development and postnatal outcomes. This study investigates the impact of maternal overfeeding during mid to late pregnancy on gene expression in the round and sirloin muscles of Hanwoo neonatal calves. Eight cows were assigned to either a control group receiving standard nutrition (100%) or a treated group receiving overnutrition (150%). After birth, tissue samples from the round and sirloin muscles of neonatal calves were collected and subjected to RNA sequencing to assess differentially expressed genes (DEGs). RNA sequencing identified 43 DEGs in round muscle and 15 in sirloin muscle, involving genes related to myogenesis, adipogenesis, and energy regulation. Key genes, including PPARGC1A, THBS1, CD44, JUND, CNN1, ENAH, and RUNX1, were predominantly downregulated. Gene ontology (GO) enrichment analyses revealed terms associated with muscle development, such as “biological regulation,” “cellular process,” and “response to stimulus.” Protein-protein interaction networks highlighted complex interactions among DEGs. Random Forest analysis identified ARC, SLC1A5, and GNPTAB as influential genes for distinguishing between control and treated groups. Overall, maternal overnutrition during mid-to-late pregnancy results in the downregulation of genes involved in muscle development and energy metabolism in neonatal Hanwoo calves. These findings provide insights into the molecular effects of maternal nutrition on muscle development.

Abstract Background Nocardia, a rare but potentially fatal pathogen, can induce systemic infections with diverse manifestations. This study aimed to investigate the tissue and organ damage caused by Nocardia farcinica (N. farcinica) in mice via different infection routes, evaluate the resulting host immune responses, and assess its invasiveness in brain tissue. Methods BALB/c mice were infected with N. farcinica through intranasal, intraperitoneal, and intravenous routes (doses: 1 × 10^8, 1 × 10^7, 1 × 10^7 CFU in 50 µl PBS). Over a 7-day period, body temperature, weight, and mortality were monitored, and samples were collected for histopathological analysis and bacterial load assessment. Serum was isolated for cytokine detection via ELISA. For RNA-seq analysis, mice were infected with 1 × 107 CFU through three infection routes, after which brain tissue was harvested. Results Intraperitoneal and intravenous N. farcinica infections caused significant clinical symptoms, mortality, and neural disruption in mice, resulting in severe systemic infection. Conversely, intranasal infection primarily affected the lungs without causing significant damage to other organs. Intraperitoneal and intravenous infections significantly increased serum cytokines, particularly TNF-α and IFN-γ. RNA-seq analysis of brains from intravenously infected mice revealed significant differential gene expression, whereas the intranasal and intraperitoneal routes showed limited differences (only three genes). The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the intravenous group were primarily related to immune processes. Conclusion The study demonstrated that intravenous N. farcinica infection induces significant clinical symptoms, triggers an inflammatory response, damages multiple organs, and leads to systemic infections.

The single-function agents with wide-spectrum activity which tend to disturb the ecological balance of oral cavity cannot satisfy dental treatment need. A multi-functional agent with specifically targeted killing property and in situ remineralization is warranted for caries management. A novel multi-functional agent (8DSS-C8-P-113) consisting of three domains, i.e., a non-specific antimicrobial peptide (AMP) (P-113), a competence stimulating peptide (C8), and an enhancing remineralization domain (8DSS), is fabricated and evaluated in this study. The findings demonstrates that 2 μM mL−1 of 8DSS-C8-P-113 eliminates planktonic Streptococcus mutans (S. mutans) without disrupting the oral normal flora. At a concentration of 8 μM mL−1, it exhibits the ability to prevent S. mutans' adhesion. Furthermore, 8DSS-C8-P-113 self-assembles a hydrogel state at the higher concentration of 16 μM mL−1. This hydrogel self-adheres on the tooth surface, resisting acid attack, eradicating S. mutans’ biofilm, and inducing mineralization in order to facilitate the repair of demineralized dental hard tissue. Its significant effectiveness in reducing the severity of dental caries is also demonstrated in vivo in a rat model. This study suggests that the multi-functional bioactive AMP 8DSS-C8-P-113 is a promising agent to specifically target pathogen, prevent tooth demineralization, and effectively induce in situ bio-mimic remineralization for the management of dental caries.

Plant volatile organic compounds are an abundant resource that can be used to explore natural gaseous fungicides. Recently, we found that (E)-2-heptenal, a green leaf volatile, could effectively inhibit the growth of Aspergillus flavus, showing promise for application as a biofumigant to prevent grain spoilage by A. flavus. In this study, the inhibitory effects of (E)-2-heptenal on A. flavus spore germination and mechanisms underlying these effects were investigated through morphological, biochemical, and transcriptomic analyses. The minimum inhibitory concentration and minimum fungicidal concentration of (E)-2-heptenal for spore germination of A. flavus were 4.0 and 6.0 µL/mL, respectively. (E)-2-heptenal treatment resulted in irregularly deformed, collapsed, and ruptured surface morphology of A. flavus spores, as well as destroyed cell wall integrity and reduced ergosterol content in A. flavus spores. Transcriptomic analysis revealed 4,312 differentially expressed genes in A. flavus spores exposed to (E)-2-heptenal, including 1,913 upregulated and 2,399 downregulated genes; these genes were mainly involved in ribosome biogenesis, cell cycle, linoleic acid metabolism, MAPK signaling, nucleoplasmic transport, meiosis, lipoic acid metabolism, DNA replication, and pyruvate metabolism pathways. (E)-2-heptenal can induce reactive oxygen species accumulation and mitochondrial dysfunction in A. flavus spores in a dose-dependent manner. Besides, DNA damage and autophagy was observed in (E)-2-heptenal-treated A. flavus spores with 4′,6-diamidino-2-phenylindole and monodansylcadaverine fluorescence staining. The findings of the present study provide insights into the underlying inhibitory mechanisms of (E)-2-heptenal on A. flavus spore germination. [ABSTRACT FROM AUTHOR]

Abstract Phenylalanine ammonia lyase (PAL) is a widely studied enzyme in plant biology due to its role in connecting primary metabolism to secondary phenylpropanoid metabolism, significantly influencing plant growth, development, and stress response. Although PAL genes have been extensively studied in various plant species but their exploration in cucumber has been limited. This study successfully identified 11 CsPAL genes in Cucumis sativus (cucumber). These CsPAL genes were categorized based on their conserved sequences revealing patterns through MEME analysis and multiple sequence alignment. Interestingly, cis-elements related to stress were found in the promoter regions of CsPAL genes, indicating their involvement in responding to abiotic stress. Furthermore, these gene’s promoters contained components associated with light, development and hormone responsiveness. This suggests that they may have roles in hormone developmental processes. MicroRNAs were identified as a key regulators for the CsPAL genes, playing a crucial role in modulating their expression. This discovery underscores the complex regulatory network involved in the plant’s response to various stress conditions. The influence of these microRNAs further highlights the complicated mechanisms that plants use to manage stress. Gene expression patterns were analyzed using RNA-seq data. The significant upregulation of CsPAL9 during HT3h (heat stress for 3 h) and the heightened upregulation of both CsPAL9 and CsPAL7 under HT6h (heat stress for 6 h) in the transcriptome study suggest a potential role for these genes in cucumber’s tolerance to heat stress. This comprehensive investigation aims to enhance our understanding of the PAL gene family’s versatility, offering valuable insights for advancements in cucumber genetics.

Abstract Background Agar-like zona pellucida (ZP) is the most common type of abnormal ZP, and is one of the causes of low fertility or infertility. However, the molecular mechanism of agar-like ZP is unclear. Single-cell RNA-sequencing (scRNA-seq) analysis was used to assess the cellular and molecular landscape of oocytes with agar-like ZP. Methods Human metaphase I (MI) oocytes were collected from four patients with agar-like ZP and four healthy donors. Total RNA was isolated, cDNA was synthesized, and libraries were generated and subsequently sequenced on a HiSeq 2500 instrument. The scRNA-seq data were analyzed with R software. Results We identified 1320 genes that were differentially expressed between agar-like ZP oocytes and healthy donor oocytes. Gene Ontology term enrichment results showed that the genes downregulated in agar-like ZP oocytes were significantly related to extracellular matrix organization, while the genes upregulated in agar-like ZP oocytes were significantly related to the regulation of response to DNA damage stimulus. The Kyoto Encyclopedia of Genes and Genomes enrichment results showed that genes were enriched in the ECM-receptor interaction pathway and focal adhesion pathway. Other signaling pathways important in oocyte development were also enriched, such as PI3K-Akt. Differential expression analysis identified UBC, TLR4, RELA, ANXA5, CAV1, KPNA2, CCNA2, ACTA2, FYN and ITGB3 as genetic markers of oocytes with agar-like ZP. Conclusions Our findings suggest that agar-like ZP oocytes exhibit significant downregulation of genes involved in the ECM-receptor interaction signaling pathway and focal adhesion pathway, which could lead to aberrant ZP formation, while the upregulated genes were significantly related to regulation of the response to DNA damage stimulus. Agar-like ZP formation may interfere with the normal exchange of signals between oocytes and perivitelline granulosa cells, thereby preventing cumulus cells from participating in oocyte DNA damage repair and causing MI arrest.

Abstract Background LRRK2-targeting therapeutics that inhibit LRRK2 kinase activity have advanced to clinical trials in idiopathic Parkinson’s disease (iPD). LRRK2 phosphorylates Rab10 on endolysosomes in phagocytic cells to promote some types of immunological responses. The identification of factors that regulate LRRK2-mediated Rab10 phosphorylation in iPD, and whether phosphorylated-Rab10 levels change in different disease states, or with disease progression, may provide insights into the role of Rab10 phosphorylation in iPD and help guide therapeutic strategies targeting this pathway. Methods Capitalizing on past work demonstrating LRRK2 and phosphorylated-Rab10 interact on vesicles that can shed into biofluids, we developed and validated a high-throughput single-molecule array assay to measure extracellular pT73-Rab10. Ratios of pT73-Rab10 to total Rab10 measured in biobanked serum samples were compared between informative groups of transgenic mice, rats, and a deeply phenotyped cohort of iPD cases and controls. Multivariable and weighted correlation network analyses were used to identify genetic, transcriptomic, clinical, and demographic variables that predict the extracellular pT73-Rab10 to total Rab10 ratio. Results pT73-Rab10 is absent in serum from Lrrk2 knockout mice but elevated by LRRK2 and VPS35 mutations, as well as SNCA expression. Bone-marrow transplantation experiments in mice show that serum pT73-Rab10 levels derive primarily from circulating immune cells. The extracellular ratio of pT73-Rab10 to total Rab10 is dynamic, increasing with inflammation and rapidly decreasing with LRRK2 kinase inhibition. The ratio of pT73-Rab10 to total Rab10 is elevated in iPD patients with greater motor dysfunction, irrespective of disease duration, age, sex, or the usage of PD-related or anti-inflammatory medications. pT73-Rab10 to total Rab10 ratios are associated with neutrophil degranulation, antigenic responses, and suppressed platelet activation. Conclusions The extracellular serum ratio of pT73-Rab10 to total Rab10 is a novel pharmacodynamic biomarker for LRRK2-linked innate immune activation associated with disease severity in iPD. We propose that those iPD patients with higher serum pT73-Rab10 levels may benefit from LRRK2-targeting therapeutics that mitigate associated deleterious immunological responses.

Abstract Reducing the levels of dietary protein is an effective nutritional approach in lowering feed cost and nitrogen emissions in ruminants. The purpose of this study was to evaluate the effects of dietary Lys/Met ratio in a low protein diet (10%, dry matter basis) on the growth performance and hepatic function (antioxidant capacity, immune status, and glycolytic activity) in Tibetan lambs. Ninety two-month-old rams with an average weight of 15.37 ± 0.92 kg were randomly assigned to LP-L (dietary Lys/Met = 1:1), LP-M (dietary Lys/Met = 2:1) and LP-H (dietary Lys/Met = 3:1) treatments. The trial was conducted over 100 d, including 10 d of adaption to the diets. Hepatic phenotypes, antioxidant capacity, immune status, glycolytic activity and gene expression profiling was detected after the conclusion of the feeding trials. The results showed that the body weight was higher in the LP-L group when compared to those on the LP-M group (P 1). Gene Ontology (GO) and correlation analyses showed that in the LP-L group, core genes (C1QA and JUNB) enriched in oxidoreductase activity were positively correlated with antioxidant indicators, while the MYO9A core gene enriched in the immune response was positively associated with immune indicators, and core genes enriched in molecular function (PDK3 and PDP2) were positively correlated with glycolysis indicators. In summary, low-protein diet with a low Lys/Met ratio (1:1) could reduce the hepatic oxidative stress and improve the glycolytic activity by regulating the expression of related genes of Tibetan sheep.

Phenylalanine ammonia lyase (PAL) is a widely studied enzyme in plant biology due to its role in connecting primary metabolism to secondary phenylpropanoid metabolism, significantly influencing plant growth, development, and stress response. Although PAL genes have been extensively studied in various plant species but their exploration in cucumber has been limited. This study successfully identified 11 CsPAL genes in Cucumis sativus (cucumber). These CsPAL genes were categorized based on their conserved sequences revealing patterns through MEME analysis and multiple sequence alignment. Interestingly, cis-elements related to stress were found in the promoter regions of CsPAL genes, indicating their involvement in responding to abiotic stress. Furthermore, these gene's promoters contained components associated with light, development and hormone responsiveness. This suggests that they may have roles in hormone developmental processes. MicroRNAs were identified as a key regulators for the CsPAL genes, playing a crucial role in modulating their expression. This discovery underscores the complex regulatory network involved in the plant's response to various stress conditions. The influence of these microRNAs further highlights the complicated mechanisms that plants use to manage stress. Gene expression patterns were analyzed using RNA-seq data. The significant upregulation of CsPAL9 during HT3h (heat stress for 3 h) and the heightened upregulation of both CsPAL9 and CsPAL7 under HT6h (heat stress for 6 h) in the transcriptome study suggest a potential role for these genes in cucumber's tolerance to heat stress. This comprehensive investigation aims to enhance our understanding of the PAL gene family's versatility, offering valuable insights for advancements in cucumber genetics. [ABSTRACT FROM AUTHOR]

Background: Marinesco-Sjögren syndrome (MSS) is an autosomal recessive neuromuscular disorder that arises in early childhood and is characterized by congenital cataracts, myopathy associated with muscle weakness, and degeneration of Purkinje neurons leading to ataxia. About 60% of MSS patients have loss-of-function mutations in the SIL1 gene. Sil1 is an endoplasmic reticulum (ER) protein required for the release of ADP from the master chaperone Bip, which in turn will release the folded proteins. The expression of non-functional Sil1 leads to the accumulation of unfolded proteins in the ER and this triggers the unfolded protein response (UPR). A dysfunctional UPR could be a key element in the pathogenesis of MSS, although our knowledge of the molecular pathology of MSS is still incomplete. Methods: RNA-Seq transcriptomics was analysed using the String database and the Ingenuity Pathway Analysis platform. Fluorescence confocal microscopy was used to study the remodelling of the extracellular matrix (ECM). Transmission electron microscopy (TEM) was used to reveal the morphology of the ECM in vitro and in mouse tendon. Results: Our transcriptomic analysis, performed on patient-derived fibroblasts, revealed 664 differentially expressed (DE) transcripts. Enrichment analysis of DE genes confirmed that the patient fibroblasts have a membrane trafficking issue. Furthermore, this analysis indicated that the extracellular space/ECM and the cell adhesion machinery, which together account for around 300 transcripts, could be affected in MSS. Functional assays showed that patient fibroblasts have a reduced capacity of ECM remodelling, reduced motility, and slower spreading during adhesion to Petri dishes. TEM micrographs of negative-stained ECM samples from these fibroblasts show differences of filaments in terms of morphology and size. Finally, structural analysis of the myotendinous junction of the soleus muscle and surrounding regions of the Achilles tendon revealed a disorganization of collagen fibres in the mouse model of MSS (woozy). Conclusions: ECM alterations can affect the proper functioning of several organs, including those damaged in MSS such as the central nervous system, skeletal muscle, bone and lens. On this basis, we propose that aberrant ECM is a key pathological feature of MSS and may help explain most of its clinical manifestations. [ABSTRACT FROM AUTHOR]

Purpose: Alzheimer's disease (AD) is a common neurodegenerative disease, which can lead to cognitive impairment and dementia. Since AD is tightly associated with aging and cellular senescence, objective of this study was to investigate the association between senescence-related genes and proteins (SRGs and SRPs) and the development of AD. Design: The whole study was based on transcriptomic analysis of control and AD brain tissues and Mendelian randomization (MR) analysis. Methods: For transcriptomic analysis, GSE5281 dataset from GEO database contains the transcriptomic data of human brain tissues (n = 161) from control group and AD patients. The expression of SRGs in control and AD brain tissues were compared by Student's t test. For MR analysis, the instrumental singlenucleotide polymorphisms (SNPs) associated with 110 SRPs were filtered and selected from a large genome-wide association study (GWAS) for plasma proteome. The causality between plasma levels of SRPs and AD was explored using GWAS data of AD from Lambert et al. (17,008 cases and 37,154 controls) and further validated by using data from FinnGen consortium (6,489 patients and 170,489 controls). MR estimate was performed using the inversevariance weighted (IVW) method and the heterogeneity and pleiotropy of results were tested. Results: Transcriptomic analysis identified 36 up-regulated (including PLAUR) and 8 down-regulated SRGs in AD brain tissues. In addition, the MR results at both discovery and validation stages supported the causality between plasma levels of PLAUR (IVW-p = 3.04E-2, odds ratio [OR]= 1.15), CD55 (IVW-p = 1.56E-3, OR= 0.86), and SERPINE2 (IVW-p = 2.74E-2, OR= 0.91) and the risk of AD. Conclusion: Our findings identified that PLAUR, as an SRG, may take part in the development of AD and found that high plasma levels of PLAUR was associated with increased risk of AD, indicating that this gene was a risk factor for this disease and providing the rationale of existing drugs or new preventative and therapeutic strategies. [ABSTRACT FROM AUTHOR]

In this study, we report the interaction between an arbuscular mycorrhizal fungus, Septoglomus constrictum, and tomato plants under heat stress. For the first time, this interaction was studied by Illumina RNA-seq, followed by a comprehensive bioinformatic analysis that investigated root and leaf tissue samples. The genome-wide transcriptional profiling displayed fewer transcriptomic changes in the root under heat-stress conditions caused by S. constrictum. The top 50 DEGs suggested significant changes in the expression of genes encoding heat-shock proteins, transporter proteins, and genes of phytohormone metabolism involving jasmonic acid signalling. S. constrictum induced the upregulation of genes associated with pathways such as 'drought-responsive' and the 'development of root hair' in the root, as well as 'glycolipid desaturation', 'intracellular auxin transport', and 'ethylene biosynthesis' in the leaf. The pathways 'biotin biosynthesis' and 'threonine degradation' were found in both investigated tissue types. Expression analysis of transcription factors showed 2 and 11 upregulated transcription factors in heat-stressed root and leaf tissues, respectively. However, we did not find shared transcription factors. Heat-stressed arbuscular mycorrhizal plants suffered less oxidative stress when exposed to high temperatures. Colorimetric tests demonstrated less accumulation of H2O2 and MDA in heat-stressed mycorrhizal plants. This phenomenon was accompanied by the higher expression of six stress genes that encode peroxidases, glutathione S-transferase and ubiquitin carboxyl-terminal hydrolase in roots and leaves. Our findings provide a new perspective on elucidating the functional metabolic processes of tomato plants under mycorrhizal-heat stressed conditions. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria (LAB) are the most common probiotics, and they present excellent inhibitory effects on pathogenic bacteria. This study aimed to explore the anti-biofilm potential of the purified active substance of Lactiplantibacillus plantarum, named Z102-E. The effects of Z102-E on Listeria monocytogenes were investigated in detail, and a transcriptomic analysis was conducted to reveal the anti-biofilm mechanism. The results indicated that the sub-MIC of Z102-E (3.2, 1.6, and 0.8 mg/mL) decreased the bacterial growth and effectively reduced the self-aggregation, surface hydrophobicity, sugar utilization, motility, biofilm formation, AI-2 signal molecule, contents of extracellular polysaccharides, and extracellular protein of L. monocytogenes. Moreover, the inverted fluorescence microscopy observation confirmed the anti-biofilm effect of Z102-E. The transcriptomic analysis indicated that 117 genes were up-regulated and 214 were down-regulated. Z102-E regulated the expressions of genes related to L. monocytogenes quorum sensing, biofilm formation, etc. These findings suggested that Z102-E has great application potential as a natural bacteriostatic agent. [ABSTRACT FROM AUTHOR]

Background: Static tumor features before initiating anti-tumor treatment were insufficient to distinguish responding from non-responding tumors under the selective pressure of immuno-therapy. Herein we investigated the longitudinal dynamics of peripheral blood inflammatory indexes (dPBI) and its value in predicting major pathological response (MPR) in non-small cell lung cancer (NSCLC). Methods: A total of 147 patients with NSCLC who underwent neoadjuvant immunochemotherapy were retrospectively reviewed as training cohort, and 26 NSCLC patients from a phase II trial were included as validation cohort. Peripheral blood inflammatory indexes were collected at baseline and as posttreatment status; their dynamics were calculated as their posttreatment values minus their baseline level. Least absolute shrinkage and selection operator algorithm was utilized to screen out predictors for MPR, and a MPR score was integrated. We constructed a model incorporating this MPR score and clinical predictors for predicting MPR and evaluated its predictive capacity via the area under the curve (AUC) of the receiver operating characteristic and calibration curves. Furthermore, we sought to interpret this MPR score in the context of micro-RNA transcriptomic analysis in plasma exosomes for 12 paired samples (baseline and posttreatment) obtained from the training cohort. Results: Longitudinal dynamics of monocyte-lymphocyte ratio, platelet-tolymphocyte ratio, platelet-to-albumin ratio, and prognostic nutritional index were screened out as significant indicators for MPR and a MPR score was integrated, which was further identified as an independent predictor of MPR. Then, we constructed a predictive model incorporating MPR score, histology, and differentiated degree, which discriminated MPR and non-MPR patients well in both the training and validation cohorts with an AUC value of 0.803 and 0.817, respectively. Furthermore, micro-RNA transcriptomic analysis revealed the association between our MPR score and immune regulation pathways. A significantly better event-free survival was seen in subpopulations with a high MPR score. Conclusion: Our findings suggested that dPBI reflected responses to neoadjuvant immuno-chemotherapy for NSCLC. The MPR score, a noninvasive biomarker integrating their dynamics, captured the miRNA transcriptomic pattern in the tumor microenvironment and distinguished MPR from non-MPR for neoadjuvant immunochemotherapy, which could support the clinical decisions on the utilization of immune checkpoint inhibitor-based treatments in NSCLC patients. [ABSTRACT FROM AUTHOR]

Atractylodes lancea rhizomes (ARs) are rich in essential oil, which contains a high amount of volatile organic compounds (VOCs), especially sesquiterpenes. The essential oil of A. lancea has high medicinal and economic value. In this study, we investigated the impact of alteration in light quality on the production and composition of VOCs in A. lancea. We applied red light, blue light, and mixed red and blue light of different ratios (red : blue = 3:1, 6:1, and 9:1) treatment on A. lancea plantlets and analyzed their VOCs by gas chromatography-mass spectrometry (GC-MS). Our results showed that light quality mainly affected the production rather than the composition of VOCs in A. lancea. We identified a total of 27 VOCs in the rhizome, 13 of them were sesquiterpenes. The concentration of sesquiterpenes increased as the proportion of red light increased. We performed transcriptomic analysis and identified differentially expressed genes (DEGs) between the white light group (the control group) and the other groups. These DEGs were enriched in the following pathways: plant-pathogen interaction, endocytosis, plant hormone signal transduction, photosynthesis-antenna proteins, photosynthesis, and circadian rhythm. We analyzed the Pearson correlation between the relative expression of the DEGs and the concentration of the key medicinal component in ARs, atractylon, and verified gene expression by RT-qPCR. The results indicated that the genes WRKY2, and MYC2, HSPs, EBF1, SAUR72, PYL4, and MKK5 of the enriched pathways were positively associated with atractylon accumulation. [ABSTRACT FROM AUTHOR]

The multisystemic effects of COVID-19 may continue for a longer time period following the acute phase, depending on the severity of the disease. However, long-term systemic transcriptomic changes associated with COVID-19 disease and the impact of disease severity are not fully understood. We aimed to investigate the impact of COVID-19 and its severity on transcriptomic alterations in peripheral blood mononuclear cells (PBMCs) following 1 year of the disease. PBMCs were isolated from the peripheral blood of healthy control donors who did not have COVID-19 (C; n = 13), from COVID-19 patients without pneumonia (NP; n = 11), and from COVID-19 patients with severe pneumonia (SP; n = 10) after 1-year of follow-up. Following RNA isolation from PBMCs, high-quality RNAs were sequenced after creating a library. Differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElncRNAs) were identified using Benjamini–Hochberg correction and they were analysed for hierarchical clustering and principal component analysis (PCA). Intergroup comparisons (C vs. NP, C vs. SP, and NP vs. SP) of DEGs and DElncRNAs were performed and hub genes were determined. Functional enrichment analyses of DEGs and DElncRNAs were made using Metascape (v3.5.20240101) and the first version of NCPATH. The RNA sequencing analysis revealed 4843 DEGs and 1056 DElncRNAs in "C vs. NP", 1651 DEGs and 577 DElncRNAs in "C vs. SP", and 954 DEGs and 148 DElncRNAs in "NP vs. SP", with 291 DEGs and 70 DElncRNAs shared across all groups, respectively. We identified 14 hub genes from 291 DEGs, with functional enrichment analysis showing upregulated DEGs mainly linked to inflammation and osteoclast differentiation and downregulated DEGs to viral infections and immune responses. The analysis showed that 291 common and 14 hub genes were associated with pneumonia and that these genes could be regulated by the transcription factors JUN and NFκB1 carrying the NFκB binding site. We also revealed unique immune cell signatures across DEG categories indicating that the upregulated DEGs were associated with neutrophils and monocytes, while downregulated DEGs were associated with CD4 memory effector T cells. The comparative transcriptomic analysis of NP and SP groups with 52 gene signatures suggestive of IPF risk showed a lower risk of IPF in the SP group than the NP patients. Our findings suggest that COVID-19 may cause long term pathologies by modulating the expression of various DEGs, DeLncRNAs, and hub genes at the cellular level. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic, which is caused by the SARS-CoV-2 virus, has resulted in extensive health challenges globally. While SARS-CoV-2 primarily targets the respiratory system, clinical studies have revealed that it could also affect multiple organs, including the heart, kidneys, liver, and brain, leading to severe complications. To unravel the intricate molecular interactions between the virus and host tissues, we performed an integrated transcriptomic analysis to investigate the effects of SARS-CoV-2 on various organs, with a particular focus on the relationship between renal failure and COVID-19. A comparative analysis showed that SARS-CoV-2 triggers a systemic immune response in the brain, heart, and kidney tissues, characterized by significant upregulation of cytokine and chemokine secretion, along with enhanced migration of lymphocytes and leukocytes. A weighted gene co-expression network analysis demonstrated that SARS-CoV-2 could also induce tissue-specific transcriptional profiling. More importantly, single-cell sequencing revealed that COVID-19 patients with renal failure exhibited lower metabolic activity in lung epithelial and B cells, with reduced ligand–receptor interactions, especially CD226 and ICAM, suggesting a compromised immune response. A trajectory analysis revealed that COVID-19 patients with renal failure exhibited less mature alveolar type 1 cells. Furthermore, these patients showed potential fibrosis in the hearts, liver, and lung increased extracellular matrix remodeling activities. However, there was no significant metabolic dysregulation in the liver of COVID-19 patients with renal failure. Candidate drugs prediction by Drug Signatures database and LINCS L1000 Antibody Perturbations Database underscored the importance of considering multi-organ effects in COVID-19 management and highlight potential therapeutic strategies, including targeting viral entry and replication, controlling tissue fibrosis, and alleviating inflammation. [ABSTRACT FROM AUTHOR]

The genetic alterations currently identified in papillary thyroid microcarcinomas (PTMCs) are insufficient for distinguishing tumors with aggressive features. We aimed to identify candidate markers associated with lateral lymph node metastasis (LLNM, N1sb disease) in patients with PTMC using transcriptomic analysis. RNA sequencing was performed on 26 matched tumor and normal thyroid tissue samples (N0, n = 14; N1b, n = 12), followed by functional enrichment analyses of differentially expressed genes (DEGs). EcoTyper was used to explore the distinct tumor microenvironment (TME). We identified 631 DEGs (213 upregulated and 418 downregulated) between N1b and N0 PTMCs. The most significantly upregulated genes in N1b were associated with tumorigenesis, adhesion, migration, and invasion. DEGs were mainly enriched in the pathways of idiopathic pulmonary fibrosis, TME, wound healing, and inhibition of matrix metalloproteases. We predicted the activation of these pathways in N1b PTMCs. N1b PTMCs had a unique TME with abundant fibroblasts and epithelial cells, associated with an increased risk of disease progression. Fibroblast marker genes, including POSTN, MMP11, TNFAIP6, and FN1, and epithelial cell marker genes, including NOX4, MFAP2, TGFVBI, and TNC, were selected. POSTN and FN1, fibroblast cell-specific genes, and NOX4 and TNC, epithelial cell-specific genes, were promising biomarkers for predicting LLNM development and recurrence in patients with PTMC. We delineated the cellular ecotypes within the TME of patients with N1b PTMC and revealed potential markers for predicting LLNM and the prognosis of PTMC. These findings provide valuable insights into the contributions of cancer-associated fibroblasts and epithelial cells to PTMC progression and metastasis. [ABSTRACT FROM AUTHOR]

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Polyalthia longifolia is well-known for its abundance of polyphenol content and traditional medicinal uses. Previous research has demonstrated that the methanolic extract of P. longifolia leaves (PLME, 1 mg/mL) possesses anti-aging properties in Saccharomyces cerevisiae BY611 yeast cells. Building on these findings, this study delves deeper into the potential antiaging mechanism of PLME, by analyzing the transcriptional responses of BY611 cells treated with PLME using RNA-sequencing (RNA-seq) technology. The RNA-seq analysis results identified 1691 significantly (padj < 0.05) differentially expressed genes, with 947 upregulated and 744 downregulated genes. Notably, the expression of three important aging-related genes, SIR2, SOD1, and SOD2, showed a significant difference following PLME treatment. The subsequent integration of these targeted genes with GO and KEGG pathway analysis revealed the multifaceted nature of PLME's anti-aging effects in BY611 yeast cells. Enriched GO and KEGG analysis showed that PLME treatment promotes the upregulation of SIR2, SOD1, and SOD2 genes, leading to a boosted cellular antioxidant defense system, reduced oxidative stress, regulated cell metabolism, and maintain genome stability. These collectively increased longevities in PLME-treated BY611 yeast cells and indicate the potential anti-aging action of PLME through the modulation of SIR2 and SOD genes. The present study provided novel insights into the roles of SIR2, SOD1, and SOD2 genes in the anti-aging effects of PLME treatment, offering promising interventions for promoting healthy aging. [ABSTRACT FROM AUTHOR]

In this study, the transcriptome profiles of tissue–cultured grapevine (Vitis vinifera L. × Vitis labrusca L.: Rose Honey) seedlings inoculated with fungal endophytes Epicoccum layuense R2-21 (Epi R2-21) and Alternaria alternata XHYN2 (Alt XHYN2), were analyzed at three different time points (6 h, 6 d, and 15 d). A total of 4783 differentially expressed genes (DEGs) was found, of which 1853 (6 h), 3878 (6 d), and 4732 (15 d) were differentially expressed relative to those of the control in endophyte Epi R2-21 treatments, while a total of 5898 DEGs, of which 2726 (6 h), 4610 (6 d), and 3938 (15 d) were differentially expressed in endophyte Alt XHYN2 treatments. DEGs enriched in secondary metabolic pathways, plant–pathogen interaction, and hormone signalling were further analysed. The upregulated DEGs in the Epi R2-21 and Alt XHYN2 treatments, both enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG), were mainly involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, stilbenoid, diarylheptanoid and gingerol biosynthesis, phenylalanine metabolism, and circadian rhythms–plant and plant–pathogen interactions, similar to the trend observed in our previous study conducted on the cultivar 'Cabernet Sauvignon' (Vitis vinifera L.). Taken together with the results obtained from the cultivar 'Cabernet Sauvignon', it was found that tissue-cultured seedlings of the cultivar 'Rose Honey' induced a stronger defence response to fungal endophyte infection than that of the cultivar 'Cabernet Sauvignon', and inoculation with the endophyte Alt XHYN2 triggered a stronger response than inoculation with the endophyte Epi R2-21. In addition, the protein–protein interaction (PPI) network revealed that the genes VIT_16s0100g00910, encoding CHS, and VIT_11s0065g00350, encoding CYP73A, were involved in secondary metabolism and thus mediated in the resistance mechanism of grapevine on both the cultivars. The results showed that inoculation with the endophytes Epi R2-21 and Alt XHYN2 had a great ability to induce defence responses and reprogram the gene expression profiles in different grapevine cultivars, which deepens our knowledge of the interaction between fungal endophytes and grapevine and gives hints for grape quality management in viticulture using candidate fungal endophytes. [ABSTRACT FROM AUTHOR]

Seed size (SS) constitutes a pivotal trait in watermelon breeding. In this study, we present findings from an examination of two watermelon accessions, namely, BW85 and F211. Seeds from BW85 exhibited a significant enlargement compared to those of F211 at 13 days after pollination (DAP), with the maximal disparity in seed length and width manifesting at 17 DAP. A comprehensive study involving both metabolic and transcriptomic analyses indicated a significant enrichment of the ubiquinone and other terpenoid-quinone biosynthesis KEGG pathways. To detect the genetic region governing seed size, a BSA-seq analysis was conducted utilizing the F2 (BW85 × F211) population, which resulted in the identification of two adjacent QTLs, namely, SS6.1 and SS6.2, located on chromosomes 6. SS6.1 spanned from Chr06:4847169 to Chr06:5163486, encompassing 33 genes, while SS6.2 ranged from Chr06:5379337 to Chr06:5419136, which included only one gene. Among these genes, 11 exhibited a significant differential expression between BW85 and F211 according to transcriptomic analysis. Notably, three genes (Cla97C06G113960, Cla97C06G114180, and Cla97C06G114000) presented a differential expression at both 13 and 17 DAP. Through annotation, Cla97C06G113960 was identified as a ubiquitinconjugating enzyme E2, playing a role in the ubiquitin pathway that mediates seed size control. Taken together, our results provide a novel candidate gene influencing the seed size in watermelon, shedding light on the mechanism underlying seed development. [ABSTRACT FROM AUTHOR]

SUMMARY The advanced model of floral morphogenesis is based largely on data from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), but this process is less well understood in the Triticeae. Here, we investigated a sterile barley (Hordeum vulgare) mutant with malformed floral organs (designated mfo1), of which the paleae, lodicules, and stamens in each floret were all converted into lemma‐like organs, and the ovary was abnormally shaped. Combining bulked‐segregant analysis, whole‐genome resequencing, and TILLING approaches, the mfo1 mutant was attributed to loss‐of‐function mutations in the MADS‐box transcription factor gene HvAGL6, a key regulator in the ABCDE floral morphogenesis model. Through transcriptomic analysis between young inflorescences of wild‐type and mfo1 plants, 380 genes were identified as differentially expressed, most of which function in DNA binding, protein dimerization, cell differentiation, or meristem determinacy. Regulatory pathway enrichment showed HvAGL6 associates with transcriptional abundance of many MADS‐box genes, including the B‐class gene HvMADS4. Mutants with deficiency in HvMADS4 exhibited the conversion of stamens into supernumerary pistils, producing multiple ovaries resembling the completely sterile multiple ovaries 3.h (mov3.h) mutant. These findings demonstrate that the regulatory model of floral morphogenesis is conserved across plant species and provides insights into the interactions between HvAGL6 and other MADS‐box regulators. [ABSTRACT FROM AUTHOR]

Key message: Saline-alkali stress induces oxidative damage and photosynthesis inhibition in H. citrina, with a significant downregulation of the expression of photosynthesis- and antioxidant-related genes at high concentration. Soil salinization is a severe abiotic stress that impacts the growth and development of plants. In this study, Hemerocallis citrina Baroni was used to investigate its responsive mechanism to complex saline-alkali stress (NaCl:Na2SO4:NaHCO3:Na2CO3 = 1:9:9:1) for the first time. The growth phenotype, photoprotective mechanism, and antioxidant system of H. citrina were studied combining physiological and transcriptomic techniques. KEGG enrichment and GO analyses revealed significant enrichments of genes related to photosynthesis, chlorophyll degradation and antioxidant enzyme activities, respectively. Moreover, weighted gene co-expression network analysis (WGCNA) found that saline-alkali stress remarkably affected the photosynthetic characteristics and antioxidant system. A total of 29 key genes related to photosynthesis and 29 key genes related to antioxidant enzymes were discovered. High-concentration (250 mmol L−1) stress notably inhibited the expression levels of genes related to light-harvesting complex proteins, photosystem reaction center activity, electron transfer, chlorophyll synthesis, and Calvin cycle in H. citrina leaves. However, most of them were insignificantly changed under low-concentration (100 mmol L−1) stress. In addition, H. citrina leaves under saline-alkali stress exhibited yellow–brown necrotic spots, increased cell membrane permeability and accumulation of reactive oxygen species (ROS) as well as osmolytes. Under 100 mmol L−1 stress, ROS was eliminate by enhancing the activities of antioxidant enzymes. Nevertheless, 250 mmol L−1 stress down-regulated the expression levels of genes encoding antioxidant enzymes, and key enzymes in ascorbate–glutathione (AsA-GSH) cycle as well as thioredoxin-peroxiredoxin (Trx-Prx) pathway, thus inhibiting the activities of these enzymes. In conclusion, 250 mmol L−1 saline-alkali stress caused severe damage to H. citrina mainly by inhibiting photosynthesis and ROS scavenging capacity. [ABSTRACT FROM AUTHOR]