Penghao Wang

The abundant skin commensal, Staphylococcus epidermidis, is the leading cause of late-onset sepsis (LOS) in preterm infants but rarely causes infections in term infants and adults. Staphylococcal virulence mechanisms and the role of the preterm immune responses in driving these life-threatening infections remain poorly understood. Using an ex vivo sepsis model, we challenged whole blood from very preterm infants (30-32 weeks gestational age, GA; n = 8), term infants (> 37 weeks GA; n = 8), and young adults (18-25 years; n = 8) with either live S. epidermidis or S. aureus (~ 10
colony-forming units, CFU/ml) for 90 min. Dual RNA-sequencing (RNA-seq) was performed to simultaneously assess host and pathogen gene expression profiles, identifying common and pathogen-specific responses across cohorts. We found shared immune processes induced in all age groups upon bacterial challenge, including cytokine (IL1A, IL1B, IL6, IFNB1) and chemokine (CCL20, CCL3, CCL7, CXCL2) signalling. Preterm infants also exhibited unique responses, such as increased platelet activation and fibrin clot formation, Wnt signalling, and hypoxia pathways in response to S. epidermidis challenge. Our findings suggest that bacterial gene co-expression, including iron acquisition and heme biosynthesis genes, are also influenced by the hosts developmental age, highlighting the complexity of host-bacterial interactions in the early stages of neonatal sepsis.

Background
The investigation of ovarian development, dysfunction, and aging is essential for female reproductive health. Despite extensive research on the cellular functions of Brefeldin A (BFA) as an intracellular transport inhibitor, its specific effects and mechanisms on ovarian development/aging remain inadequately understood.

Methods
Mice and porcine oocytes/granulosa cells (GCs) were treated with BFA. Morphological and omics analyses (including Western blot, real-time polymerase chain reaction (RT-PCR), transcriptomics, and metabolomics) were conducted.

Results
In 3-week-old female mice, BFA treatment significantly suppressed oocyte maturation, induced apoptosis, and increased estradiol and LH levels. This treatment upregulated apoptosis-related genes while downregulating proliferation-associated genes. Additionally, BFA elevated senescence markers (p21 and p26) and decreased the activity of the longevity gene SIRT6. In porcine oocytes, BFA reduced the maturation rate and lowered mRNA levels of key maturation-related genes, LHX8 and GDF9. In porcine GCs, BFA increased apoptosis and upregulated genes such as Caspase-3, BAX, and P21, while downregulating genes associated with proliferation and longevity. Similar effects were observed in 12-month-old female mice, indicating consistency across age groups. Metabolomic analysis in these mice revealed that BFA primarily impacted pathways related to steroid biosynthesis, ovarian steroidogenesis, and estrogen signaling. Transcriptomic analysis in 12-month-old female mice further demonstrated that BFA disrupted ovarian function through multiple mechanisms, including modulation of the GnRH signaling pathway, activation of the FOXO pathway, and interference with meiosis-related gene expression.

Conclusion
Our findings are pivotal for advancing the understanding of ovarian aging, dysfunctions, and diseases, and ultimately facilitate addressing BFA's potential adverse effects on reproductive health/aging.

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

Artificial Intelligence (AI) has emerged as a transformative tool in precision agriculture, facilitating datadriven decision-making and crop improvement. In the context of agricultural crops, data from multiple modalities, such as phenotypic traits, genomic markers, and environmental conditions, offer diverse insights into crop development and yield potential. However, single-modality approaches may fail to capture the complex interplay between genomics, environment, and other factors affecting crop traits. To address this challenge, this study investigates the integration of multimodal data to improve genotype-to-phenotype predictions. Focusing on barley (Hordeum vulgare L.), a globally and nationally important cereal crop, we propose a new barley-Multimodal Deep Learning (barley-MMDL) model to predict flowering time and grain yield using heterogeneous multimodal datasets. The model combines Convolutional Neural Networks (CNNs) to process high-dimensional genomic markers with Long Short-Term Memory (LSTM) networks to capture temporal patterns in environmental data. These modality-specific latent features are then fused to enable joint optimization of feature extraction and prediction in an end-to-end manner. The proposed barleyMMDL model achieved the lowest RMSE values of 8.84 for flowering time and 778.50 for grain yield, outperforming baseline unimodal and multimodal models. These results demonstrate the improved predictive capability of barleyMMDL and underscore the potential of multimodal data integration to advance prediction capability in precision agriculture and contribute to sustainable agricultural practices.

Ovarian aging significantly contributes to the decline of the female reproductive system, adversely affecting fertility and endocrine homeostasis. To address the challenges posed by reproductive aging, natural products have shown promising preventive and therapeutic effects. Here, we investigated the beneficial effects of natural compound celastrol on ovarian development and aging, together with its underlying mechanisms. We found that celastrol administration at a concentration of 3 mg/kg promoted follicle development in young mice and enhanced porcine oocyte maturation, while regulating granulosa cell proliferation and apoptosis. In 12-month-old mice (equivalent to middle-aged adults), celastrol exhibited similar beneficial effects. Transcriptomic analysis revealed that differentially expressed genes post-celastrol treatment were associated with steroid biosynthesis, estrogen signaling pathways, type 2 diabetes, insulin secretion, meiosis, and apoptosis. Additionally, insulin receptor substrate 1 (IRS1), an adapter protein in insulin signaling, was shown to advance puberty in young mice and to facilitate oocyte maturation. Overexpression of IRS1 in oocytes promoted follicular development and oocyte maturation, resulting in enhanced steroid hormone levels, whereas IRS1 knockdown inhibited these processes. Our findings indicate that celastrol may regulate ovarian development and aging by modulating IRS1 expression and its related pathways, suggesting celastrol as a novel small-molecule compound targeting IRS1, and offering new perspectives for potential therapeutic strategies against reproductive aging and infertility.

Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identify a secretory effector candidate (FgEC10) that is essential for the virulence of F. graminearum. FgEC10 interacts strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerates its degradation via the 26S proteasome pathway. In addition, we show that TaFAH interacts with proteasome 26S subunit, non-ATPases 12 (TaPSMD12) and that FgEC10 enhances the interaction between TaFAH and TaPSMD12. RNA silencing or overexpression of TaFAH in wheat plants shows that TaFAH positively regulates wheat FHB resistance. Overexpression of TaFAH promotes the expression of genes associated with disease resistance and the heading period. Metabolomic analysis reveals that overexpression of TaFAH increases the levels of several amino acids in wheat, and exogenous application of some of these amino acids show an increase in F. graminearum resistance in the wheat spike and seedling. Collectively, our study reveals a pathogenic mechanism and provides a valuable gene resource for improving FHB resistance and promoting heading in wheat.

The oriental fruit fly, Bactrocera dorsalis, is a highly destructive pest in fruits, vegetables and flowers with heat treatment being common for its control in internationally traded produce. However, heat treatment can adversely affect quality, which limits its application. This study aimed to develop a novel control strategy combining phosphine fumigation with heat treatment (P + H), demonstrating a significant synergistic effect in controlling B. dorsalis. We conducted transcriptomic analysis and qRT-PCR validation to explore this synergistic effect. P + H significantly increased the expression of heat shock proteins (HSP), but their levels were lower than those induced by heat treatment alone. RNAi-based experiments confirmed the association between HSP gene expression and insect mortality, further supporting the important role of HSP genes in response to heat treatment. Functional enrichment analysis indicated that the MAPK/ERK signaling pathway and HSF-1 dephosphorylation dynamically regulate HSP genes expression under P + H treatment. Additionally, energy allocation toward cellular repair may further limit HSP gene synthesis, affecting insect tolerance to heat response. These findings provide insights into the molecular bases for the synergism of P + H treatment, highlighting that HSP gene regulation plays as critical role in insect stress resistance and offering a novel approach to pest control.
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•P + H shows a strong synergistic effect against B. dorsalis.•P + H increases HSP expression but less than heat treatment alone.•MAPK/ERK and HSF-1 dephosphorylation regulate HSP expression under P + H.•Phosphine acts as a biological regulator of insect stress resistance.

Multiple phytohormones, including gibberellin (GA), abscisic acid (ABA), and indole-3-acetic acid (IAA), regulate seed germination. In this study, a barley aldehyde oxidase 1 (HvAO1) gene was identified, which is located near the SD2 (seed dormancy 2) region at the telomeric end of chromosome 5H. A doubled-haploid population (AC Metcalfe/Baudin) was used to characterize HvAO1 and validated its association with seed germination and malting quality. Aldehyde oxidase is predicted to catalyse the oxidation of various aldehydes, such as indoleacetaldehyde and abscisic aldehyde, into IAA and ABA, which is the final step of IAA/ABA biogenesis. This process influences the final IAA/ABA concentration in the seed, affecting the seed dormancy. Sequence analysis revealed substantial variations in the HvAO1 promoter regions between AC Metcalfe and Baudin. The combining seed germination tests, genetic variation analysis, gene expression, and phytohormone measurements showed that Baudin, which displays strong seed dormancy, has a specific sequence variation in the promoter region of the HvAO1 gene. This variation is associated with a higher expression level of the HvAO1 gene and an increased level of ABA than those in AC Metcalfe, which shows weak dormancy and lacks this sequence variation. In addition to its strong effect on the SD2 gene, HvAO1 shows excellent potential to fine-tune malting quality and seed dormancy, as evidenced by genotyping with HvAO1-specific markers, dormancy phenotypes, and malting quality. Our findings provide a new strategy for introducing favourable HvAO1 alleles to achieve the desired level of seed dormancy and high malting quality in barley.

A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.