Search Results (58)

The ‘Tenuifoliae irises’ are a distinctive group of beardless, rhizomatous perennial irises, which are characterised by their somewhat vertical rhizomes, typically clothed at the apex with long maroon-brown, sharp fibrous remains of leaf sheaths; perianth tube long, filiform to scapiform; stigma bilobed; capsules often trigonous to six-ribbed, apically beaked; and seeds angulose to subcubic or pyriform, lacking fleshy appendages, and with testa hard, irregularly wrinkled. The representatives of the aggregate are mostly native to the dry steppes and grasslands from lowland to high mountain habitats of Central and Eastern Asia, extending westwards to the Black Sea and Caspian regions. Morphological classification of the ‘Tenuifoliae irises’ recognises about ten to eleven species, which are arranged into two genera, Sclerosiphon and Cryptobasis. Diverse molecular research recovered members of the ‘Tenuifoliae irises’ in contrasting placements within the ‘Iris-flower clade’. Sometimes, Sclerosiphon was sister to Eremiris, but Cryptobasis aligned with the ‘Spuria irises’ (Chamaeiris) and the ‘Spanish irises’ (Xiphion and related genera); in other cases, both Sclerosiphon and Cryptobasis formed a clade sister to Chamaeiris, or Cryptobasis alone was identified as the basal member of the Iris s.l. clade, positioned immediately after Siphonostylis. To examine these taxonomic discrepancies within a rigorous molecular systematic framework and using 12 reliably authenticated specimens, we generated 24 sequences of the matK gene (12) and the trnL (UAA)–trnF (GAA) loci (12) from members of the ‘Tenuifoliae irises’. These sequences were subsequently incorporated into a comprehensive dataset of the ‘Iris-flower clade’, enabling a broader analytical assessment. The obtained three-taxon statement hierarchy of patterns and maximum likelihood phylogenetic trees both recover the ‘Tenuifoliae irises’ as monophyletic and sister to Chamaeiris, and in turn to the ‘Xiphion s.l. clade’. We also found Sclerosiphon and Cryptobasis as sister genera. The morphological and karyological data supporting those relationships are discussed, which allow getting back to Rodionenko’s sources and recovering Sclerosiphon in his original sense, alongside Cryptobasis. Furthermore, the molecular results allow us to expand Sclerosiphon to include the Eastern Chinese members of the aggregate. In consequence, five new combinations (one series and four species) are established in the genus, one lectotype is designated, and data on nomenclature, distribution and ecology of the accepted species are reported. Full article

Background: Menstrual migraine (MM), including pure menstrual migraine (PMM) and menstrually related migraine (MRM), is characterized by attacks occurring in close temporal association with menstruation and is often more severe, longer lasting, and less responsive to treatment than non-menstrual migraine. Prostaglandin-mediated inflammation and calcitonin gene-related peptide (CGRP) release play a key role in MM pathophysiology. Phycocyanin (PC) and palmitoylethanolamide (PEA) are nutraceutical compounds with anti-inflammatory, analgesic, and neuroprotective properties that may be beneficial as short-term perimenstrual prophylaxis. Objectives: To evaluate the effectiveness of an oral supplementation combining phycocyanin and palmitoylethanolamide as a short-term prophylaxis for menstrual migraine in a real-world clinical setting, a retrospective observational study without a control group was conducted in five Italian centers between May 2023 and June 2025. Methods: Clinical records of 800 women were reviewed, and 220 patients receiving perimenstrual supplementation with phycocyanin and palmitoylethanolamide were screened. Sixty-one women diagnosed with migraine without aura, according to the International Classification of Headache Disorders, met all inclusion criteria and were analyzed. Phycocyanin and palmitoylethanolamide were taken at a dosage of two capsules daily from five days before to five days after the onset of menstruation for three consecutive months. Outcomes during the perimenstrual window were compared with a three-month period without supplementation. Primary outcomes included migraine severity, frequency, and duration of the attacks; secondary outcomes included analgesic consumption and menstrual migraine-associated symptoms. Results: Among the 61 included patients, phycocyanin and palmitoylethanolamide supplementation was associated with a significant reduction in migraine severity across all monitored perimenstrual days (p < 0.0001). While the overall monthly frequency of migraine attacks did not change, the number of migraine days during the perimenstrual window significantly decreased from the first month of supplementation (p < 0.05). Moreover, migraine duration during the perimenstrual window was significantly reduced at one, two, and three months of phycocyanin and palmitoylethanolamide supplementation compared with baseline. Analgesic use and the number of days with migraine-associated symptoms (nausea, vomiting, photophobia/phonophobia) were also significantly reduced. Treatment was well tolerated. Conclusions: In this real-world retrospective study, perimenstrual supplementation with phycocyanin and palmitoylethanolamide was associated with reduced severity, duration, and perimenstrual frequency of menstrual migraine attacks, along with decreased analgesic use, suggesting a safe and potentially beneficial short-term prophylactic strategy for women with menstrual migraine. Full article

Encapsulation is a major cellular defense reaction in lepidopterans. However, in the oriental armyworm (Mythimna separata), the molecular regulators that coordinate hemocyte adhesion and multilayer capsule assembly remain poorly defined. In this study, we identified Mythimna separata encapsulation related gene 1 (MysERG1) as a novel cellular immune regulatory gene. MysERG1 transcripts were most abundant in hemocytes and were notably upregulated in adherent hemocytes as well as in samples of capsules, indicating an association with adhesion-dependent hemocyte activation. Following separation of granulocytes and plasmatocytes, MysERG1 expression was observed to be higher in adherent plasmatocytes than in adherent granulocytes. However, recombinant MysERG1 selectively increased granulocyte adhesion but did not significantly affect plasmatocyte adhesion and was specifically localized on granulocytes. Additionally, recombinant MysERG1 enhanced hemocyte aggregation on foreign surfaces, highlighting its functional role in facilitating encapsulation. Functional knockdown using double-stranded RNA significantly reduced the size of the capsules, indicating that MysERG1 is required for robust capsule formation. This study identifies MysERG1 as a novel factor involved in hemocyte cooperation during encapsulation in M. separata and presents a conceptual framework for inter-hemocyte communication mechanisms in lepidopteran cellular immunity. Full article

H-NS (histone-like nucleoid-structuring protein) is a global regulator affecting diverse bacterial processes. This study aimed to elucidate the regulatory role of H-NS in the virulence of Klebsiella pneumoniae (K. pneumoniae), particularly in relation to capsule synthesis and anchoring. A clinically isolated ST11-KL64 strain of K. pneumoniae FK6741 with low virulence was used. The role of H-NS was evaluated using colony morphology, the string test, viscosity measurement, capsule quantification, transmission electron microscopy, growth curve, biofilm assay, a mouse infection model, transcriptomic analysis, and RT-qPCR. Deletion of hns converted FK6741 into a hypermucoid phenotype in the positive string test; capsule quantification and transmission electron microscopy (TEM) showed increased polysaccharide chains but a reduced and tightly bound capsule. The mutant was initially found to grow slowly but formed stronger biofilms. In vivo, it displayed reduced virulence but induced stronger inflammation. Molecular assays revealed upregulation of capsule synthesis genes (galF, wzi, wcaJ, and wzc) and downregulation of wabG, which is involved in capsule anchoring. H-NS represses capsule synthesis genes, limiting capsule formation in K. pneumoniae. In contrast, loss of H-NS downregulates wabG, a key gene involved in GalA-mediated capsule anchoring, resulting in unstable surface attachment and loss of capsular polysaccharides. Consequently, these unanchored polysaccharides fail to confer effective protection, resulting in reduced bacterial virulence. Full article

Objectives: To explore the genetic basis of phage resistance in sequentially generated capsular mutants of phage-resistant Klebsiella pneumoniae using an established phage library. Methods: Sequential induction strategies were employed to obtain phage-resistant K. pneumoniae capsular mutants by exposing ST11-K64 K. pneumoniae Kp2325 to different single phages. Whole genome sequencing and bioinformatic analysis were used to elucidate the capsular-related genetic changes in phage-resistant mutants. Phenotypic changes were assessed through gene complementation, growth assays, phage cleavage spectrum analysis, TEM for phage morphology, CPS analysis, biofilm formation, and virulence assays. Results: Three sequentially generated phage-resistant K. pneumoniae capsular mutants were obtained, designated R1, R2 and R3. The narrowing of the phage cleavage spectrum and the evolutionary trade-offs of biological phenotypes were observed. Key genetic changes included: (1) ISKpn26 insertion disrupting wcaJ in R1; (2) combined wcaJ insertion and 9-bp deletion in waaH in R2; and (3) CPS gene cluster deletion in R3 were identified as key mechanisms of phage resistance in K. pneumoniae mutants R1, R2 and R3, respectively. Conclusions: Sequential exposure to different single phages led to rapid evolution of phage resistance in K. pneumoniae via genetic mutations that disrupt capsular synthesis. These findings highlight the critical role of bacterial capsule in phage–host interactions and emphasize the need to use phage cocktails targeting different types of receptors to counteract the evolution of bacterial defense mechanisms in phage therapy. Full article

Dry seed longevity varies considerably among species, but little is known about its relation with the climate and the molecular mechanisms that determine seed lifespan. Salicaceae species, with more than 620 species worldwide, are known to produce short-lived seeds, making them particularly good models to explore ageing processes in the glassy state rather than under accelerated ageing. We compared seed lifespan for 13 species of Salix and Populus across a broad geographical range (up to 2200 m a.s.l.). High-quality seeds were obtained by optimizing collection time (just before capsule dehiscence) and post-harvest handling (i.e., the use of negative pressure to remove seed hairs). At optimal moisture contents (MCs) between 6 and 9%, most species seeds demonstrated minimal decreases in viability after storage at −20 °C or in liquid nitrogen for 3 years. Dry room (15% RH, 15 °C) storage differentiated between species’ seed lifespans (P₅₀s) of c. 150 to >1200 d. Unlike Salix, Populus species from warm wet environments tended to produce longer-lived seeds in dry storage. Based on transcriptome data on Populus davidiana (longer-lived) and Populus euphratica (shorter-lived), we revealed high correlations between late seed maturation genes, such as 60% of HSP and 67% of LEA genes showed higher expression in P. davidiana seeds, while 70% of WRKY transcription factors showed significantly higher expression in P. euphratica seeds. For these two species, genes related to oxidative stress might be the most important contributor to different seed longevity in the dry glassy state. Full article

Transcriptomic profiling is a powerful tool for dissecting the cellular and molecular complexity of ocular tissues, providing insights into retinal development, corneal disease, macular degeneration, and glaucoma. With the expansion of microarray, bulk RNA sequencing (RNA-seq), and single-cell RNA-seq technologies, artificial intelligence (AI) has emerged as a key strategy for analyzing high-dimensional gene expression data. This review synthesizes AI-enabled transcriptomic studies in ophthalmology from 2019 to 2025, highlighting how supervised and unsupervised machine learning (ML) methods have advanced biomarker discovery, cell type classification, and eye development and ocular disease modeling. Here, we discuss unsupervised techniques, such as principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), and weighted gene co-expression network analysis (WGCNA), now the standard in single-cell workflows. Supervised approaches are also discussed, including the least absolute shrinkage and selection operator (LASSO), support vector machines (SVMs), and random forests (RFs), and their utility in identifying diagnostic and prognostic markers in age-related macular degeneration (AMD), diabetic retinopathy (DR), glaucoma, keratoconus, thyroid eye disease, and posterior capsule opacification (PCO), as well as deep learning frameworks, such as variational autoencoders and neural networks that support multi-omics integration. Despite challenges in interpretability and standardization, explainable AI and multimodal approaches offer promising avenues for advancing precision ophthalmology. Full article

Posterior capsule opacification (PCO), a frequent complication of cataract surgery, arises from dysregulated wound healing and fibrotic transformation of residual lens epithelial cells. While transcriptomic and machine learning (ML) approaches have elucidated fibrosis-related pathways in other tissues, the molecular divergence between regenerative and fibrotic outcomes in the lens remains unclear. Here, we used an ex vivo chick lens injury model to simulate post-surgical conditions, collecting RNA from lenses undergoing either regenerative wound healing or fibrosis between days 1–3 post-injury. Bulk RNA sequencing data were normalized, log-transformed, and subjected to univariate filtering prior to training LASSO, SVM, and RF ML models to identify discriminatory gene signatures. Each model was independently validated using a held-out test set. Distinct gene sets were identified, including fibrosis-associated genes (VGLL3, CEBPD, MXRA7, LMNA, gga-miR-143, RF00072) and wound-healing-associated genes (HS3ST2, ID1), with several achieving perfect classification. Gene Set Enrichment Analysis revealed divergent pathway activation, including extracellular matrix remodeling, DNA replication, and spliceosome associated with fibrosis. RT-PCR in independent explants confirmed key differential expression levels. These findings demonstrate the utility of supervised ML for discovering lens-specific fibrotic and regenerative gene features and nominate biomarkers for targeted intervention to mitigate PCO. Full article

Background: Pyoderma is a superficial bacterial infection that is considered the formation of pus-containing lesions on the skin occurring in animals. Staphylococci, including Staphylococcus aureus and Staphylococcus pseudintermedius, that cause pyoderma in pet animals is a global health concern. The objectives of this study were to investigate antibiotic-resistant staphylococci isolated from pyoderma in dogs and cats and to analyse whole genome sequences of multidrug-resistant (MDR) staphylococci. Methods: A total of 56 pyoderma swabbing samples from 42 dogs and 14 cats located in Southern Thailand was collected to isolate staphylococci. Antibiotic susceptibility and antibiotic-resistant genes of staphylococcal isolates were investigated. Furthermore, the representative MDR isolates were investigated using whole genome sequence analysis. Results: 61 isolates were identified as staphylococci, which can be classified into 12 different species, mostly including 13 S. intermedius (13.26%), 13 S. saprophyticus (13.26%), 8 S. sciuri (8.16%), and Staphylococcus cohnii (8.16%). Remarkably, the main pyoderma-causing species that were isolated in this study were S. aureus (5.10%) and S. pseudintermedius (3.06%). Most staphylococci were resistant to penicillin G (30%), and the blaZ gene was found to be the highest prevalence of the resistance genes. Both MDR-S. aureus WU1-1 and MDR-S. pseudintermedius WU48-1 carried capsule-related genes as main virulence factor genes. Interestingly, MDR-S. pseudintermedius WU48-1 was resistant to seven antibiotic classes, which simultaneously carried blaZ, mecA, aac, dfrK, aph3, and tetM. Genes related to antibiotic efflux were the highest proportion of the mechanism found in both representatives. Remarkably, SCCmec cassette genes were found in both isolates; however, the mecA gene was found only in MDR-S. pseudintermedius WU48-1. In addition, these were mostly carried by macrolide- and tetracycline-resistance genes. Mobile gene transfer and horizontal gene transfer events frequently contain genes involved in the antibiotic target alteration mechanism. Conclusions: This study found that MDR staphylococci, especially S. aureus and S. pseudintermedius, are important in animals and owners in terms of One Health concern. The information on whole genome sequences of these MDR staphylococci, particularly antimicrobial resistance genes, mobile genetic elements, and horizontal gene transfer events, can help to understand gene transmission and be applied for antibiotic resistance surveillance in veterinary medicine. Full article

The degeneration of germplasm is a key factor limiting the yield and quality of Gastrodia elata Blume. Sexual reproduction is a primary method to address this degeneration, while the number of flowers and capsules is directly related to sexual reproduction. However, the genetic mechanisms underlying the high flower/fruit-bearing traits in G. elata remain unclear. We first compared the quantitative and qualitative traits during the flowering to fruiting period of G. elata, including bolting height, flowering quantity, flowering time, fruiting quantity, capsule spacing, seed quality, etc. The natural materials were selected by multi-capsule and few-capsule for transcriptome analysis to screen the differentially expressed genes (DEGs); the candidate gene GePIF4 was suspected to regulate the formation of multiple flowers and fruits. It was confirmed that GePIF4 has multiple biological functions in the overexpression of transgenic lines, including increasing numbers of vegetative propagation corms (VPCs) and promoting the growth of G. elata. Through comparative transcriptomic analysis of EV and OE-GePIF4 transgenic lines, the transcriptional regulatory network of GePIF4 was identified, and transient expression of GePIF4 was demonstrated to significantly promote gastrodin accumulation. The dual-LUC assay and in vitro yeast one hybrid results showed that GePIF4 could directly bind to GeRAX2 to regulate multi-capsule formation, and GePIF4 could directly bind to GeC4H1 to promote gastrodin accumulation. Therefore, we elucidate the role of GePIF4 in multi-capsule formation and secondary metabolite accumulation, thereby laying the groundwork for the genetic improvement of G. elata germplasm resources. Full article

Avian pathogenic Escherichia coli (APEC) causes bloodstream infections mainly by resisting the bactericidal action of host serum. Although various protein and polysaccharide factors involved in serum resistance have been identified, the role of small non-coding RNA (sRNA) in serum resistance has rarely been studied. The sRNA RyhB contributes to serum resistance in APEC, but the regulation mechanism of RyhB to serum resistance-related targets remains unknown. Here, we studied the regulatory mechanism of RyhB on capsule synthesis and how RyhB regulates serum resistance, macrophage phagocytosis resistance, and pathogenicity to natural hosts by regulating capsule synthesis. The results showed that RyhB upregulates capsular synthesis by interacting with the promoter regions of the capsule gene cluster and activating the translation of the capsule. The deletion of ryhB and/or neu reduced the ability of resistance to serum, macrophage phagocytosis, and pathogenicity of APEC in ducks. It can be concluded that RyhB directly upregulates the expression of capsular gene cluster and capsular synthesis and then indirectly promotes resistance to serum and macrophage phagocytosis and pathogenicity to ducks. Full article

Erwinia are widely known as phytopathogenic bacteria, but among them, there are also plant-friendly strains that can promote plant growth (PGPR). The Erwinia-like strain OPT-41 was isolated from Triticum aestivum seedlings as a potential PGPR. The cells (0.9–1.3 × 1.5–3.1 µm) of this microorganism are Gram-negative, rod-shaped, motile (with peritrichous flagella), and non-spore- and non-capsule-forming. The 16S rRNA gene sequence analyses showed it is located in the Erwiniaceae family and has a pairwise similarity above the species delineation threshold of 98.65% with several of its members: Erwinia tasmaniensis (99.21%), Candidatus Pantoea bathycoeliae (98.93%), Pantoea agglomerans (98.87%), Erwinia endophytica (98.83%), Erwinia persicina (98.82%), Erwinia billingiae (98.76%) and Erwinia aphidicola (98.75%). Whole genome-based taxonomy performed on the Type (Strain) Genome Server clarified the status of strain OPT-41, detecting it as a potential new species in the genus Erwinia. The microorganism under study was the most closely related to the type strain of E. phyllosphaerae, demonstrating 27.2% similarity in dDDH, 83.44% similarity in OrthoANIu, and 1.9% difference in G+C content. The major fatty acids of strain OPT-41 were 9 C_16:1, C_14:0, and C_16:0. A combination of genome-based taxonomy and traditional polyphasic taxonomy clearly indicated that strain OPT-41 belongs to a novel Erwinia species, for which the name E. plantamica sp. nov was proposed. OPT-41 (=IBPPM 712=VKM B-3873D=CCTCC AB 2024361) has been designated as the type strain. In addition, OPT-41 was found to have low degradation potential for host plant pectins and proteins and be friendly in Triticum aestivum and Hordeum vulgare crops. Full article

DNA methylation is a critical mechanism for regulating gene expression in bacteria and plays an essential role in bacterial pathogenesis. A mutant, WC1535ΔhsdM, lacking hsdM encoding a DNA methyltransferase was constructed using homologous recombination technology. The growth, hemolytic activity, and capsule formation of the mutant were analyzed. The dynamic distribution of the wild-type (WT) and mutant strains in tilapia tissues after artificial infection was determined. The adhesion, invasion, anti-phagocytic, and whole-blood survival abilities of the WT and mutant strains were analyzed. Tilapia were intraperitoneally injected with the WT or mutant strains, and the LD₅₀ values were determined. The expression levels of the immune-related genes in tilapia were analyzed by qRT-PCR. The mutant showed faster growth during the logarithmic growth period (5–10 h) and lower hemolytic activity than the WT strain. Mutant loads in tilapia tissues were significantly lower than those of the WT strain. Mutant strain adhesion to epithelial cells was significantly reduced, it was more easily engulfed by macrophages, and it had decreased intracellular survival. The LD₅₀ of the mutant was 2.06 times higher than that of the WT strain, indicating decreased pathogenicity. Expression levels of immune-related genes IL-1β, IL-6, IFN-γ, and TNF-α in tilapia induced by the mutant were lower than those by the WT strain. In conclusion, the WC1535ΔhsdM mutant exhibited an increased growth rate and decreased hemolytic activity, tissue colonization, and pathogenicity, indicating that HsdM could regulate S. agalactiae growth and pathogenicity. This study provides new insights into the pathogenesis of piscine S. agalactiae. Full article

Klebsiella pneumoniae represent a common invasive infection etiological agent, whose potential carbapenem-resistance and hypermucoviscosity complicate the patient’s management. Infection development often derives from gastrointestinal colonization; thus, it is fundamental to monitor asymptomatic K. pneumoniae colonization through surveillance protocols, especially for intensive care and immunocompromised patients. We described a six-month routine screening protocol from the Policlinico of Catania (Italy), while blood samples were collected from the same patients only in cases of a systemic infection suspicion. All the patients who had dissemination episodes were furtherly investigated through next-generation sequencing, analyzing both colonizing and disseminating strains. This study documents emerging invasive sequence types such as ST101, ST307, and ST395, mainly revealing blaNDM or blaKPC genes, along with siderophores and hyperproduction capsule markers as virulence factors. Most of the detected factors are presumably related to a specific plasmid content, which are extremely varied and rich. In conclusion, active surveillance through sequencing is essential to enhance awareness of local epidemiology within high-risk multi-drug resistance areas. A random sequencing analysis on the most warning microorganisms could enhance sequence typing (ST) awareness within specific settings, allowing for better prevention control strategies on their eventual persistence or diffusion. Full article

Cataracts remain the leading cause of visual impairment worldwide, yet the underlying molecular mechanisms, particularly in age-related cataracts (ARCs), are not fully understood. The Notch signaling pathway, known for its critical role in various degenerative diseases, may also contribute to ARC pathogenesis, although its specific involvement is unclear. This study investigates the role of Notch signaling in regulating ferroptosis in lens epithelial cells (LECs) and its impact on ARC progression. RNA sequencing of anterior lens capsule samples from ARC patients revealed a significant downregulation of Notch signaling, coupled with an upregulation of ferroptosis-related genes. Notch1 expression decreased, while ferroptosis markers increased in an age-dependent manner. In vitro, upregulation of Notch signaling alleviated ferroptosis by decreasing ferritin heavy chain 1 (FTH1) and p53 levels while enhancing the expression of nuclear factor erythroid 2-related factor 2 (Nrf2), glutathione peroxidase 4 (GPX4), and solute carrier family 7 member 11 (SLC7A11). Conversely, inhibition of Notch signaling exacerbated ferroptosis, as evidenced by reduced Nrf2, GPX4, and SLC7A11 expression. These findings suggest that downregulation of Notch signaling promotes ferroptosis in LECs by impairing the Nrf2/GPX4 antioxidant pathway, thereby contributing to ARC development. This study offers new insights into ARC pathogenesis and highlights the Notch signaling pathway as a potential therapeutic target for preventing or mitigating ARC progression. Full article