Search Results (52)

Cibotium barometz (L.) J. Sm., a medicinally significant fern in traditional Chinese medicine, is little explored at the genomic level regarding its bioactive compounds. Using an integrated approach combining Illumina and PacBio sequencing technologies, we profiled its root, rachis, and pinna transcriptomes, identifying 12,718, 21,341, and 11,441 unigenes, respectively. Our analysis systematically characterized the transcriptional features of transcription factors (TFs), simple sequence repeats (SSRs), long non-coding RNAs (lncRNAs), and differentially expressed genes (DEGs). Enrichment analyses highlighted the roles of highly expressed unigenes in secondary metabolism. Seventeen key enzymes involved in polysaccharide biosynthesis showed tissue-specific expression patterns. Notably, total polysaccharide content correlated positively with UDP-arabinose 4-epimerase (UXE) expression but negatively with phosphoglucomutase (PGM) and 3,5-epimerase/4-reductase (UER1). Flavonoid accumulation inversely correlated with chalcone synthase (CHS) expression. Two lignin pathways (H-lignin and G-lignin) were characterized, with phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and cinnamyl alcohol dehydrogenase (CAD) as key genes. The absence of ferulate-5-hydroxylase (F5H) explains the undetected S-lignin pathway. Regulatory network analysis revealed positive correlations between PAL expression and NAC72/NAC78/WRKY35 and C4H expression and WRKY65/WRKY69/WRKY71, while a negative correlation was revealed between flavonoid 3′,5′-hydroxylase (F3′5′H) and MYB3R4. This study provides comprehensive transcriptomic insights into C. barometz bioactive compound biosynthesis, serving as a foundation for mechanistic research. Full article

(1) Purpose: The study investigated the correlation between variations in body mass index (BMI) and tear crystallization class according to the Masmali classification. Moreover, it examined the potential diagnostic value of a patterning test within the population affected by obesity. (2) Methods: A total of 61 patients were investigated, with ages ranging from 25 to 72 years (median age [interquartile range] = 39.0 [26] years). BMI values ranged from 19.1 to 47.5 kg/m², with a median BMI (interquartile range) of 29.3 (12.1) kg/m². (3) Results: The Kruskal–Wallis test was used to assess differences in BMI across the Masmali classes and revealed statistically significant disparities between at least two groups (p = 0.024). The rank η² value of 0.094 shows a small-to-moderate effect size, suggesting that approximately 9% of the variance in rank distributions is explained by the Masmali classification. The post hoc Dunn test with Bonferroni and Holm corrections showed that patients classified as Masmali grade 2 exhibited a significantly higher BMI compared to those in grade 0 (p = 0.009), whereas no statistically significant differences were identified between grades 0 and 1 or between grades 1 and 2. The analysis of variance (ANOVA) revealed a statistically significant difference among Masmali Classes 0, 1, and 2 with respect to the number of branching structures in dried tear samples analyzed at a brightness threshold of 220. The effect size (η² = 0.263) shows that approximately 26% of the variability in branching number can be attributed to the severity of tear film dysfunction as defined by the Masmali classification. Accordingly, as the Masmali score increases, the number of branches decreases significantly, particularly among patients with elevated BMI. (4) Conclusion: The findings suggest that when classified according to the Masmali scale the dry eye syndrome exhibits a distinct crystallization pattern in patients with excess body weight. Specifically, higher BMI values are associated with a marked decrease in the number of fern-like branches identified in the tear ferning test. Full article

Objectives: The study examined tear and serum alterations using the ferning test and quantified the number of branches formed during the controlled drying of these biological fluids (tears and serum), in order to identify a potential diagnostic patterning test in individuals with obesity. Methods: A total of 61 patients aged between 25 and 72 years were enrolled (median age [interquartile range] = 39.0 [26] years). BMI values ranged from 19.1 to 47.5 kg/m², with a median BMI (interquartile range) of 29.3 (12.1) kg/m². Results: The Kruskal–Wallis test showed statistically significant differences among at least two Schirmer classes with respect to the number of branches observed in dried tears at a brightness threshold of 220 (H(2) = 8.485, p = 0.014). According to the Dunn post hoc test, Schirmer Class 1 showed a markedly lower number of branches compared with Classes 2 and 3 (p < 0.031 and p < 0.021), whereas no significant difference was found between Classes 2 and 3. The Kruskal–Wallis test further suggested the presence of statistically significant differences in the number of branches in dried serum, quantified using ImageJ2 at a brightness threshold of 190, across visceral fat classes (H(2) = 9.583, p = 0.008). Dunn’s post hoc tests revealed that the number of branches in serum analyzed at a brightness threshold of 190 was significantly higher in visceral fat class 3 compared to class 1 (p_holm = 0.006), while no statistically significant differences were observed between classes 1 and 2 or between classes 2 and 3 (p_holm > 0.05). Conclusions: In addition to other obesity-specific complications patients with obesity exhibit an increased risk of developing dry eye syndrome. The combined assessment of DPT in both the tear film and serum may represent a new method for analyzing obesity-associated biomarkers. Further studies are required to determine the sensitivity and specificity of these approaches in diagnosing systemic alterations induced by excess adipose tissue. Full article

Pigmentary keratitis (PK) is a prevalent ocular surface disease in Pug dogs, yet comparative evidence on topical immunosuppressants remains limited. This prospective comparative clinical study evaluated the efficacy and safety of two agents with distinct mechanisms—tacrolimus, a calcineurin inhibitor, and sirolimus, an mTOR inhibitor—for the treatment of PK. Thirty-two Pugs (63 eyes) were randomly assigned to receive either 0.03% tacrolimus or 0.03% sirolimus three times daily for six months. Tear film quantity and quality were assessed using the Schirmer tear test, tear break-up time, and Ferning patterns, alongside serial clinical scoring of corneal pigmentation and ocular surface signs. Both treatments improved tear-film parameters, although only tacrolimus produced statistically significant increases in tear production and more frequent formation of a pigment-free “clear line,” indicating enhanced pigment regression. Pigment lightening and transparency recovery improved similarly in both groups. Adverse events—including blepharospasm, diffuse corneal oedema, and complicated ulcers—occurred more frequently in the sirolimus group, suggesting a comparatively less favorable short-term safety profile. Overall, both tacrolimus and sirolimus demonstrated therapeutic benefit in PK, although tacrolimus showed superior quantitative efficacy and better tolerability. Further long-term studies are warranted to clarify safety considerations and to optimize immunomodulatory strategies for this breed-specific condition. These findings suggest tacrolimus may be considered a first-line immunomodulatory therapy for PK in Pug dogs. Full article

RNA editing is a crucial mechanism regulating gene expression in plant organellar genomes, which optimizes protein structures through base substitution and plays a vital role in plant growth, development, and stress adaptation. This study revises the conventional understanding restricting MORF proteins to seed plants by reporting their first identification in ferns, an early vascular plant lineage. We sequenced chloroplast genomes of O. japonica and P. vachellii, revealing one MORF9 homolog in O. japonica and three homologs (MORF1/8/9) in P. vachellii through comparative transcriptomics and structural validation. All identified MORF proteins harbor conserved MORF-box domains, suggesting structural and potentially functional conservation with angiosperms. Crucially, MORF members differentially regulate organellar RNA editing: chloroplast editing frequencies are predicted to show dose-dependent enhancement (0.7–1.0 in conserved sites), potentially influenced by MORF presence or copy number. In O. japonica, chloroplast editing exhibits tissue-specific patterns (conserved sites 0.7–1.0; tissue-specific sites lower efficiency at 0.1–0.2), while this study’s mitochondrial editing results show a balanced frequency distribution (0–1 range). Amino acid substitution analysis demonstrates MORF-mediated hydrophobic optimization (Ser→Leu > 30%, Pro→Leu > 18%), likely underpinning fern adaptability. This work provides crucial initial evidence for a conserved MORF-mediated RNA editing module shared between these early vascular plants (ferns) and angiosperms, offering fundamental insights into the evolutionary trajectory of plant organellar gene regulation. Full article

Dry eye disease (DED) is a multifactorial condition characterized by insufficient tear film stability and ocular discomfort. Conventional artificial tears offer limited efficacy due to short precorneal residence time. This study aimed to develop and optimize ion-sensitive in situ gelling formulations based on low-acyl gellan gum (GG) and arabinogalactan (AG) to enhance retention and therapeutic efficacy in DED. Various buffer systems were screened to identify optimal gelation conditions upon interaction with artificial tear fluid (ATF). Formulations were characterized by pH, osmolality, wettability, thermal behavior, viscosity, and viscoelastic properties. A Design of Experiments (DoE) approach was employed to understand the influence of GG and AG concentrations on rheological behavior. The selected formulation, GG(0.1%)/AG(0.2%), demonstrated a significant viscosity increase upon ATF dilution, suitable viscoelastic properties, enhanced mucoadhesion compared to hyaluronic acid, improved ferning patterns, no cytotoxic effects, and stability over time. In vivo studies in rabbits confirmed prolonged precorneal retention of the fluorescently labeled formulation. These results suggest that the GG/AG-based hydrogel is a promising strategy for improving the performance of artificial tears in DED treatment. Full article

Background: Sarcoidosis is a systemic inflammatory disease characterized by the formation of non-caseating granulomas, predominantly affecting the lungs and lymph nodes. However, the disease can affect any organ, including the eye, where it most commonly manifests as uveitis and dry eye disease (DED). The Ferning Test (FT), a non-invasive method for tear film analysis, offers insight into tear quality. Through this study, we aimed to evaluate the ability of the FT to diagnose and differentiate DED in patients with sarcoidosis. Methods: The study included a sample of 30 patients, divided into three groups, each consisting of 10 patients: one group of patients with sarcoidosis and dry eye disease (S-DED), one group of patients with DED without other systemic pathologies, and a control group of healthy individuals. Tear film samples were collected from the right eye of each participant, without stimulation, by microcapillarity. A drop of tear was spread on a microscope slide, allowed to dry, and then examined under a microscope to analyze the crystallization pattern. Results: Microscopic analysis revealed a significant difference in the structure and morphology of crystallization, as well as in the number of formed branchings, in sarcoidosis patients compared to patients in the other two groups. This finding suggests a distinct alteration in tear film composition in patients with sarcoidosis. Conclusions: Based on these results, the FT represents a valuable and promising tool for the diagnosis of DED associated with sarcoidosis. Being a non-invasive, easy-to-perform, and inexpensive test, it can be widely implemented in any ophthalmology department, opening perspectives for the test to become an important component among the diagnostic elements of dry eye syndrome in patients with sarcoidosis. Full article

Dryopteris fragrans (L.) Schott synthesizes volatile sesquiterpenes through the mevalonate pathway (MVA), in which 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) serves as the key rate-limiting enzyme. Although HMGR plays a crucial role in terpenoid biosynthesis, its functional characteristics in D. fragrans and its involvement in stress responses remain unclear. This study identified three HMGR genes (DfHMGR1/2/3) from the transcriptome data of D. fragrans. Bioinformatics analysis revealed that the encoded proteins are localized to the endoplasmic reticulum and share high sequence similarity with fern homologs. Under abiotic stress conditions, DfHMGRs exhibited differential expression patterns, with marked upregulation under salt and drought stress. To validate the functions of these genes, we generated transgenic Nicotiana tabacum L. plants overexpressing DfHMGRs. Compared with wild-type controls, the transgenic lines showed enhanced tolerance to drought and heat stress. Promoter analysis identified functional regulatory regions controlling DfHMGR expression, and co-expression network analysis predicted 21 potential transcriptional regulators. This study validates the function of D. fragrans HMGRs in a heterologous system and provides candidate genes for improving stress resistance in plants. Full article

cangas are iron-rich outcrops where rupestrian fields develop in the Carajás Mountain Range (CMR). canga formations are ancient ecosystems characterized by high levels of endemic and threatened plant species that thrive on iron-rich substrates in the southeastern Amazon uplands. The recent taxonomic validation of these species enables more accurate distribution modeling across past, present, and future time scales. This work presents a comprehensive palynological database for the Amazon canga vegetation, resulting from extensive field and herbarium surveys, as well as the compilation and taxonomic validation of species in the Carajás Mountain Range (CMR). This atlas includes 204 plant species: 10 ferns and lycophytes, 62 monocots, and 132 eudicots and magnoliids (mainly herbs, lianas, and trees). Most flowering plants are pollinated by bees, with secondary pollination by other insects and wind. The taxa co-occur in two geoenvironments: (1) forested slopes and caves over plinthosols and ferralsols and (2) slopes with canga vegetation over plinthosols. Seventeen species are potential domesticates used by Indigenous peoples. This highlights canga vegetation as a unique and diverse ecosystem with various survival strategies, emphasizing the need for precise habitat definitions in paleoenvironmental and paleoclimate reconstructions. This atlas provides a valuable reference for palynological studies, enhancing the vegetation reconstruction, climate history analysis, pre-Columbian influences on vegetation patterns, and ecological monitoring. Full article

Background: Dihydroflavonol 4-reductase (DFR) is a key enzyme in the flavonoid biosynthetic pathway that regulates anthocyanin and proanthocyanidin accumulation in plants. Although DFR genes have been studied in various species, their origin of the DFR gene family, its distribution across the plant kingdom, and the reasons behind the emergence of different DFR subtypes Methods: This study performed a whole-genome analysis of DFR genes in 237 plant species, including algae, mosses, ferns, gymnosperms, and angiosperms, integrating phylogeny, conserved motifs, duplication mechanisms, positive selection, and expression pattern analyses. Results: These results indicate that the DFR gene family originated from the common ancestor of extant ferns and seed plants, and the emergence of asparagine (Asn)-type and aspartic (Asp)-type DFRs is associated with gymnosperms. Notably, we report for the first time the presence of Asn-type, Asp-type, and arginine (Arg)-type DFRs in some species, which breaks the previous notion that Arg-type DFRs are exclusive to ferns. Tandem duplication is considered the primary driving force behind the expansion of the DFR family and is associated with the formation of different DFR subtypes. Furthermore, Asn-type DFRs were highly expressed during the early stages of seed development, suggesting their important role in seed development. Conclusions: Overall, this study revealed the dynamic evolutionary trajectory of the DFR gene family in plants, providing a theoretical foundation for future research on DFR genes. Full article

Understanding the species diversity distribution of lycophytes and ferns is crucial for identifying biodiversity hotspots and conservation planning. Northeast China, a biodiversity-sensitive area affected by climate change, lacks comprehensive information on diversity and distribution patterns of these plants. To address this gap, we sorted out all naturally distributed lycophyte and fern species recorded in the region, analyzed their diversity, frequency, and threatened status. Correlation and regression analyses were also conducted with geographic gradients at the county level. Our study identified a total of 143 taxa (species and intraspecific taxa) belonging to 48 genera of 19 families of lycophytes and ferns in Northeast China, with terrestrial (85 spp.) and epilithic (55 spp.) life forms dominating. Species with frequencies below 10.00% comprised 75.52% of the total. Notably, five species were listed as threatened in the Red List of China’s Biodiversity, highlighting the urgency for conservation measures. Overall, species diversity decreased from low to high latitudes, but increased with maximum elevation and elevation range. High diversity areas were concentrated mainly in Da Hinggan Mountains, Xiao Hinggan Mountains, and Changbai Mountains, which correspond to the main mountainous terrain of Northeast China. Changbai Mountains exhibited the highest diversity, establishing itself as a pivotal diversity center for lycophytes and ferns in the region. Exploring the diversity and distribution of lycophytes and ferns is crucial for understanding their interactions with environmental gradients, and thereby supporting significant biodiversity conservation efforts in Northeast China. Full article

Global change influences species diversity patterns. Compared with seed plants, ferns are more sensitive to temperature and humidity changes and are an ideal group for studying species diversity patterns under future climate changes. Polypodiaceae, which has important ecological and application value, such as medicinal and ornamental value, is one of the most widely distributed fern families, with rich species diversity. Here, we explore the changes in the species diversity patterns of Polypodiaceae and their influencing factors. We collected more than 300,000 data points on the distribution of Polypodiaceae to map actual current species diversity patterns. We used Maxent to establish current and future potential species distribution models using 20 predictors and determined the current species diversity patterns using the actual current species diversity patterns and current potential species distribution model method. Multiple linear regression and random forest models were used to evaluate the effects of climate factors on the species diversity patterns of Polypodiaceae. We evaluated the effects of future climate changes on the species diversity of Polypodiaceae. The species diversity of Polypodiaceae increased gradually from higher to lower latitudes and the centers were concentrated in the low latitudes of tropical rainforests. There were four distribution centers across the world for Polypodiaceae: central America, central Africa, southern Asia, and northern Oceania. The species diversity of Polypodiaceae was greatly affected by precipitation factors rather than temperature factors. Under future climate change scenarios, species diversity is expected to shift and accumulate toward the equator in mid-to-low latitudes. Species diversity is projected to remain concentrated in low-latitude regions but will tend to aggregate towards higher altitude areas as global temperatures rise, with precipitation during the warmest season identified as the most influential factor. Full article

The family Onocleaceae represents a small family of terrestrial ferns, with four genera and around five species. It has a circumboreal to north temperate distribution, and exhibits a disjunct distribution between Eurasia and North America, including Mexico. Historically, the taxonomy and classification of this family has been subject to debate and contention among scholars, leading to contradictory classifications and disagreements on the number of genera and species within the family. Furthermore, due to this disjunct intercontinental distribution and the lack of detailed study across its wide range, this family merits further study to clarify its distributional pattern. Maximum likelihood and Bayesian phylogenetic reconstructions were based on a concatenated sequence dataset for 17 plastid loci and one nuclear locus, which were generated from 106 ingroup and six outgroup taxa from three families. Phylogenetic analyses support that Onocleaceae is composed of four main clades, and Pentarhizidium was recovered as the first branching lineages in Onocleaceae. Molecular dating and ancestral area reconstruction analyses suggest that the stem group of Onocleaceae originated in Late Cretaceous, with subsequent diversification and establishment of the genera Matteuccia, Onoclea, Onocleopsis, and Pentarhizidium during the Paleogene and Neogene. The ancestors of Matteuccia, Onoclea, and Onocleopsis could have migrated to North America via the Beringian land bridge or North Atlantic land bridge which suggests that the diversification of Matteuccia + Onoclea + Onocleopsis closely aligns with the Paleocene-Eocene Thermal Maximum (PETM). In addition, these results suggest that Onocleaceae species diversity peaks during the late Neogene to Quaternary. Studies such as this enhance our understanding of the mechanisms and climatic conditions shaping disjunct distribution in ferns and lycophytes of eastern Asia, North America, and Mexico and contribute to a growing body of evidence from other taxa, to advance our understanding of the origins and migration of plants across continents. Full article

We present a mathematical framework for analyzing fractal patterns in AI-generated images using persistent homology. Given a text-to-image mapping $M:T\to I$, we demonstrate that the persistent homology groups $H_k\left(t\right)$ of sublevel set filtrations ${\left\{f^{-1}\left((-\infty ,t]\right)\right\}}_{t\in \mathbb{R}}$ characterize multi-scale geometric structures, where $f:M\left(p\right)\to \mathbb{R}$ is the grayscale intensity function of a generated image. The primary challenge lies in quantifying self-similarity in scales, which we address by analyzing birth–death pairs $(b_i,d_i)$ in the persistence diagram $PD\left(M\right(p\left)\right)$. Our contribution extends beyond applying the stability theorem to AI-generated fractals; we establish how the self-similarity inherent in fractal patterns manifests in the persistence diagrams of generated images. We validate our approach using the Stable Diffusion 3.5 model for four fractal categories: ferns, trees, spirals, and crystals. An analysis of guidance scale effects $\gamma \in [4.0,8.0]$ reveals monotonic relationships between model parameters and topological features. Stability testing confirms robustness under noise perturbations $\eta \le 0.2$, with feature count variations $\Delta {\mu }_f<0.5$. Our framework provides a foundation for enhancing generative models and evaluating their geometric fidelity in fractal pattern synthesis. Full article

Yuanjiang dry–hot valley is located in the southwest of mainland China. It is a sparsely vegetated area with a fragile arid ecosystem. Although the valley previously had forest cover, it has become a tropical montane savannah in recent decades. Mechanisms controlling plant species distribution in such dry–hot valleys are unclear. Clarifying this will be beneficial to sustainable ecosystem management in dry–hot valleys. This study explored the relationship between diversity patterns of plant species and their environments in the lowland of this dry–hot valley. To achieve this, transects and plots were arranged along the river channel. Alpha and beta diversity indices were calculated to quantify biodiversity changes between species and environments. Estimated species, rarity, and abundance indices were also utilized to examine the correlation among species, their population size, and their environment: Species_estimated (expected number of species in t pooled plots), Singletons (the number of species with only one individual in t pooled plots), Uniques (the number of species living in one plot in t pooled plots), ACE (species richness estimator with coverage-based abundance), ICE (species richness estimator with coverage-based incidence), and Chao2 (species richness estimator extrapolated from Singletons). Fifty years of meteorological records, including temperature and precipitation, were utilized as climate variables. The results indicated the following findings: (1) alpha diversity was higher closer to the river, whereas the beta diversity was higher towards the lower sections of the river (Bray–Curtis < 0.5), but this trend was reversed in the perpendicular transects; (2) total phosphorous (TP) and total potassium (TK) were higher on flatter ground, tending to be associated with raised nitrogen (TN) and organic matter (OM); (3) soil nutrients were higher towards the lower sections of the river, corresponding to an increased number of species; (4) water supply determined plant distribution, with soil condition determining water retention; (5) the estimated species and their rarity and abundance indices were associated with proximity to the river, indicating heterogeneity of habitats and soil condition; and (6) fern species could be used as indicators representing the xeric environment of Yuanjiang dry–hot valley. Plant cover was reduced at low altitudes, with high temperatures and a low water supply. These results draw attention to the need for specific policy formation to protect the microhabitats and manage the environment of the Yuanjiang valley. Full article