Search Results (244)

Understanding the genetic basis of agronomic traits in quinoa adapted to the Qinghai–Tibet Plateau is essential for developing high-yield cultivars, as conventional breeding is constrained by limited molecular tools. In this study, 300 cultivated accessions were evaluated for five quantitative traits, and whole-genome resequencing generated 3.69 million high-quality SNPs. Population structure analysis and genome-wide association study (GWAS) were conducted, with integration of seed developmental transcriptomes to refine trait-associated loci. A highly admixed genetic background (K = 7) was revealed, and 11 significant QTLs across seven chromosomes were identified, involving genes related to metabolism, transport, and cell-wall formation. Among these, CesA4 (CQ042210) showed a strong association with thousand grain weight (TGW) and a distinct expression maximum at the early seed-filling stage. These results provide a genomic framework for understanding trait variation in plateau-adapted quinoa and highlight promising targets for marker-assisted breeding. Full article

Background: Tracheobronchopathia osteochondroplastica (TO) is a rare benign disorder characterized by submucosal cartilaginous and osseous nodules of the tracheobronchial tree, typically sparing the posterior membranous wall. Involvement of the vocal cords is exceedingly rare and may result in critical airway obstruction. The underlying genetic and molecular mechanisms of TO remain largely unexplored. Case presentation: We report a rare case of TO extending from the vocal cords to the bronchi in a 76-year-old man who initially presented with pneumonia and later developed acute respiratory failure due to severe airway narrowing, necessitating emergency tracheostomy. Bronchoscopy and computed tomography revealed diffuse calcified nodules involving the anterior and lateral airway walls, including the subglottic region. Histopathology demonstrated chronic inflammatory cell infiltration with squamous metaplasia. To explore the molecular basis of this condition, whole-genome sequencing (WGS) was performed using peripheral blood samples—the first such application in TO. WGS identified 766 germline mutations (including 27 high-impact variants) and 66 structural variations. Candidate genes were implicated in coagulation and inflammation (KNG1), arachidonic acid metabolism and extracellular matrix remodeling (PLA2G4D), ciliary dysfunction and mineralization (TMEM67), vascular calcification (CDKN2B-AS1), smooth muscle function (MYLK4), abnormal calcification (TRPV2, SPRY2, BAZ1B), fibrotic signaling (AHNAK2), and mucosal barrier integrity (MUC12/MUC19). Notably, despite systemic germline mutations, calcification was restricted to the airway. Conclusions: This case highlights that TO with vocal cord involvement can progress beyond a benign course to cause life-threatening airway obstruction. Integrating clinical, histological, and genomic findings, we propose a novel pathophysiological model in which systemic genetic susceptibility interacts with local immune cell infiltration and fibroblast-driven extracellular matrix remodeling, resulting in airway-restricted dystrophic calcification. This first genomic characterization of TO provides new insights into its pathogenesis and suggests that multi-omics approaches may enable future precision medicine strategies for this rare airway disease. Full article

Drought severely limits plant growth, threatening global food security and biodiversity. This review provides a comprehensive overview of the recent advances in plant responses to drought, ranging from initial sensing to physiological adaptation, as well as guidelines for experimental design. We focus on key regulatory components, specifically the ABA signaling core (PYR/PYL/RCARs, PP2C phosphatases, and SnRK2 kinases) and ROS signaling. We provide a detailed description of transcriptional networks, highlighting the pivotal roles of DREB, NAC, and MYB transcription factors in coordinating gene expression. Furthermore, we explore downstream tolerance strategies, including osmoprotectant (e.g., proline) accumulation, cell wall remodeling involving expansins and pectin methylesterases, as well as stomatal regulation. We also discuss how combining genetics with multi-omics and high-throughput phenotyping bridges the gap between molecular mechanisms and whole-plant physiological performance. Ultimately, these insights provide a foundation for refining research approaches and accelerating the development of drought-resilient crops to sustain agricultural productivity and ecosystem stability in increasingly arid environments. Full article

Background: Infections caused by the multidrug-resistant pathogen Mycobacterium abscessus (Mab) are notoriously difficult to treat. The novel β-lactamase inhibitor durlobactam, in combination with β-lactams, shows potent bactericidal activity against Mab, but the potential for acquired resistance remains a clinical concern. Objectives: To identify and characterize mechanisms of acquired resistance to durlobactam in Mab. Methods: In vitro single-step resistance selection was performed by plating wild-type Mab ATCC 19977 and by transcriptional silencing using a CRISPR interference (CRISPRi) system. Minimum inhibitory concentrations (MICs) were determined by both an agar-based method and broth microdilution. Results: Whole-genome sequencing of durlobactam-resistant mutants identified loss-of-function mutations in ponA1, a gene encoding a class A penicillin-binding protein involved in cell wall synthesis. Targeted deletion of ponA1 (ΔponA1) and CRISPRi-mediated knockdown of ponA1 expression both recapitulated the resistance phenotype, resulting in a significant increase in the durlobactam MIC on solid agar media. Strikingly, broth microdilution MICs remained largely unaffected. Conclusions: Inactivation of the peptidoglycan synthase PonA1 is a novel mechanism of resistance to durlobactam in Mab that is phenotypically expressed only during growth on solid surfaces. This finding identifies a specific genetic pathway for resistance and highlights that standard broth-based susceptibility testing could miss clinically relevant resistance mechanisms. Full article

Extracellular vesicles (EVs) secreted by Fusarium oxysporum play an important role in the process of its infestation of the host, but the in vitro research system for EVs of F. oxysporum (Fo-EVs) has not yet been improved, and the mechanism of its action remains unclear. In this study, particle size distribution, particle concentration, number of particles per unit of protein, number of particles per unit of mycelial biomass, and concentration of contaminated proteins were used as indicators to evaluate the yield and purity of Fo-EVs. The optimal method for Fo-EV preparation and extraction was screened by comparing liquid culture, solid culture, and solid culture with enzymatic cell wall hydrolysis. The optimal system for Fo-EVs separation and purification was screened by a pairwise combination of three primary methods (Ultracentrifugation (UC), Ultrafiltration (UF), and Polyethylene glycol precipitation method (PEG)) and two secondary methods (Size-exclusion chromatography (SEC) and Aqueous two-phase system (ATPS)), respectively. The protein composition was identified via mass spectrometry technology, followed by GO annotation and GO enrichment analysis using whole-genome proteins as the background. Based on these steps, a Fo-EV protein library was constructed to reveal Fo-EV’s most active biological functions. The results showed that solid culture combined with the UC-SEC method could effectively enrich Fo-EVs with a typical cup-shaped membrane structure. The obtained Fo-EVs had an average particle size of 253.50 nm, a main peak value of 200.60 nm, a particle concentration of 2.04 × 10¹⁰ particles/mL, and a particle number per unit protein of 1.09 × 10⁸ particles/μg, which were significantly superior to those of other combined methods. Through proteomic analysis, 1931 proteins enriched in Fo-EVs were identified, among which 350 contained signal peptides and 375 had transmembrane domains. GO enrichment analysis revealed that these proteins were mainly involved in cell wall synthesis, vesicle transport, and pathogenicity-related metabolic pathways. Additionally, 9 potential fungal EV markers, including Hsp70, Rho GTPase family, and SNARE proteins, were screened. This study constructed an isolation system and a marker database for Fo-EVs, providing a methodological and theoretical basis for in-depth analysis of the biological functions of Fo-EVs. Full article

The escalating crisis of antibiotic resistance, particularly concerning foodborne pathogens such as Staphylococcus aureus and its biofilm contamination, has emerged as a major global challenge to food safety and public health. Biofilm formation significantly enhances the pathogen’s resistance to environmental stresses and disinfectants, underscoring the urgent need for novel antimicrobial agents. In this study, we isolated Bacillus strain B673 from the saline–alkali environment of Xinjiang, conducted whole-genome sequencing, and applied antiSMASH analysis to identify ribosomally synthesized and post-translationally modified peptide (RiPP) gene clusters. By integrating an LSTM-Attention-BERT deep learning framework, we screened and predicted nine novel antimicrobial peptide sequences. Using a SUMO-tag fusion tandem strategy, we achieved efficient soluble expression in an E. coli system, and the purified products exhibited remarkable inhibitory activity against Staphylococcus aureus (MIC = 3.13 μg/mL), with inhibition zones larger than those of the positive control. Molecular docking and dynamic simulations demonstrated that the peptides can stably bind to MurE, a key enzyme in cell wall synthesis, with negative binding free energy, suggesting an antibacterial mechanism via MurE inhibition. This study provides promising candidate molecules for the development of anti-drug-resistant agents and establishes an integrated research framework for antimicrobial peptides, spanning gene mining, intelligent screening, efficient expression, and mechanistic elucidation. Full article

We report the first identification of several large (1.4–2.2 MDa), highly stable protein–peptide complexes in various organs and tissues (body wall, gonads, respiratory trees, gut, and coelomic fluid) of the sea cucumber Paracaudina chilensis. Gel filtration and transmission electron microscopy methods were used to estimate the molecular weights and sizes of the complexes. According to light scattering assay data, these multiprotein complexes undergo significant dissociation only in the presence of 3.0 M MgCl₂ or 8.0 M urea containing 0.1 M EDTA and DTT. Analysis of the complexes using SDS-PAGE and MALDI mass spectrometry showed that all complexes contain numerous proteins (>10 kDa), whose number and composition vary among organs. Additionally, using MALDI mass spectrometry, it was shown that the whole-organism complexes contain 254 distinct peptides (<10 kDa). The peptide content in organ-specific complexes decreases in the following order: respiratory trees (104) > coelomic fluid (76) > body wall (64) > gut (58) > gonads (55). In contrast to individual proteins and peptides, multiprotein complexes have expanded possibilities, since they can interact with various molecules and cells. Thus, they can perform the functions of all peptides and proteins located on their surfaces. We propose that the unique protein and peptide composition of each complex facilitates the specific biological functions of its respective organ. Full article

Sulfiting agents are common preservatives in the food and beverage industry to inhibit spoilage microorganisms. Sulfite produced by the dissolution of sulfur dioxide (SO₂) in water is used as a microbial inhibitor and antioxidant during winemaking. Thus, sulfite resistance is a desirable trait for wine yeasts. However, consumer health concerns regarding SO₂ exposure require a better understanding of the molecular basis of sulfite resistance/response. In this study, we have developed a highly SO₂-stress-resistant Saccharomyces cerevisiae strain (F3) using evolutionary engineering by repeated batch selection at gradually increased potassium metabisulfite (K₂S₂O₅) levels. F3 was resistant to 1.1 mM K₂S₂O₅ stress, which was strongly inhibitory to the reference strain, and cross-resistant to oxidative, heat, and freeze–thaw stresses. F3 also had enhanced cell wall integrity and altered carbon metabolism, indicating its potential for industrial applications, including winemaking. Comparative whole genome sequencing revealed point mutations in SSU1 and FZF1 that are related to SO₂ transport; ATG14, related to autophagy; and other genes involved in vacuolar protein sorting. Comparative transcriptomic analysis showed significant upregulation of SSU1 and differential expression of genes related to transport and carbohydrate metabolism. These findings may shed light on the molecular mechanisms contributing to SO₂ resistance and industrial robustness in S. cerevisiae. Full article

In this study, a comprehensive approach to the taxonomy and the distribution areas of Cornus mas (commonly known as cornelian cherry) is presented, considering the superior valorization of bioactive compounds through co-microencapsulation in a unique matrix combination, together with probiotic bacteria. According to the phytochemical profile, the whole plant of cornelian cherry includes 101 chemical compounds, classified as follows: polyphenols, terpenoids, carotenoids, vitamins, carbohydrates, acids, and hydrocarbons. In general, the bioactive compounds are highly sensitive to digestion and external factors, such as oxygen, pH, temperature, etc. In order to improve the bioaccesibility and the storage stability of the polyphenols, a solid–liquid ultrasound assisted method was applied to deliver an anthocyanin-enriched extract, which was microencapsulated together with Lacticaseibacillus casei (L. casei) by freeze-drying in a unique combination of whey protein isolate (WPI) and maltodextrin (MD) as wall materials. Two powders were obtained, with and without the probiotic bacteria. The data obtained in this study showed a high encapsulation efficiency (82.16–88.95%) of anthocyanins, whereas for L. casei, the microencapsulation efficiency reached 80%. The co-microencapsulated powder showed a viable cell count of 3.80·10⁹ CFU/g dry matter (D.M.). The microencapsulated powders showed a significant amount of total polyphenols (8.30–13.00 mg of gallic acid equivalent per gram D.M.). Furthermore, the in vitro digestibility of the anthocyanins highlighted the protective effect of the microencapsulation matrix in the stomach, whereas a slow release was observed in the simulated intestinal conditions. Furthermore, after 21 days of storage, the lactic acid bacteria viability was high (2.53 × 10⁹ CFU/g dry matter), which confirmed the functionality and the nutraceutical value of the co-microencapsulated powder. Full article

4-vinylguaiacol (4-VG) is a commercially important compound due to its characteristic clove-like aroma and its use as a flavoring in the food, beverage, and cosmetics industries. However, its extraction from natural sources or by a chemical method is expensive. The bioconversion of ferulic acid (FA) to 4-VG via microorganisms is an alternative, considering the market trend toward biotechnological and environmentally friendly processes and products. This study aimed to evaluate the tolerance of the bacterial strain Brucella intermedia (basonym Ochrobactrum intermedium) TG 3.48 to FA, its bioconversion to 4-VG, and the activity of the FA decarboxylase enzyme (FADase), which is key to the 4-VG production process. The strain tolerated FA concentrations up to 700 mg L⁻¹. When the microorganism grew at 300 mg L⁻¹ FA in Mineral Liquid Medium (MLM), it converted 99.5% of FA to 4-VG within 12 h. The FADase activity was cell-associated with 5.17 U mL-1 in the whole cell, 4.40 U mL⁻¹ in the intracellular extract, and 3.54 U mL⁻¹ in the cell wall fragments, while the specific activity was 778.90 U mg⁻¹. Full article

Skin hyperpigmentation disorders represent a major dermatological challenge, and safe alternatives to conventional depigmenting agents remain scarce. Probiotics and their postbiotic derivatives have emerged as promising natural candidates; however, only a few bacterial strains have been investigated for melanogenesis-inhibitory activity, and their true potential remains largely unexplored. Here, we report for the first time the biosafety profile and anti-melanogenic activity of Lactobacillus salivarius BGHO-1 and Lactobacillus paracasei BGSJ2-8, and assess their possible use in the treatment of skin hyperpigmentation. Two complementary zebrafish-based approaches were employed: (i) image-assisted analysis of pigmentation patterns, melanocyte morphology, and melanocytotoxicity, and (ii) quantitative melanin analysis, enabling integrated safety and efficacy evaluation. We investigated both native and heat-inactivated preparations, including whole cultures, cell-free supernatants, isolated cells, and separated cell walls/membranes and cytoplasmic fractions. While several fractions demonstrated the ability to inhibit melanogenesis, the cell wall/membrane fraction was the most potent, reducing melanin content by 64% compared to untreated embryos, while causing no systemic side effects and preserving melanocyte structure. Furthermore, this fraction did not elicit inflammatory responses or neutropenia, underscoring its favorable safety profile at anti-melanogenic doses. Collectively, this study identifies specific postbiotics as effective and safe modulators of melanogenesis and highlights their translational potential in developing novel approaches for treating skin hyperpigmentation. Full article

Mining novel Streptomyces species from extreme environments provides a valuable strategy for the discovery of new antibiotics. Here, we report a strain of Streptomyces sp. HMX87^T, which exhibits antimicrobial activity and was isolated from desert soil collected in the Tuha Basin, China. Molecular taxonomic analysis revealed that the 16S rRNA gene sequence of strain HMX87^T shares the highest similarity with those of Streptomyces bellus CGMCC 4.1376^T (98.5%) and Streptomyces coerulescens DSM 40146^T (98.43%). In phylogenetic trees, it formed a distinct branch. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain HMX87^T and the above two type strains were below the thresholds of 95% and 70%, respectively, confirming that strain HMX87^T represents a novel species within the genus Streptomyces, for which the name Streptomyces hamibioticus sp. nov. is proposed. Physiologically, the strain HMX87^T grew at temperatures ranging from 25 to 37 °C, tolerated pH values from 5 to 12, and survived in NaCl concentrations of 0% to 8% (w/v). Chemotaxonomic characterization indicated the presence of LL-diaminopimelic acid (LL-DAP) in the cell wall, ribose and galactose as whole-cell hydrolysate sugars, MK-9(H8) (66.3%) as the predominant menaquinone, and iso-C_16:0 (25.94%) and anteiso-C_15:0 (16.98%) as the major fatty acids characteristics that clearly distinguish it from its closest relatives. Whole-genome sequencing of strain HMX87^T revealed an abundance of genes associated with high-temperature tolerance, salt-alkali resistance, and antimicrobial activity. The genomic features and secondary metabolic potential reflect its adaptation to extreme environmental conditions, including high temperature, salinity, alkalinity, strong ultraviolet radiation, and oligotrophic nutrients. The strain HMX87^T has been deposited in the Czech Collection of Microorganisms (CCM 9454^T) and the Guangdong Microbial Culture Collection Center (GDMCC 4.391^T). The 16S rRNA gene and whole-genome sequences have been submitted to GenBank under accession numbers PQ182592 and PRJNA1206124, respectively. Full article

Glands from Nepenthes pitcher secrete various substances, including digestive enzymes, and absorb nutrients from digested prey. Due to the extreme specialization of these glands, they are an interesting model for studying secretory cells’ structure and activity. This study aimed to fill the gap in the literature concerning the immunocytochemistry of Nepenthes digestive glands in the major cell wall polysaccharides and glycoproteins. To do this, the localization of the cell wall components in the cell walls of glandular cells was performed using whole-mount immunolabeled glands of Nepenthes albomarginata. Also, we wanted to check to what extent the cuticles of glandular cells with discontinuities would be a barrier to the antibodies. The technique used allowed for the localization of de-esterified pectic homogalacturonans in the outer walls of gland cells. The remaining antibodies (which detect esterified pectins, hemicelluloses, and arabinogalactan protein) marked only debris or secretion residues on the gland or epidermal surfaces. Positive labeling with LM19 and CCRC-M38 antibodies suggests the presence of pectic homogalacturonan in the very superficial part of the glands’ cell walls, so they were easily accessible to antibodies. Full article

Basal stem rot caused by Fusarium solani is among the most destructive soil-borne diseases affecting passion fruit (Passiflora spp.). While biological control employing antagonistic microorganisms offers a promising plant protection strategy, reports on antagonists specifically targeting passion fruit basal stem rot remain limited. Here, a screen for F. solani antagonists led to the identification of Bacillus velezensis strain L11-7, whose whole genome was subsequently sequenced. Pot experiments demonstrated that strain L11-7 significantly reduced the severity of stem basal rot, achieving control efficiencies of 92.85%, and exhibited broad antagonistic properties against other plant pathogenic fungi. L11-7 possesses cellulase, glucanase, and protease activities, alongside capabilities for nitrogen and phosphorus production. L11-7 was identified as B. velezensis through morphological analysis, 16S rRNA, gyrB, and rpoB gene sequencing, and whole-genome analysis. Its genome features a single circular 3.97 Mb chromosome harboring 13 s metabolite biosynthetic gene clusters (e.g., fengycin, surfactin, macrolactin H, bacillaene, difficidin) and genes encoding essential cell wall hydrolases. Several genes related to plant growth promotion, including those involved in nitrogen fixation and IAA production, are also present. These results indicate that B. velezensis L11-7 is a prospective biocontrol agent against passion fruit basal stem rot and has plant growth-promoting properties. Full article

Screens for specific phenotypes have long been a cornerstone of biology. Here, we present an updated synthesis of our large-scale visual screens for Arabidopsis (Arabidopsis thaliana) mutants that exhibit leaf morphology defects. In our 2009 review, we used phenotypes to group the leaf mutants that we had isolated and characterized since 1992; here, by contrast, we functionally classified the mutations that we studied over the last 16 years based on the biological programs they disrupt. Since 2009, we have identified and analyzed 38 genes required for proper leaf development; these genes are involved in translation, chloroplast function, cell wall construction, auxin homeostasis, microRNA biogenesis, and epigenetic regulation. Many of the identified mutants have pleiotropic phenotypes, consistent with the central roles of the affected pathways in development. In this review, we systematically link morphological traits to specific molecular dysfunctions, highlighting the enduring utility of forward genetic approaches. We found that the Arabidopsis leaf is a model organ of a model organism, and we have used this model-in-a-model system to dissect whole-plant traits such as cell proliferation and expansion, and to improve our understanding of the genetic control of plant form and size. Full article