Search Results (934)

Antibiotic misuse accelerates resistance dissemination via plasmid conjugation, but quorum sensing (QS) regulatory mechanisms remain undefined. Using Escherichia coli (E. coli) MG1655 conjugation models (RP4-7/EC600 plasmids), we demonstrate that long-chain acyl-homoserine lactones (C10/C12-HSL) enhance transfer frequency by up to 7.7-fold (200μM C12-HSL; p < 0.001), while quorum-quenching by sub-inhibitory vanillin suppressed this effect by 95% (p < 0.0001). C12-HSL compromised membrane integrity via ompF upregulation (4-fold; p < 0.01) and conjugative pore assembly (trbBp upregulated by 1.38-fold; p < 0.05), coinciding with ROS accumulation (1.5-fold; p < 0.0001) and SOS response activation (recA upregulated by 1.68-fold; p < 0.001). Crucially, rpoS and rmf deletion mutants reduced conjugation by 65.5% and 55.8%, respectively (p < 0.001), exhibiting attenuated membrane permeability (≤65.5% reduced NPN influx; p < 0.0001), suppressed ROS (≤54% downregulated; p < 0.0001), and abolished transcriptional induction of conjugation/stress genes. Reciprocal RpoS–RMF (ribosomal hibernation factor) crosstalk was essential for AHL responsiveness, with deletions mutually suppressing expression (≤65.9% downregulated; p < 0.05). We establish a hierarchical mechanism wherein long-chain AHLs drive resistance dissemination through integrated membrane restructuring, stress adaptation, and RpoS–RMF-mediated genetic plasticity, positioning QS signaling as a viable target for curbing resistance spread. Full article

Rice seed storage proteins (SSPs) play a critical role in determining the nutritional quality, cooking properties, and digestibility of rice. To enhance seed quality, CRISPR/Cas9 genome editing was applied to modify SSP composition by targeting genes encoding 13 kDa prolamins and type A glutelins. Three CRISPR/Cas9 constructs were designed: one specific to the 13 kDa prolamin subfamily and two targeting conserved GluA glutelin regions. Edited T₀ and T₁ lines were generated and analyzed using InDel analysis, SDS-PAGE, Bradford assay, and RP-HPLC. Insertions were more frequent than deletions, accounting for 56% and 74% of mutations in prolamin and glutelin genes, respectively. Editing efficiency varied between sgRNAs. All lines with altered protein profiles contained InDels in target genes. SDS-PAGE confirmed the absence or reduction in bands corresponding to 13 kDa prolamins or GluA subunits, showing consistent profiles among lines carrying the same construct. Quantification revealed significant shifts in SSP composition, including increased albumin and globulin content. Prolamin-deficient lines showed reduced prolamins, while GluA-deficient lines exhibited increased prolamins. Total protein content was significantly elevated in all edited lines, suggesting enrichment in lysine-rich fractions. These findings demonstrate that CRISPR/Cas9-mediated editing of SSP genes can effectively reconfigure the rice protein profile and enhance its nutritional value. Full article

Medicago falcata is one of the most important perennial forage legumes in the Medicago genus. In this study, we reported the complete chloroplast genome of two M. falcata ecotypes grown in different regions, and compared them with those of Medicago truncatula and Medicago sativa. We found that the M. falcata chloroplast genome lacks a typical quadripartite structure, containing 78 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. They shared high conservation in size, genome structure, gene order, gene number and GC content with those of M. truncatula and M. sativa. High nucleotide diversity occurred in the coding gene regions of rps16, rps3, and ycf4 genes. Meanwhile, mononucleotide repeats are the most abundant repeat type, followed by the di-, tri-, tetra-, and pentanucleotides, and forward repeats were more abundant than reverse and palindrome repeats for all these three Medicago species. Phylogenetic analyses using both coding sequences and complete chloroplast genomes revealed that M. falcata shares the closest phylogenetic relationship with M. hybrida and M. sativa. This study provided valuable information for further studies on the genetic relationship of the Medicago genus. Full article

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus Sassafras has long been controversial. Chloroplast (cp) evolution of Sassafras has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of Sassafras, and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 Sassafras ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (ccsA-ndhD, trnH-psbA, rps15-ycf1, and petA-psbJ) and 672 cp microsatellites were identified for Sassafras. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that Sassafras constituted a monophyletic clade and grouped a sister branch with the Cinnamomum sect. Camphora within the tribe Cinnamomeae. Divergence time between S. albidum and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), S. tzumu diverged from S. randaiense at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of Sassafras. Overall, our study clarified the evolution pattern of Sassafras cp genomes and elucidated the phylogenetic position and divergence time framework of Sassafras. Full article

A novel barna-like virus was found to be associated with field-collected Afrina sporoboliae plant-parasitic nematodes. The positive-sense, single-stranded RNA genome of this virus, named Afrina barna-like virus (AfBLV), comprises 4020 nucleotides encoding four open reading frames (ORFs). ORF 1 encodes a protein product spanning a transmembrane, a peptidase, and VPg domains, whereas an overlapping ORF 2 encodes an RNA-dependent RNA polymerase (RdRP). ORF2 may be expressed via a −1 translational frameshift. In phylogenetic reconstructions, the RdRP of AfBLV was placed inside a separate clade of barna and barna-like viruses related to but distinct from the genera in the Solemoviridae and Alvernaviridae families, within the overall lineage of Sobelivirales. ORF 3 of AfBLV encodes a protein product of 206 amino acids (aa) long with homology to a putative protein encoded by a similarly positioned gene of an uncharacterized virus sequence identified previously as Barnaviridae sp. ORF 4 encodes a 161 aa protein with no significant similarities to sequences in the GenBank databases. AfBLV is the first barnavirus found in a nematode. Sequence comparisons of the AfBLV genome and genomes of other barna-like viruses suggested that a recombination event was involved in the evolution of AfBLV. Analyses of the phylogeny of RdRPs and genome organizations of barna-like and solemo-like viruses support the re-classification of Barnavirus and Dinornavirus genera as members of the Solemoviridae family. Full article

Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes of four Rosa species: R. acicularis, R. iliensis, R. laxa, and R. spinosissima. In addition to the plastome, we sequenced the nuclear ribosomal internal transcribed spacer (ITS). Results: Plastomes ranged in size from 157,148 bp (R. iliensis) to 157,346 bp (R. laxa). In each plastome, 136 genes were annotated, comprising 90 protein-coding, 38 tRNA, and eight rRNA genes. A total of 905 SSRs were identified, ranging from 224 (R. acicularis) to 229 in R. spinosissima. Nine highly variable regions were detected, including two coding genes (rps16 and ycf1) and seven intergenic spacers (ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), rpl14-rpl16, trnR(UCU)-atpA, trnD(GUC), trnG(UCC)-trnfM(CAU), and psbE-petL). Maximum Likelihood (ML) phylogenetic analyses based on the complete plastome and ycf1 gene datasets consistently resolved the Rosa species into three major clades, with strong bootstrap support. In contrast, the ML tree based on ITS resolved species into four clades but showed lower bootstrap values, indicating reduced resolution compared to plastid datasets. Conclusions: Our findings underscore the value of plastome data in resolving phylogenetic relationships within the genus Rosa. Full article

Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article

Background/Objectives: Senior-Loken syndrome (SLS) is a rare autosomal recessive renal–retinal disease caused by mutations in 10 genes. This study aimed to review the ophthalmic findings, renal function, and genotypes of Korean SLS cases. Methods: We retrospectively reviewed 17 genetically confirmed SLS patients in Korea, including 9 newly identified cases and 8 previously reported. Comprehensive ophthalmologic evaluations and renal assessments were conducted. Genetic testing was performed using whole-genome sequencing (WGS), whole-exome sequencing (WES), or Sanger sequencing. Results: Among the 17 patients, patients with NPHP1 mutations were most common (35.3%), followed by those with NPHP4 (29.4%), IQCB1 (NPHP5, 29.4%), and SDCCAG8 (NPHP10, 5.9%) mutations. Patients with NPHP1 mutations showed retinitis pigmentosa (RP) sine pigmento and preserved central vision independent of renal deterioration. Patients with NPHP4 mutations showed early renal dysfunction. Two patients aged under 20 maintained relatively good visual function, but older individuals progressed to severe retinopathy. Patients with IQCB1 mutations were generally prone to early and severe retinal degeneration, typically manifesting as Leber congenital amaurosis (LCA) (three patients), while two patients exhibited milder RP sine pigmento with preserved central vision. Notably, two out of five (40.0%) maintained normal renal function at the time of diagnosis, and both had large deletions in IQCB1. The patient with SDCCAG8 mutation exhibited both end-stage renal disease and congenital blindness due to LCA. Wide-field fundus autofluorescence (AF) revealed perifoveal and peripapillary hypoAF with a perifoveal hyperAF in younger patients across genotypes. Patients under 20 years old showed relatively preserved central vision, regardless of the underlying genetic mutation. Conclusions: The clinical manifestation of renal and ocular impairment demonstrated heterogeneity among Korean SLS patients according to causative genes, and the severity of renal dysfunction and visual decline was not correlated. Therefore, simultaneous comprehensive evaluations of both renal and ocular function should be performed at the initial diagnosis to guide timely intervention and optimize long-term outcomes. Full article

Background: Alcohol-associated liver disease (ALD) is characterized by gut–liver axis dysfunction and metabolic dysregulation, yet the therapeutic potential of probiotics remains underexplored. This study aimed to investigate the protective effects and mechanisms of Lacticaseibacillus paracasei 36 (LP36) against ethanol-induced ALD in mice. Methods: Mice were pretreated with LP36 prior to ethanol exposure. Liver injury was assessed through serum ALT/AST levels, hepatic steatosis (TC/TG content), and ethanol detoxification capacity (ADH/ALDH activity). Intestinal barrier integrity was evaluated via Mucin2 and ZO-1 expression, and gut microbiota alterations were analyzed by 16S rRNA sequencing. Hepatic transcriptomics (RNA-seq) was performed to identify key regulatory pathways. Results: LP36 significantly attenuated ethanol-induced liver injury, evidenced by reduced ALT/AST, improved hepatic steatosis (lower TC/TG), and enhanced ADH/ALDH activity. Mechanistically, LP36 restored intestinal barrier function (upregulated Mucin2 and ZO-1), modulated gut microbiota (suppressed Parasutterella, Romboutsia, and Christensenellaceae_R-7_group; enriched Faecalibaculum and Tuzzerella), and reduced systemic inflammation. Transcriptomics revealed LP36-mediated rescue of AMPK signaling, involving regulation of Stk11, Prkag3, lipid synthesis genes (Fasn, Acaca), and metabolic modulators (Creb3l3, G6pc3, mTOR, Rps6kb2).Conclusions: LP36 ameliorates ethanol-induced ALD by enhancing intestinal barrier integrity, reshaping gut microbiota, and restoring AMPK-dependent metabolic homeostasis. These findings highlight LP36 as a promising probiotic candidate for ALD prevention. Full article

During aging, the brain vasculature undergoes significant deterioration characterized by increased arterial tortuosity, compromised blood–brain barrier integrity, and reduced cerebral blood flow, all of which contribute to various neurological disorders. Thus, understanding the mechanisms underlying aging-related cerebrovascular defects is critical for developing strategies to alleviate aging-associated neurological diseases. In this study, we investigated the role of aging-related genes in brain vascular development using zebrafish as an in vivo model. By thoroughly analyzing scRNA-seq datasets of mid- and old-aged brain vascular endothelial cells (human/mouse), we found ribosomal protein S20 (rps20) significantly down-regulated during aging. qPCR analysis and whole-mount in situ hybridization validated a high expression of rps20 during early zebrafish development, which progressively decreased in adult and aged zebrafish brains. Functional studies using the CRISPR/Cas9-mediated knockout of rps20 revealed an impaired growth of central arteries in the hindbrain and a marked increased intracranial hemorrhage incidence. Mechanistically, qPCR analysis demonstrated a significant downregulation of vegfa, cxcl12b, and cxcr4a, key signaling molecules required for hindbrain vascular development, in rps20-deficient embryos. In conclusion, our findings demonstrate that rps20 is essential for proper brain vascular development and the maintenance of vascular homeostasis in zebrafish, revealing a novel mechanism by which aging-related genes regulate brain vascular development. This study provides new insights that may aid in understanding and treating aging-associated vascular malformations and neurological pathologies. Full article

To compare the clinical characteristics of inherited retinal diseases (IRDs) caused by biallelic versus monoallelic variants in the RP1, BEST1, and PROM1 genes. A total of 52 patients (26 female) with genetically confirmed IRDs were retrospectively selected from the records of the Harkness Eye Institute Clinical Coordinating Center at Columbia University Irving Medical Center. In RP1, 3 individuals with biallelic variants and 22 patients with monoallelic variants classified as pathogenic or likely pathogenic were selected. In BEST1, eight individuals with biallelic variants and nine individuals with monoallelic variants classified as either pathogenic or likely pathogenic were included. In PROM1, four individuals with biallelic variants and six patients with monoallelic variants classified as pathogenic or likely pathogenic were selected. All patients underwent multimodal retinal imaging and, when available, full-field electroretinography (ffERG). In all three genes, individuals with biallelic variants had markedly earlier disease onset and more severe phenotypes. In RP1, on SD-OCT, foveal involvement was observed in all biallelic cases (3/3, 100%) and in 4/22 (18%) monoallelic cases. In BEST1, the average age of onset in the biallelic cohort was 7.12 years, and the average age was 32.7 years in the monoallelic cohort. Four of eight (50%) patients in the biallelic group were additionally found to have widespread serous lesions outside of the central macula. This finding was not observed in the monoallelic group. Three of eight (38%) biallelic BEST1 patients had moderate reductions in their photopic flicker. All monoallelic BEST1 patients had photopic responses within the normal range. PROM1 biallelic cases showed severe functional impairment on ffERG, while most monoallelic cases retained normal responses. In the biallelic cohort, four of four (100%) of patients had severely attenuated or extinguished photopic responses. In the monoallelic PROM1 group, four of five (80%) monoallelic PROM1 patients had normal photopic responses, and P2-2 had mildly attenuated photopic responses. Individuals with biallelic variants exhibited earlier disease onset, more severe retinal degeneration, and significantly reduced retinal function compared with those with monoallelic variants. These observations highlight the role of loss-of-function mechanisms in more aggressive disease courses and underscore the importance of considering zygosity when determining prognosis and planning gene-based therapies. Full article

Rhododendron purdomii Rehder & E. H. Wilson (Ericaceae) is a threatened ornamental and medicinal shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China. To facilitate its conservation and utilization, the complete chloroplast genome of Rh. purdomii was sequenced, assembled, and characterized. The cp genome exhibited a typical quadripartite structure with a total length of 208,062 bp, comprising a large single copy (LSC) region of 110,618 bp, a small single copy (SSC) region of 2606 bp, and two inverted repeat (IR) regions of 47,419 bp each. The overall GC content was 35.81%. The genome contained 146 genes, including 96 protein-coding genes, 42 transfer RNA genes, and 8 ribosomal RNA genes. Structure analysis identified 67,354 codons, 96 long repetitive sequences, and 171 simple sequence repeats. Comparative genomic analysis across Rhododendron species revealed hypervariable coding regions (accD, rps9) and non-coding regions (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which may serve as potential molecular markers for genetic identification. Phylogenetic reconstruction confirmed the monophyly of Rhododendron species and highlighted a close relationship between Rh. purdomii and Rh. henanense subsp. lingbaoense. These results provide essential genomic resources for advancing taxonomic, evolutionary, conservation, and breeding studies of Rh. purdomii and other species within the genus Rhododendron. Full article

Halophyte plants, with genes responsive to abiotic stress, are promising candidates to enhance crop stress tolerance, but reliable RT-qPCR analysis requires the precise selection of candidate reference genes (CRGs) due to their inconsistent expression across tissues and stress conditions. In this study eight CRGs of A. littoralis, AlEF1A, AlRPS3, AlGTFC, AlRPS12, AlUBQ2, AlTUB6, AlACT7, and AlGAPDH1, were analyzed to assess their stability for the normalization of RT-qPCR data under polyethylene glycol (PEG, 20% w/v for drought simulation), abscisic acid (ABA, 100 μM), and cold stress (4 °C) treatments. The result of the algorithms suggested different CRGs for different treatments or tissue types. However the comprehensive analysis indicates that AlEF1A is the most stable CRG for PEG-treated leaf tissue, but AlTUB6 is preferable for PEG-treated root tissue, while for PEG-treated leaf and root tissues, AlEF1A can be suggested. For cold-stressed leaf and/or root samples, AlRPS3 was the most stable. For ABA-treated leaf and root tissues, AlGTFC and AlEF1A were the most stable CRGs, respectively, whereas AlTUB6 was suggested for ABA-treated leaf and root tissues. Collectively, for all stresses combined (PEG, ABA, and cold), AlGTFC was the most stable CRG in leaf samples, while AlRPS3 was the most stable in root samples and combined leaf and root samples. The validation analysis indicates a statistically significant difference (p value < 0.05) between normalization with the most and least stable CRGs. This research suggests reliable tissue-specific RGs for A. littoralis under abiotic stresses that can enhances the accuracy of gene expression quantification. Full article

Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterized by progressive photoreceptor degeneration and vision loss. While current management is largely supportive—relying on visual aids, orientation training, and nutritional supplementation—these interventions offer only symptomatic relief and do not halt disease progression. Advances in molecular genetics have led to the development of targeted treatments, including gene replacement therapy, RNA-based therapies, and CRISPR/Cas9 gene editing, offering promising strategies for disease modification. The approval of voretigene neparvovec for RPE65-associated RP marked a milestone in gene therapy, while ongoing trials targeting mutations in RPGR, USH2A, and CEP290 are expanding therapeutic options. Optogenetic therapy and stem cell transplantation represent additional strategies, particularly for patients with advanced disease. Challenges persist in delivery efficiency, immune responses, and treating large or dominant-negative mutations. Non-viral vectors, nanoparticle systems, and artificial intelligence-guided diagnostics are being explored to address these limitations and support personalized care. This review summarizes the current and emerging therapeutic landscape for RP, highlighting the shift toward precision medicine and the need for continued innovation to overcome genetic and phenotypic variability. Full article

Background: Sedum, with the largest number of species in the family Crassulaceae, is a taxonomically complex genus and an important group of horticultural plants within this family. Despite extensive historical research using diverse datasets, the branching patterns within this genus and the family remain debatable. Methods: In this study, we conducted sequencing and comparative analyses of plastomes from eight Sedum species, focusing on the diversities in nucleotide, microsatellite repeats, putative RNA editing, and gene content at IR junctions. The phylogenetic inferences were further conducted at the order level—Saxifragales. Results: Our IR junction analyses of the eight investigated Sedum species detected a unique 110 bp IR extension into rps19, a feature highly conserved across Crassulaceae species, indicating a remarkably family-specific pattern. Additionally, we obtained 79 PCGs from 148 Saxifragales species and constructed a phylogenetic tree using a larger set of plastomes than in previous studies. Our results confirm the polyphyly of Sedum and reveal that S. emarginatum is more closely related to S. makinoi than to S. alfredii, which is sister to S. plumbizincicola. Furthermore, we also performed analyses of codon usage, putative RNA editing sites, and microsatellite repeats. Conclusions: These findings and the generated sequence data will enrich plastid resources and improve understanding of the evolution of Sedum, Crassulaceae, and Saxifragales. Full article