Genes最新文献

Background/objectives: The widespread use of antibiotics in livestock has raised concerns about commensal gut bacteria, such as lactic acid bacteria (LAB), acting as reservoirs for antimicrobial resistance. This study aimed to characterize the antibiotic resistance profiles of LAB isolated from livestock feces by combining phenotypic susceptibility testing with whole-genome sequencing (WGS) to identify antibiotic resistance genes (ARGs) and their genomic context.

Methods: Four LAB strains from farm animal fecal samples were subjected to antibiotic susceptibility testing for 9 antibiotics (ampicillin, gentamicin, kanamycin, clindamycin, chloramphenicol, erythromycin, streptomycin, tetracycline, and vancomycin) using MIC determinations. WGS was performed on each isolate to detect ARGs using curated databases and to determine the chromosomal or plasmid location of these genes.

Results: All four isolates exhibited phenotypic resistance to at least one antibiotic class, most frequently to aminoglycosides. However, discrepancies between phenotype and genotype were noted: resistance to aminoglycosides was common despite the absence of known aminoglycoside-resistance genes, suggesting intrinsic, uptake-related mechanisms. In contrast, one strain carried the chromosomal lsa(D) gene but remained susceptible to clindamycin. WGS revealed that all strains harbored the chromosomal van(T) gene, while one isolate carried three additional plasmid-borne ARGs-erm(B), cat(A), and tet(W)-conferring resistance to macrolide-lincosamide-streptogramin antibiotics, chloramphenicol, and tetracycline. Another strain encoded van(Y), lsa(D), and arr on its chromosome. The detection of multiple plasmid-located ARGs in a single LAB isolate highlights their potential for horizontal gene transfer.

Conclusions: This study provides a detailed phenotypic and genomic insight into antibiotic resistance in gut-derived LAB from livestock. The findings highlight that commensal LAB can harbor clinically relevant ARGs-sometimes on mobile genetic elements-without always expressing corresponding resistance phenotypes. Such LAB may serve as a hidden reservoir for antibiotic resistance, raising the risk of ARG dissemination through the food chain. These results underscore the importance of vigilant monitoring and genomic screening of LAB, especially those considered for use in foods or feed, to ensure they do not contribute to the spread of antimicrobial resistance.

Background/Objectives: Sites of ribosomal RNA genes are the most widely documented regions of chromosomes in various groups of eukaryotes, including insects. Data on the number and chromosomal location of 45S rDNAs (25S, 5.8S, and 18S rDNA) are actively used to study the diversity of karyotypes, the organization of individual chromosomes, and the evolution of entire genomes. In true bugs (suborder Heteroptera), the number and chromosomal distribution of 18S rDNA loci are currently known for less than 0.5% of described species. Although some patterns of rDNA distribution can already be identified both in individual taxa of true bugs and in the suborder as a whole, there are still negligible data. In order to expand our understanding of the diversity of rDNA distribution in Heteroptera, we studied for the first time the location of 18S rDNA in 13 species from 13 genera (seven families) of the infraorders Cimicomorpha and Pentatomomorpha (=Terheteroptera, the terminal group of Heteroptera). Methods: Fluorescence in situ hybridization (FISH) with an 18S rDNA probe was used in our study. Results: In total, we have identified three main types of rDNA arrangement: (1) on autosomes, (2) on the X chromosome, and (3) on autosomes and on the X chromosome simultaneously. In most of the studied species, 18S rDNA loci were detected in the terminal position on one pair of autosomes. Conclusions: This study contributed to the understanding of the chromosomal distribution of rDNA loci in the infraorders Cimicomorpha and Pentatomomorpha and confirmed the importance of rDNA in the reorganization of the genomes of Heteroptera as a whole.

Background/Objectives: The PB family of "cut-and-paste" DNA transposons shows great promise as genetic manipulation tools while significantly impacting eukaryotic genome evolution. However, their evolutionary profile in beetles (Coleoptera), the most species-rich animal order, remains poorly characterized. Methods: A local tBLASTN search was conducted to mine PiggyBac (PB) transposons across 136 coleopteran insect genomes, using the DDE domain of the PB transposase as the query. Multiple sequence alignment was performed with MAFFT, and a maximum likelihood phylogenetic tree of the transposase DDE domains was constructed using IQ-TREE. Evolutionary dynamics were analyzed by means of K-divergence. Results: Our study reveals PB transposons are widely distributed, highly diverse, and remarkably active across beetles. We detected PB elements in 62 of 136 examined species (45%), classifying them into six distinct clades. A total of 62 PB-containing species harbored intact copies, with most showing recent insertions (K divergence ≈ 0), indicating ongoing transpositional activity. Notably, PB elements from Harmonia axyridis, Apoderus coryli, and Diabrotica balteata exhibit exceptional potential for genetic tool development. Structurally, intact PB elements ranged from 2074 to 3465 bp, each containing a single transposase ORF (500-725 aa). All were flanked by terminal inverted repeats and generated TTAA target site duplications. Conclusions: These findings demonstrate PB transposons have not only shaped historical beetle genome evolution but continue to drive genomic diversification, underscoring their dual significance as natural genome architects and promising biotechnological tools.

Background: Kenaf (Hibiscus cannabinus L.) is an important fiber crop belonging to the genus Hibiscus in the Malvaceae family. Research on its chloroplast genome holds significant importance for deciphering the evolutionary relationships of the Hibiscus species, developing genetic markers, and promoting kenaf (H. cannabinus) genetic breeding.

Methods: Based on high-throughput sequencing technology, this study completed the sequencing and assembly of the kenaf (H. cannabinus) chloroplast genome.

Results: (1) The kenaf (H. cannabinus) chloroplast genome exhibits a typical circular quadripartite structure with a total length of 163,019 bp, including a large single-copy region (LSC) of 90,467 bp, a small single-copy region (SSC) of 19,486 bp, and a pair of inverted repeat regions (IRa/IRb) of 26,533 bp each. The total GC content is 36.62%, among which, the IR region has the highest GC content (42.61%) and the SSC region the lowest (30.87%). (2) A total of 131 genes were annotated, including 85 mRNAs, 37 tRNAs, 8 rRNAs, and 1 pseudogene. Their functions cover photosynthesis (e.g., pet and atp family genes), self-replication (e.g., rpl, rps, and rpo family genes), and genes with unknown functions (e.g., ycf1 and ycf2). A codon usage bias analysis revealed that the relative synonymous codon usage (RSCU) value of the stop codon UAA is the highest (1.6329), and codons ending with A/U are preferentially used (e.g., GCU for alanine with RSCU = 1.778). (3) A repeat sequence analysis identified various interspersed repeat sequences (predominantly 30~31 bp in length, with a relatively high proportion in the 30~40 bp range, including forward and palindromic types) and simple sequence repeats (cpSSRs). Among them, single-base repeat SSRs account for the highest proportion (e.g., (A)8 and (T)9), and specific SSR primers were designed. (4) A comparative evolutionary analysis indicated that the Ka/Ks ratios (nonsynonymous substitution rate/synonymous substitution rate) of core chloroplast genes (e.g., rps2 and rpoC2) in kenaf (H. cannabinus) are all less than 1 (0.145~0.415), suggesting that they are under purifying selection. The collinearity similarity of chloroplast genomes between kenaf (H. cannabinus) and its closely related species reaches over 99.97%, and the IR region boundaries are relatively conserved. The phylogenetic tree shows that kenaf (H. cannabinus) clusters with closely related Hibiscus species with a 100% bootstrap value, indicating a close genetic relationship.

Conclusions: This study provides basic data for the functional analysis of the kenaf (H. cannabinus) chloroplast genome, the phylogeny of Hibiscus, and the utilization of genetic resources.

Background/objectives: Knee osteoarthritis (KOA) is a multifactorial and degenerative disease. Growth differentiation factor 5 (GDF5) polymorphism rs143384 G > A is associated with reduced gene expression and musculoskeletal pathologies. This study aimed to evaluate the association between this functional polymorphism and clinical variability and disease severity among patients with KOA in an admixed population.

Methods: This cross-sectional observational study enrolled 224 Brazilian patients with KOA, who were evaluated and classified according to disease severity.

Results: The median age was 64 (44-84) years; 75.9% of the patients were female, 50.9% were shorter than 1.60 m, and 67.4% were obese or morbidly obese. The disease severity distribution was 64.7% grades I-III and 35.3% IV-V. Patients with KOA who were over 70 years had significantly more advanced grades (OR = 9.3; 95% CI = 3.4-26), in either female group (OR = 8.2; 95% CI = 2.6-26). The minor allele frequency of the GDF5 rs143384 A variant was 41.7% in the overall KOA case group, increasing with disease severity (39.7% in grades I-III versus 45.6% in IV-V). After adjusting for the confounding factors (age and BMI) the GDF5 GA + AA genotype was significantly associated with higher KOA severity IV-V in female patients (OR = 2.5; 95% CI = 1.2-5.3). Additionally, the mean height of female KOA patients with the GDF5 GA + AA genotype (1.56 ± 0.07 m) was significantly shorter than that of patients with the GG genotype (1.59 ± 0.08 m).

Conclusions: The GDF5 rs143384 polymorphism was associated with greater KOA severity and shorter stature in female patients. These results suggest that this variant may contribute to phenotypic variability in patients with knee osteoarthritis, helping to refine clinical characterization and stratification in this population, contributing to personalized diagnoses and guiding future changes in treatment guidelines for knee osteoarthritis.

Background: The transcription factor FOXM1 is a master regulator of the cell cycle and is implicated in various cell fate decisions. However, its functional role and regulatory network in human Wharton's jelly mesenchymal stem cells (WJ-MSCs) remain poorly defined. This study aimed to elucidate the comprehensive function of FOXM1 in maintaining WJ-MSC stemness, proliferation, and survival, and to delineate the underlying molecular mechanisms.

Methods: We used RNA Interference to knock down FOXM1 in WJ-MSCs. The phenotypic impacts were assessed through CCK-8, colony formation, migration, and flow cytometry assays. We analyzed transcriptomic changes using RNA-seq and verified the results through qRT-PCR and Western blotting.

Results: Knockdown of FOXM1 significantly reduced the expression of core pluripotency factors (OCT4, SOX2, and NANOG), impairing stem cell identity and abolishing colony formation and migration capacities. Furthermore, FOXM1 deficiency induced G0/G1 phase cell cycle arrest, downregulated CCND1, and triggered apoptosis through a mechanism involving p53 accumulation, an increased BAX/BCL-2 ratio, and Caspase-3 activation. RNA-seq analysis further corroborated the systematic downregulation of cell cycle pathways and upregulation of apoptotic pathways upon FOXM1 deficiency.

Conclusions: Our findings establish FOXM1 as a critical regulatory node that integrates stem cell identity with proliferative and survival signals to maintain WJ-MSC homeostasis. This study redefines FOXM1's role in stem cell biology and provides a theoretical foundation for enhancing the therapeutic efficacy of WJ-MSCs by modulating this key factor.

Background/Objectives: The further application of high-coverage whole genome sequencing in fields such as paleogenomics, forensic investigations, and conservation genomics is impeded by two major barriers: extremely high costs and stringent sample requirements. Utilizing low-coverage sequencing offers a practical solution to these constraints; however, this approach introduces a primary challenge-the necessity to reconstruct distorted genomic information for downstream analysis. Methods: Analytical experiments conducted on low- to medium-coverage sequencing data confirmed the accuracy of several existing methods for inferring relationships up to the third degree and distinguishing unrelated individuals. Subsequently, efforts were made to evaluate allele-frequency-independent methods within animal genomics, where analyses are likely to encounter challenges such as uncertain allele frequencies, diverse sample types, and suboptimal sample quality. Kinship inference was performed on a total of 33 pairs of animal samples across three species, comprising nine parent-offspring pairs and four full-sibling pairs. Results: The analysis revealed that two efficient algorithm implementations (READ and KIN) successfully identified all unrelated pairs. Notably, among the various algorithms utilized, only KIN exhibited confusion between first- and second-degree relationships when subjected to. Conclusions: This study has filled a critical gap in the existing literature by conducting a comprehensive evaluation of various algorithms on low-coverage sequencing data derived from authentic human and animal samples, accompanied by detailed ground truth-a vital task that has been overlooked.

Background: Acute otitis media (AOM) is one of the most common pediatric infections. We aimed to investigate the bacterial profile of AOM in children, the serotype distribution, and the main genetic virulence factors involved in adhesion, immune evasion, and tissue spread. Methods: In total, 121 AOM cases involving children aged 0 to 14 years were studied. Middle ear fluids (MEF) (n = 42) and nasopharyngeal samples (n = 79) were collected. All strains were identified using routine microbiological tests, conventional PCRs and real-time PCR methods. Molecular serotyping was performed for S. pneumoniae and H. influenzae isolates. An immunofluorescence serotyping technique was employed for M. catarrhalis. Target genetic factors were determined for all involved bacterial agents using singleplex or multiplex PCRs. Results: We analyzed 148 nasopharyngeal and MEF. Among 121 AOM cases, a total of 127 bacterial agents were identified, including S. aureus (n = 41), S. pneumoniae (n = 28), H. influenzae (n = 23), M. catarrhalis (n = 19), and S. pyogenes (n = 16). The leading three serotypes among S. pneumoniae were: 19A (18.0%), 6A (14.3%), and 15B (14.3%). 91.3% of H. influenzae isolates were non-typeable (lacking a capsule-NTHi). The M. catarrhalis isolates were distributed in serotypes A (57.9%), B (26.3%), and C (15.8%). Presence of pili type 1 was detected in 21.4% pneumococci, and the fimbrial gene hifA was found in 34.8% of the H. influenzae strains. In 73.6% of the M. catarrhalis strains, ompCD was identified, while 84.2% contained ompE. 62.5% of the S. pyogenes isolates harbored the sdc gene, and 56.2% possessed the sdaD gene, predominantly in the MEF isolates. The cna adhesin was found in 28.0% of the S. aureus strains. Conclusions: The monitoring of bacterial pathogens responsible for otitis media, along with their serotype distribution and the prevalence of genetic factors involved in disease pathogenesis, is essential for public health and can help predict disease severity and treatment options.

Background: Prostate cancer remains a major contributor to cancer-related morbidity and mortality worldwide, emphasizing the need for safer and more effective therapeutic options. Andrographolide, a diterpenoid lactone derived from Andrographis paniculata, has shown promising anticancer activity, yet its effects on microRNA (miRNA) regulation in prostate cancer remain insufficiently explored.

Methods: In this study, we evaluated the cytotoxic and molecular effects of andrographolide on two human prostate cancer cell lines, PC3 and LNCaP, along with HEK-293 cells as a noncancerous model.

Results: Cell viability assessment using the MTT assay revealed dose-dependent cytotoxicity, with 24 h IC₅₀ values of 82.31 µM for PC3, 68.79 µM for LNCaP, and 133.9 µM for HEK-293 cells. Subsequent expression analysis of key oncogenic and tumor suppressor miRNAs demonstrated that andrographolide induced the upregulation of miR-16-5p, miR-34a-5p, and miR-200a-5p miRNAs implicated in apoptosis, proliferation control, and androgen receptor signaling. In contrast, the expression of oncomiRs miR-21-5p and miR-221-5p showed minimal or nonsignificant changes, reflecting the complex and context-specific roles of miRNAs in prostate cancer. Gene expression profiling further indicated differential transcriptional responses between the two prostate cancer cell lines, consistent with their distinct molecular backgrounds.

Conclusions: Although HEK-293 cytotoxicity and previously reported nephrotoxic effects warrant caution, these results support the potential of andrographolide as an adjuvant phytochemical capable of modulating clinically relevant miRNAs in prostate cancer. Future studies investigating optimized delivery systems and validating direct miRNA targets may help advance andrographolide toward safer and more targeted therapeutic applications.

Background/Objectives: Myotonic dystrophy type 1 (DM1) is a rare, multisystemic disorder caused by an expanded (CTG)n repeat in the DMPK gene. Although DM1 has been studied in several populations, access to molecular diagnosis and comprehensive care remains limited in many low- and middle-income countries. This study provides an updated overview of DM1 in Mexico, from diagnostic implementation to patient management, describing key clinical and genetic findings. Methods: We conducted a nationwide, 15-year prospective study at Mexico's National Reference Center for neuromuscular diseases. A total of 853 individuals at risk were subjected to clinical and molecular evaluation using PCR, TP-PCR, and SP-PCR, encompassing symptomatic, pre-symptomatic, prenatal, and preimplantation genetic diagnosis. Socioeconomic, clinical, and molecular variables were analyzed. Results: A total of 488 individuals were confirmed as DM1 carriers, with the most prevalent phenotypes being classic (36.5%) and juvenile (28.5%). Genomic analysis revealed a correlation between CTG tract sizes and phenotypes. Intriguingly, interrupted CTG repeat tracts were identified in 2.8% of DM1 carriers, who exhibited milder clinical phenotypes and a reduced degree of somatic and intergenerational instability. Survival analysis revealed a reduction in symptom-free survival in patients with larger expansions, while interrupted CTG tracts were associated with delayed onset. Conclusions: The centralization of diagnostic services in Mexico resulted in regional disparities, impacting early diagnosis and family planning. This study highlights the clinical and molecular diversity of DM1 in a Latin American population and underscores the urgent need for decentralized diagnostic services, integrated care models, and tailored prognostic tools in underserved settings.