Search Results (188)

Aphids are important agricultural pests that interact with diverse bacterial taxa living within or associated with their bodies. Some bacteria, such as the obligate symbiont Buchnera aphidicola, provide essential nutritional functions and are predominantly inherited vertically, whereas other aphid-associated bacteria may have more variable distributions and ecological roles. In this study, we investigated patterns of association between aphid evolutionary relationships and selected bacterial taxa. Aphids were identified using morphological characteristics and mitochondrial cytochrome c oxidase subunit I (COI) sequences, and host phylogenetic relationships were reconstructed using mitochondrial DNA data. We then compared the host phylogeny with that of the obligate symbiont Buchnera aphidicola based on 16S rRNA sequences and screened aphid specimens for selected aphid-associated bacteria (Wolbachia, Pantoea, and Arsenophonus) using diagnostic PCR assays. The host and Buchnera phylogenies showed significant global congruence, consistent with a strong long-term host-associated evolutionary relationship and predominantly vertical inheritance of Buchnera. In contrast, the selected aphid-associated bacteria showed heterogeneous detection patterns across the sampled aphid taxa. Pantoea was detected relatively frequently and across a broad range of sampled hosts, whereas Wolbachia and Arsenophonus showed more variable and restricted detection patterns. Given the small and uneven sample sizes among aphid species, these findings are interpreted as descriptive screening patterns rather than species-level prevalence estimates. Overall, the results highlight contrasting patterns of host-associated evolution between Buchnera and other aphid-associated bacteria and provide a basis for further investigation of the ecological and evolutionary processes underlying these associations. Full article

Background: Spinal muscular atrophy (SMA) is mainly caused by biallelic SMN1 inactivation. While most patients carry homozygous deletions, 3–5% are compound heterozygotes, making molecular diagnosis challenging. Methods: A tiered diagnostic strategy was applied to 17 pediatric patients, combining copy number analyses (MLPA and targeted long-read sequencing, tLRS), sequence variant detection (RT-PCR cloning and sequencing, allele-specific long-range PCR with nested PCR, and tLRS), and structural variant analysis (ultra-long-read sequencing, Ultra-LRS). Results: Copy numbers were concordant between MLPA and tLRS. MLPA-suggested gene conversions were confirmed by tLRS, while discordant total copy numbers were resolved as large deletions by Ultra-LRS. RT-PCR cloning, and sequencing identified SMN1 variants in 11/12 cases and confirmed aberrant splicing in three cases, but failed for large deletions. AS-LR-PCR with nested PCR characterized the variants in 13/15 but failed in gene conversion cases. tLRS achieved definitive diagnosis in all cases, and Ultra-LRS precisely delineated breakpoint junctions of two large deletions. Conclusions: A hierarchical complementary strategy integrating copy number, sequence, and structural analyses is essential for the accurate diagnosis of compound heterozygous SMA. Full article

Background: Esophagogastric cancer (EGC), encompassing oesophageal, gastroesophageal junction (GEJ), and proximal gastric malignancies, remains a major contributor to global cancer mortality. Neoadjuvant therapy, chemotherapy (CT) or chemoradiotherapy (CRT) is now standard for locally advanced, resectable disease. However, variability in treatment response and survival outcomes continues to challenge therapeutic optimisation. Methods: This systematic review followed the PRISMA 2020 guidelines and included studies published between January 2020 and September 2025. Eligible studies enrolled adult patients with resectable EGC treated with neoadjuvant CT or CRT, reporting data on pathological response (pathological complete response (pCR) or tumour regression grade (TRG)) and survival outcomes [overall survival (OS), disease-free survival (DFS)]. Sixty studies (18 randomised controlled trials and 42 cohort analyses) were included for qualitative synthesis. Results: Across all regimens, pCR rates ranged from 8% to 49%, with CRT achieving higher pCR (mean 33%) and major TRG response (63%) compared to CT alone (pCR 22%, TRG 48%). Immunotherapy-enhanced protocols (IO-CRT and IO-CT) demonstrated the most promising outcomes, reaching mean pCR rates up to 48–50%. Patients with complete or major regression consistently achieved superior OS and DFS, confirming pathological response as a consistent prognostic marker for long-term survival. Significant clinical heterogeneity was observed across histological subtypes (SCC vs. AC), treatment intensity, and surgical timing, while methodological heterogeneity stemmed from variations in TRG systems, follow-up duration, and reporting standards. Conclusions: Pathological response is consistently associated with survival following neoadjuvant therapy in EGC, yet its predictive power is modulated by tumour histology and treatment modality. Standardisation of TRG assessment, integration of molecular biomarkers, and harmonisation of study design are essential for improving comparability and advancing personalised, multimodal strategies in oesophagogastric oncology. Full article

Neonatal sepsis remains a leading cause of morbidity and mortality in the first month of life, yet its presentation is nonspecific, and its microbiological confirmation is uniquely difficult. Low-circulating bacterial loads, small obtainable blood volumes, frequent intrapartum antibiotic exposure, and the ambiguity of skin-commensal isolates erode the sensitivity and specificity of blood culture, the long-standing reference standard, so that most evaluated infants are treated empirically despite sterile cultures. This review synthesizes current evidence on the integrated microbiological evaluation of the newborn: the host- and specimen-related diagnostic challenge; the etiologic spectrum and its antimicrobial-resistance burden; conventional culture; rapid and molecular methods, including mass spectrometry and syndromic and broad-range PCR; metagenomic and cell-free-DNA sequencing; host-response biomarkers; and antimicrobial-susceptibility determination. The evidence indicates that newer methods accelerate or supplement culture but do not yet replace it, each addressing one limitation while introducing caveats of its own. Notably, much of the evidence for direct-from-blood molecular testing, microbial cell-free DNA, and metagenomic sequencing is extrapolated from adults, whereas neonatal data are stronger for several biomarkers. The greatest benefit arises from integrating complementary modalities within diagnostic- and antimicrobial-stewardship frameworks. Neonatal-specific validation, standardized thresholds, and outcome-driven trials remain the principal priorities. Full article

The Asian green mussel Perna viridis is expanding across coastal systems of the Americas, creating demand for curated molecular references to support biosecurity, aquaculture monitoring, and comparative invasion studies. Here, we report the first complete mitochondrial genomes of invasive P. viridis from Brazil and the southwestern Atlantic, generated from two specimens collected in Santa Catarina, currently the southernmost documented sector of the Brazilian range. Long-range PCR, Oxford Nanopore sequencing, read-supported assembly, manual annotation, comparative mitogenomics, nucleotide-diversity analysis, protein-level divergence, and phylogenomic inference were used to generate and evaluate complete mitochondrial references. The two circular assemblies were 16,015 bp and 16,011 bp and contained 38 annotated features, including 13 protein-coding genes, 23 tRNAs, and two rRNAs, all on the H strand, with an identical A+T content of 67.5%. Pairwise comparisons among the four complete P. viridis mitogenomes analyzed showed high overall similarity but retained 20–125 SNPs/mismatches and one to 12 indel events. Gene order was conserved within P. viridis but differed from P. canaliculus and P. perna, and phylogenomics placed the Brazilian assemblies within the P. viridis clade. These curated mitogenomes provide initial complete mitochondrial references for future marker testing and comparative studies of P. viridis in the southwestern Atlantic, but the two-specimen dataset should not be used to infer population origin, invasion routes, or connectivity. Full article

Hosta ventricosa, also known as blue plantain lily, is an important traditional herbal medicinal and ornamental plant in China. Prior to this study, no virus has been reported to infect H. ventricosa plants. Based on RNA-seq, transmission electron microscopy, and RT-PCR analyses, we have demonstrated that the H. ventricosa plant showing leaf chlorosis, mottle, mosaic, and crinkling symptoms was co-infected with hosta virus X (HVX) and a novel luteovirus, which we tentatively named hosta ventricosa luteovirus (HVLV). The genome of HVLV is a 5723 nt long, positive-sense, and single-stranded RNA with seven open reading frames (ORFs). Phylogenetic analysis based on the amino acid (aa) sequence of the viral RNA-dependent RNA polymerase (RdRp) revealed that HVLV is clustered within the genus Luteovirus. The HVLV RdRp shares 9.75–45.17% aa sequence identity with the 14 closely related luteoviruses. The P1–2 and P3–5 proteins of HVLV were identified as potential viral pathogenicity determinants through the PVX heterologous expression in Nicotiana benthamiana plants. Moreover, P2, P5 and P3–5 proteins of HVLV have been found to exhibit RNA silencing suppression activities. Additionally, we have successfully constructed an infectious cDNA clone of HVLV and uncovered that this infectious cDNA clone can infect N. benthamiana plants through agroinfiltration. These findings have expanded our understanding of luteoviruses and their host range. Full article

This study established long-term wastewater surveillance of Aichi virus (AiV) in Maryland. AiV, a member of the Kobuvirus genus associated with acute gastroenteritis, has established itself as an integral marker for wastewater-based monitoring; however, two key research questions remain unaddressed for the Baltimore metropolitan area: (1) whether AiV is consistently detectable in municipal wastewater throughout the year, and (2) whether its concentrations exhibit a measurable seasonal pattern. To address these hypotheses, influent samples were collected on a weekly basis from WWTP-A and WWTP-B from January to December 2023 (with grab sampling conducted at WWTP-A and automated collection deployed for the influent sampling of the water treatment plant B). All samples (n = 51) were subjected to PEG 8000 concentration, RNA extraction, cDNA synthesis, and RT-qPCR quantification. We observed AiV RNA in 94.12% of the samples from both facilities (25/51 at WWTP-A and 23/51 at WWTP-B) with concentrations that ranged from 2.5 to 3.63 log₁₀ gc/L and a seasonal pattern showing consistent declines: loads for WWTP-A declining from winter (3.58 log₁₀ gc/L) to fall (2.56) and for WWTP-B from winter (3.28 log₁₀ gc/L) to fall (2.31). The year-round constant AiV presence provides a strong basis for its use as a stable viral marker within wastewater-based epidemiology efforts. Full article

Background: Early feeding practices are among the most influential determinants of the infant oral microbiota during the first years of life. Breastfeeding provides bioactive components—immunoglobulins, human milk oligosaccharides (HMOs), and commensal bacteria—that may shape microbial colonisation patterns with long-term implications for oral health. However, the nature, magnitude, and clinical relevance of these effects remain poorly characterised, particularly with regard to early childhood caries (ECC) risk. Objectives: The primary objective was to evaluate the association between early feeding practices and oral microbiota composition during infancy. A secondary exploratory objective was to assess whether feeding-associated microbiota differences had been linked to subsequent dental caries outcomes. Methods: A systematic review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, and Embase were searched from January 2010 to June 2026. Eligible studies compared at least two feeding groups and measured oral microbiota directly using culture-independent methods (16S rRNA gene sequencing, metagenomics, or quantitative PCR targeting multiple taxa). Study selection, data extraction, and risk of bias assessment using the ROBINS-E tool were performed independently. Qualitative synthesis was conducted given clinical and methodological heterogeneity. Results: Of 8582 records identified, 12 studies met the inclusion criteria (sample size range: 12–448 participants; age range at microbiota assessment: 2 days–14 years, although eligibility was based on feeding exposure during infancy; six countries). Most included studies reported differences in oral microbiota composition associated with feeding type. During the first months of life, breastfed infants generally showed lower oral microbial diversity and higher abundance of Lactobacillus, the Streptococcus mitis group and Bifidobacterium compared with formula-fed infants, who exhibited greater alpha diversity, higher transmission of maternal oral bacteria, and higher abundance of Prevotella and Actinomyces. Effects were most pronounced in the first three months of life and attenuated by 12 months in most cohorts. Only one study reported subsequent dental caries outcomes after early-life microbiota assessment, finding that Streptococcus cristatus abundance at three months was associated with dental caries at nine years of age, and that longer breastfeeding duration (≥12 months) was associated with a distinct microbiota profile and lower caries rates in this single available longitudinal study. Risk of bias was low in two studies, moderate in six, and high in four. Publication bias could not be formally evaluated. Conclusions: Early feeding practices are associated with measurable differences in oral microbiota composition during infancy, particularly during the first months of life. However, evidence linking these microbiota differences to subsequent dental caries outcomes remains extremely limited, with only one included study assessing later caries development. Therefore, the clinical significance of feeding-associated microbiota profiles remains uncertain and should be investigated through well-designed prospective longitudinal studies. Full article

Background/Objectives: Melophagus ovinus is an economically important ectoparasite of small ruminants with a broad global distribution. Although mitochondrial genomes are widely used in population genetic studies, the D-loop region of M. ovinus remains poorly characterized because its high AT content and repetitive structure complicate amplification, assembly, and sequencing. Methods: We sequenced the mitochondrial genome of M. ovinus collected from Qinghai using an integrative approach combining Illumina paired-end sequencing, targeted PCR amplification, and Nanopore long-read sequencing. Comparative genomic analysis was performed against published mitogenomes from Gansu (MH024396) and Xinjiang (NC_037368). Results: The Qinghai mitochondrial genome contained the typical 37 mitochondrial genes within a 14,728 bp conserved region. Comparative analysis revealed exceptionally high conservation (>99.6% sequence identity) among Qinghai, Gansu, and Xinjiang isolates outside the D-loop region. Notably, the D-loop exhibited length polymorphism, with different assembly strategies or samples yielding lengths ranging from 317 bp to 2385 bp. Targeted long-read sequencing of ten individuals identified a predominant D-loop variant of approximately 844 bp in nine samples and a markedly shorter variant of approximately 164 bp in one sample. The short variant was characterized by extensive deletions and a novel 45 bp insertion. Support for this variant was obtained from independent Illumina DNA-seq, RNA-seq, Nanopore sequencing, and de novo assembly analyses. Conclusions: This study provides preliminary evidence for D-loop structural heterogeneity in M. ovinus, suggesting remarkable length polymorphism and complex indel patterns that require further validation. These findings significantly expand the genomic resources available for this important veterinary parasite and establish a foundation for future population genetic and evolutionary studies. Full article

Recent evidence has highlighted the crucial role of non-coding genetic elements in regulating gene expression and has been linked to a broad range of biological functions. Notably, dysregulation of long non-coding RNAs has been strongly associated with tumorigenesis and cancer progression. Background/Objectives: This study aimed to investigate the potential association between the H19 rs3741219 T>C, MEG3 rs7158663 G>A, POLR2E rs3787016 T>C, and ANRIL rs10757274 A>G variants and Breast Cancer (BC) susceptibility, as well as their relationship with clinicopathological characteristics in Mexican patients. Methods: DNA was obtained from peripheral blood samples of 505 women (254 patients and 251 control females). Genotyping was performed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methodology. Associations were calculated using odds ratios (ORs), with p-values adjusted by the Bonferroni test (p < 0.012). In silico analyses were conducted to predict the functional impact of the variants associated. Results: Patients carrying the C/C genotypes in H19 rs3741219 and POLR2E rs3787016 variants showed increased susceptibility to developing BC and with clinical and pathological characteristics (age at diagnosis, TNM stage, histologic type and molecular subtype) (p < 0.001). Conclusions: The results suggest that H19 rs3741219 and POLR2E rs3787016 variants significantly influence BC risk. Full article

This study aimed to evaluate whether serum from patients with primary antiphospholipid syndrome (APS) is associated with changes in the expression of long non-coding RNAs (lncRNAs) in endothelial cells. Human umbilical vein endothelial cells (HUVECs) were cultured with serum from 12 female patients with APS or 8 age-matched healthy female controls. The expression levels of HIF1A-AS1, OIP5-AS1, and GAS5 were quantified by RT-qPCR. Exposure of HUVECs to APS serum was associated with reduced expression of HIF1A-AS1 and OIP5-AS1 compared with cells stimulated with control serum. The median HIF1A-AS1 expression levels were 0.08 a.u. (interquartile range, 0.06–0.10) in APS-stimulated cells versus 0.14 a.u. (0.08–0.16) in controls (p = 0.044). Likewise, OIP5-AS1 levels were 0.09 a.u. (0.01–0.16) in APS-stimulated cells versus 2.24 a.u. (0.70–3.55) in controls (p = 0.018). In contrast, GAS5 expression did not differ significantly between groups (340 a.u. (310–3940 versus 358 a.u. (163–445); p = 0.290). In this proof-of-concept study, serum from APS patients was associated with selective downregulation of HIF1A-AS1 and OIP5-AS1 in endothelial cells. These findings support a potential link between circulating APS-related factors and endothelial lncRNA expression; however, no mechanistic or functional conclusions can be drawn. Full article

Survivors of childhood leukemia are at increased risk of long-term skeletal complications, including reduced bone mineral density (BMD). Vitamin D deficiency and genetic variations in the vitamin D receptor (VDR) gene are important factors influencing bone health, yet their combined effects remain insufficiently studied, particularly in North African populations. This case-control study included 130 survivors of childhood acute lymphoblastic leukemia (ALL) in remission (age range: 5–26 years) and 110 age- and sex-matched healthy controls recruited from Beni Messous Hospital. BMD was assessed at the lumbar spine and femoral neck using dual-energy X-ray absorptiometry and expressed as z-scores. Serum 25-hydroxyvitamin D levels were measured, and VDR polymorphisms (FokI, ApaI, and BsmI) were analyzed using PCR-RFLP. Hypovitaminosis D was observed in 43.85% of patients at diagnosis and 23.07% after remission. Survivors had significantly lower BMD compared with controls at both the lumbar spine (z-score: −4.26 ± 0.75 vs. 0 ± 1, p < 0.001) and femoral neck (−3.78 ± 0.45 vs. 0 ± 1, p < 0.001). Reduced BMD for age was identified in 30% of patients. Variant genotypes TT (FokI), AA (BsmI), and CC (ApaI) were more frequent in patients and were associated with lower BMD (p < 0.0001). These findings suggest that hypovitaminosis D and VDR polymorphisms may be associated with bone health in survivors of childhood leukemia. The coexistence of these factors may contribute to interindividual variability in BMD. Full article

Background/Objectives: Acrodermatitis chronica atrophicans (ACA), a late cutaneous manifestation of Lyme borreliosis, presents with a broad clinical spectrum. Most commonly, a characteristic bluish-red patchy rash, but it can also appear as unilateral limb swelling. This study aimed to characterize the clinical manifestations, diagnostic workup, and outcomes of patients with ACA in a tertiary setting in Denmark. Methods: Retrospective cohort study including all patients diagnosed with ACA at Copenhagen University Hospital-Rigshospitalet between 2017 and 2025. Results: Forty patients were included (median age 57 years; 63% female), with a median BMI of 24.5 [range 15.6–36.3]. Symptom duration was long (median 1 year). All patients presented with a skin rash. The most common location was the lower extremity, 26/40 (65%). Local edema and neuropathic pain were common (20/40) 50% and (23/40) 55%, respectively. A total of 13/40 patients underwent lymphoscintigraphy, which was deemed pathological in 7/13 (54%). The patients presenting with edema underwent significantly more imaging procedures, median 3 (range 1–5) vs. 0 (range 0–2), p < 0.005; they were younger, median age 49 years (range 17–76) vs. median 65 (range 30–81), p = 0.03; but did not differ in BMI, median 26.6 (range 19.0–36.2) versus median 23.8 (range 15.6–36.3), p = 0.48. All patients were Borrelia burgdorferi (Bb) IgG seropositive. Borrelia-specific PCR was positive in 6/13 (46%). Histopathology supported the diagnosis in 19/20 (95%). Clinical evaluation of the treatment response at 3 months was good in 33/40 (83%). Conclusions: Edema/swelling due to lymphatic obstruction is a common presentation of ACA in the tertiary setting, resulting in extensive diagnostic workup. The condition is associated with younger age but not BMI, sex, or immunodeficiency. Raised awareness and earlier testing for Bb IgG in serum seem warranted. Full article

Buckling-restrained braces (BRBs) are widely used to improve the seismic performance of high-rise and long-span structures. This study proposes a triple-tube GFRP–steel buckling-restrained brace (TTGS-BRB) as a lightweight and corrosion-resistant energy-dissipating member for such structures. To investigate its hysteretic behavior, pseudo-static tests were conducted on two scaled TTGS-BRB specimens with different wrapping orientations and end details, and a finite element model was established and validated against the test results for further parametric analyses. The test results showed that the specimen with the ±30° wrapping configuration and end stiffeners exhibited better hysteretic performance than the 90° specimen without end stiffeners, with the yield force increasing from 147.98 kN to 161.68 kN, the cumulative plastic deformation (CPD) increasing from 7.49 to 209.56, and the cumulative plastic energy (CPE) increasing from 5.25 to 199.12. Based on the validated finite element model, the effects of fiber wrapping orientation, end stiffeners, interfacial gap, P_cr/P_y ratio, and steel tube diameter-to-thickness ratio on the hysteretic performance of full-scale TTGS-BRBs were systematically investigated. The numerical results indicate that wrapping orientations within the range of ±0° to ±45°, end stiffening at both ends, an interfacial gap of 1.5 mm between GFRP and steel, an appropriate P_cr/P_y ratio, and a steel tube diameter-to-thickness ratio of less than 24 are beneficial for improving the hysteretic performance of TTGS-BRBs. These findings provide useful references for the design and application of TTGS-BRBs in practical engineering. Full article

Accurate detection of all types of mitochondrial DNA (mtDNA) variants, including single large-scale mtDNA deletions (SLSMDs) and multiple mtDNA deletions (MMDs), along with heteroplasmy quantification, is essential for Primary Mitochondrial Disease (PMD) diagnosis. This study compares amplification-free PacBio long-read sequencing (LRS) mtDNA analysis with long-range PCR-based targeted mtDNA sequencing by short-read sequencing (SRS) in terms of detection sensitivity and accuracy. In total, 17 samples, including 4 SLSMD cases (3 blood, 1 muscle), 9 MMD muscle samples, and 4 deletion-negative controls (1 blood, 3 muscle), were sequenced using the PacBio Sequel IIe. Our findings demonstrate LRS’s efficacy in detecting single nucleotide variants (SNVs) and large mtDNA deletions with precise breakpoints. LRS can accurately detect and distinguish SLSMD from MMD, providing deletion heteroplasmy without the need for a second methodology. Deletion heteroplasmy computed from LRS was highly correlated with the Droplet Digital PCR (ddPCR) estimates (Pearson’s r2 = 0.95). While LRS can detect SNVs with approximately 5% heteroplasmy, only variants exceeding 10% heteroplasmy can attain 100% sensitivity, specificity, and precision when compared to those previously identified through clinical testing. In conclusion, our findings establish PacBio LRS as a robust tool for comprehensive mtDNA analysis capable of accurately detecting and quantifying heteroplasmic mtDNA variants and complex deletions. Full article