Search Results (3,439)

Copy number variation (CNV) is a common source of genomic structural variation by altering the number of DNA fragments, which in turn affects phenotypic variation and gene expression levels. However, there have been no reports of CNV in Chinese jujube (Ziziphus jujuba Mill.). In this study, we identified 16,570 CNVs from “Yuhong” × “Jiaocheng 5” and 140 hybrid progeny materials, of which 3607 CNVs were deletion type and 12,963 CNVs were duplication type. The distribution of CNVs in the Chinese jujube genome was systematically described, and the CNV genetic map of the whole genome level of the Chinese jujube hybrid offspring was constructed. Based on the field investigations, 13 individuals with severe black spot disease and no disease were analyzed for trait association. A total of 1837 CNVs were detected at the significant level of association, of which 1371 were duplication type and 466 were deletion type. And the GO (Gene Ontology) annotation item identified a systemic acquired resistance (SAR), and eight genes related to disease resistance were screened by the annotation. After validation by qPCR, these results further support the potential role in regulating black spot disease resistance. The constructed genome-wide CNV map of the hybrid progeny of Chinese jujube provides a new way of thinking for understanding the genetic basis of phenotypic variation of complex traits in Chinese jujube. Full article

Common vetch (Vicia sativa L.) is a globally green manure and forage crop, cultivated extensively worldwide. Its seeds serve as an important concentrated feed. Due to the late release of the reference genome, few studies were conducted to analyze the genetic mechanisms of grain yield, which hindered the progress of common vetch breeding. Marker-assisted selection (MAS) is the best and most effective way to accelerate the genetic improvement of grain yield-related traits in common vetch. In this study, we performed a genome-wide association study (GWAS) using the high-density single nucleotide polymorphism (SNP) data obtained through re-sequencing to better understand the genetic basis of grain yield-related traits. In total, six grain yield-related traits were evaluated in 172 accessions mainly sourced from China and Russia, across four environments, including branches per plant (NB), pod length (PL), number of pods per plant (NP), number of grains per pod (NG), hundred-grain weight (HGW), and grain yield (GY). Population structure analysis of the 172 accessions revealed four distinct subpopulations, exhibiting strong geographical correlation. In total, 38 loci have been identified as significantly associated with six grain yield-related traits, accounting for 13.3–31.7% of the phenotypic variances. Among them, qGY1.1 and qNG1.1, qNG2.2 and qPL2.1, qNG3.2 and qGY3.2, qNG4.1 and qPL4.1, qGY4.1 and qHGW4.1, qNG6.1 and qPL6.1, and qNB6.2 and qGY6.2 exhibit overlapping regions, suggesting that these regions are pleiotropic and should be prioritized for further research and breeding. In total, 12 candidate genes encoding auxin response factor, F-box repeat protein, gibberellin receptor, serine/threonine-protein kinase-like protein, and cellulose synthase-like protein were identified. Furthermore, we successfully developed and verified a kompetitive allele-specific PCR (KASP) marker (Kasp-NB6.2) for the number of branches. These findings provide molecular insights into grain yield-related traits in common vetch and offer valuable loci and molecular tools for MAS breeding. Full article

Climate change and injudicious nitrogen addition alter the soil physico-chemical properties and microbial activity in oligotrophic forest soil, which disrupts the nitrogen cycle balance. Nevertheless, recommended fertilizer forms and levels are considered to be crucial for stable nitrogen application. We established a short-term field trial for the first time using a randomized complete block design under the yellow larch forest, with six treatments applied, including urea CO(NH₂)₂, ammonium chloride NH₄Cl, and sodium nitrate NaNO₃ at concentrations of 10 and 20 kg N hm⁻² yr⁻¹, each extended by three replicates. The gene abundances were measured using quantitative PCR (qPCR), in which the abundance levels of AOA (amoA) and nirS were higher under high CO(NH₂)₂ 2.87 × 10¹⁰ copies g⁻¹ dry soil and low NO₃⁻ 8.82 × 10⁹ copies g⁻¹ dry soil, compared to CK, representing 2.8-fold and 1.5-fold increases, respectively. We found niche partitioning as revealed despite AOA (amoA) increasing in number, AOB (amoA) contributing more to ammonia oxidation while nirS proved opportunistic under stress conditions. This was supported by distinct significant correlations among factors, in which soil urease enzymatic activity (S-UE) was associated with AOA (amoA) and nirK, while AOB (amoA) and nirS positively correlated with NH₄⁺ content and soil potential of hydrogen (pH), respectively. Among the applied treatments, high-level NO₃⁻ increased total nitrogen content and had a significant effect on soil N-acetyl-β-d-glucosaminidase (S-NAG) and soil acid protease (S-ACPT) activity. In summary, we observed an increase in Larix olgensis growth with high nitrogen retention. Full article

Double-petal ornamental pomegranate presents for its enhanced ornamental value. Thus, cultivation techniques that promote petaloidy while modulating related gene expression are desired. To screen out the efficient treatments of plant growth regulator and key genes that enhance petaloidy, this study treated the flower buds of double- and single-petal ornamental pomegranate varieties with different concentrations of plant growth regulators naphthaleneacetic acid (NAA), methyl jasmonate (MeJA), abscisic acid (ABA), and ethephon (ETH) and quantified the number of petalized stamens (NOPSs) and the number of petals (NOPs) in both varieties. Furthermore, we investigated the expression levels of the genes flavin-containing monooxygenase (YUC), IAA-amino acid hydrolase (ILR1),indole-3-acetic acid-amido synthetase (GH3.17), auxin transporter (LAX2), auxin response factor (ARF), auxin-induced in root cultures protein (AIR12), jasmonic acid-amido synthetase (JAR1), and ABA stress ripening-induced protein (ASR) under the different treatments and analyzed their role in regulating relevant phenotypic traits. Plant growth regulator experiments demonstrated that NAA (10 mg/L) significantly increased the number of petalized stamens (NOPSs) and petals (NOPs), MeJA (100 mg/L) significantly increased the number of petalized stamens, while neither ABA nor ETH induced this morphological shift. qRT-PCR analysis confirmed that NAA upregulated ILR1, LAX2, ARF, and JAR1 in the stamens of single-petal flowers (StSi) and double-petal flowers (StDo) and petals of single-petal flowers (PeSi) and double-petal flowers (PeDo), with their expression levels strongly positively correlated with NOPS in both single- and double-petal flowers and NOP in double-petal flowers. MeJA upregulated ILR1, GH3.17, LAX2, ARF, and JAR1 in StDo and PeDo and was strongly positively correlated with NOPS and NOP in double-petal flowers. Consequently, NAA (10 mg/L) and MeJA (100 mg/L) were efficient treatments, and ILR1, GH3.17, LAX2, ARF, and JAR1 were identified as key genes in NAA- and MeJA-mediated petaloidy in ornamental pomegranates. Our results provide theoretical support for identifying the formation mechanism and improving industrial cultivation techniques for double-petal pomegranates. Full article

Aerobic soils serve as significant sinks for atmospheric methane, with their effectiveness influenced by the diversity and activity of soil methanotrophs. Land-use changes, particularly the conversion of natural ecosystems to agriculture, can substantially alter these microbial communities. A promising strategy to restore methane oxidation capacity is the introduction of active, ambient methane-oxidizing bacteria. The stable methane-oxidizing microbial consortium T1, dominated by Methylocystis (74%), was isolated from the soil of the unique Chernevaya Taiga forest ecosystem. The effects of inoculating this consortium were evaluated in a four week laboratory incubation experiment, using microcosms of soddy-podzolic agro-soil. Methane oxidation potential was assessed to measure methanotroph activity; methanotrophs were quantified using qPCR targeting pmoA genes; and the diversity of soil microbial communities was examined through 16S rRNA gene profiling. Inoculated soils exhibited significantly higher methane oxidation potentials compared to non-inoculated soils. Furthermore, pmoA gene copy numbers in the inoculated soils were significantly elevated (10⁶ copies pmoA g⁻¹), indicating stable persisted methanotrophic populations throughout the incubation period. These findings suggest that enriched methanotrophic consortium inoculation into agro-soils may be a promising strategy for restoring methane-oxidizing activity. Full article

Introduction: Scrub typhus is caused by Gram-negative bacteria, Orientia tsutsugamushi. Humans are the dead-end host of scrub typhus. Currently, there is no vaccine available. The disease can be fatal without appropriate treatment. Here, we present the circulating OT genotypes in Malaysia and a tsa56-based single PCR to detect and determine OT genotypes, which is an approach to replace the time-consuming traditional nested PCR. Methods: The patients’ blood or tissue samples (n = 1200), received from all hospitals in Malaysia from December 2022 to November 2024, were screened for rickettsial infections. Both htrA qPCR and nested PCR were performed to detect the presence of OT DNA. Simultaneously, a selection of DNA was evaluated for the new single PCR protocol and confirmed with Sanger sequencing. Results: We report that Pahang state of Peninsular Malaysia presents the highest number of acute scrub typhus infections in Malaysia within the 24 months period. There are four genotypes circulating in the Malaysian population. OT genotype Gilliam (n = 31, 29.2%) and Karp (n = 31, 29.2%) are the predominant OT genotypes in Malaysia, followed by TA763 (n = 22, 20.8%) and Kato (n = 22, 20.8%). The single-run PCR presents longer sequence size and similar results with the nested PCR. Conclusions: Acute scrub typhus infection is not rare in Malaysia and should be considered for undifferentiated febrile illness. The single-run PCR protocol is time-saving and a promising approach for OT detection and genotype analysis in a single run to complement a clinical diagnostic setting and surveillance. Full article

Background: Since liquid-based cytology (LBC) has replaced the conventional Papanicolaou test in cervical cancer screening programs, pre-analytical procedures—particularly the choice of LBC collection media—have become crucial to ensure the accuracy of high-risk (HR) HPV DNA testing. This study aims to evaluate whether the newly developed CytoPath^® LBC medium can serve as a reliable alternative to standard solutions. Methods: This study exploited cell lines to evaluate the stability, integrity, and recovery rate of genomic DNA at different fixation time points (1, 7, 14 and 40 days) and serial dilutions (1:5, 1:10 and 1:20) extracted from cell lines. These samples have also undergone quantitative Real-Time PCR (qPCR) based HR-HPV test to assess the relative performance of the new preservative solution in detecting viral DNA with respect to the standard reference. Results: Cervical cell lines preserved in both media demonstrated consistent DNA stability over time. DNA yields were comparable between the two media. Notably, the DNA Integrity Number (DIN) was higher in samples fixed with the CytoPath^® solution. HR-HPV detection by qPCR showed equivalent performance, regardless of the fixative used. Conclusions: The CytoPath^® fixative solution represents a valid alternative to standard preservation media, offering improved DNA integrity while maintaining equivalent performance in HR-HPV qPCR testing. Full article

To broaden the informational scope of existing fuzzy frameworks and enhance their flexibility in representing and processing uncertainty, we propose a novel p,q-rung triangular orthopair fuzzy number (p,q-RTOFN). To enhance the aggregation capability of fuzzy data, we develop a p,q-rung triangular orthopair fuzzy weighted power Bonferroni mean (p,q-RTOFWPBM) operator that integrates the strengths of the Bonferroni mean and power average operators. We formally establish its theorems, proofs, and key properties, including symmetry and idempotency. Furthermore, we extend the complex proportional assessment (COPRAS) method to the p,q-RTOF environment, resulting in a p,q-RTOF-PBM-COPRAS model. This model effectively incorporates both positive and negative evaluation information under uncertainty, thereby reducing information loss and improving decision accuracy. A case study on urban smart farm selection confirms the feasibility and superiority of the proposed approach. This study introduces the p,q-RTOFN framework with extended informational scope, develops a hybrid p,q-RTOFWPBM operator, and incorporates these advances into an extended COPRAS method to achieve more accurate multi-criteria decision-making under uncertainty. Full article

In this study, we aimed to evaluate physiological and agronomic traits in 120 sugarcane genotypes under early drought stress conditions in a field trial across various soil types. The experiment used a split-plot arrangement, with a randomized complete block design and two replications. Two different water regimes were assigned to the main plot: (1) non-water stress (CT) and (2) drought (DT) at the early growth stage, during which sugarcane was subjected to drought stress by withholding water for 4 months. The subplot consisted of 120 sugarcane genotypes. The stalk height, stalk diameter, number of stalks, photosynthetic traits including SPAD chlorophyll meter reading (SCMR) and maximum quantum efficiency of photosystem II photochemistry (Fv/Fm), and normalized difference vegetation index (NDVI) were measured at 3, 6, and 9 months after planting (MAP). Yield and yield component parameters were measured at 12 MAP. Drought treatments lead to significant changes in various physiological traits in the sugarcane. Clustering analysis classified 36 sugarcane varieties grown in sandy loam soil and 15 genotypes in loam soil into two main clusters. In sandy loam soils, Biotec4 and CO1287 exhibited outstanding performance in drought conditions, delivering high cane yields. Meanwhile, in loam soil, MPT13-118, MPT07-1, Q47, F174, MPT14-1-902, and UT1 exhibited the best drought tolerance. Under drought conditions, cluster 1 showed higher values for SCMR, NDVI, height growth rate (HGR), cane yield, and drought tolerance index compared to cluster 2. These findings suggest that breeders can utilize these genotypes to enhance drought resistance, and the identified physiological traits can assist in selecting stronger candidates for drought tolerance. Full article

Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for the analysis and diagnosis of numerous diseases. The gut microbiome is an intricate ecosystem, coordinated by the interaction of various microbes and the metabolites produced by them, which helps in developing and sustaining immunity and homeostasis. A healthy gut microbiome is driven by different factors, such as nutrition, lifestyle, etc. The current study examines the association of diet to gut microbiome dysbiosis and its role in various disease conditions. Gut microbiome data was collected from 73 patients and tested at BioAro Inc. lab, using shotgun metagenomics through next generation sequencing. It was then analyzed and compared with data from 20 healthy subjects from HMP database. An in-house bioinformatics pipeline (PanOmiQ) and Pathogen Fast Identifier were utilized for secondary analysis, while tertiary analysis was accomplished using R software. Results showed a higher number of opportunistic pathogen microorganisms in the gut microbiome of subjects consuming a meat diet, as compared to those consuming a plant diet. These opportunistic pathogens included Ruminococcus torques (>3.34%), Ruminococcus gnavus (>2.22%), and Clostridium symbiosum (>1.87%). The study also found a higher relative abundance of these pathogens in cancer patients, as compared to healthy subjects. We also observed a highly significant (p < 0.0001) correlation of a meat diet with obesity in comparison to the subjects on a plant diet and the healthy subjects. Our findings suggest that patients following a plant diet have a lower relative abundance of pathogens that are associated with cancer and obesity. These findings provide critical insight into how we can use shotgun metagenomics to study the composition and diversity of the gut microbiome and the effects of a diet on the gut microbiome and its role in metabolic diseases. This is the first report investigating gut microbiota using shotgun metagenomics, correlating with different diseases and diet followed, which might impact the presence of opportunistic pathogens or keystones species. Additionally, it can provide valuable insights to physicians and dietetic practitioners for providing personalized treatment or customizing a diet plan. Full article

Background: Duchenne Muscular Dystrophy (DMD) is an X-linked recessive neuromuscular disorder that is characterized by progressive muscle weakness, musculoskeletal limitations, and pulmonary involvement, with cardiomyopathy and cardiovascular complications being a primary cause of morbidity and mortality. With advances in respiratory care, cardiac involvement has become the leading cause of death. There is growing interest in systemic inflammatory indices as potential predictors of cardiovascular involvement. This study aimed to evaluate the prognostic value of inflammatory markers—neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), systemic inflammatory response index (SIRI), systemic immune-inflammation index (SII), and pan-immune inflammation value (PIV)—in children with DMD and to explore their association with cardiac findings. Methods: In this retrospective study, 25 male patients diagnosed with DMD and 25 age-matched healthy male controls were evaluated between January 2021 and July 2024. Demographic and clinical data, hematologic and biochemical parameters, and inflammatory indices were recorded. Cardiovascular involvement was assessed using electrocardiography (ECG) and transthoracic echocardiography (TTE). Group comparisons were performed using independent t-tests, while ROC and Pearson correlation analyses were used for diagnostic performance and associations. Results: Pathological Q waves were the most frequent ECG abnormality (24%), and 16% of patients had echocardiographic abnormalities. While most systemic inflammatory indices (NLR, MLR, SIRI, SII, PIV) did not significantly distinguish cardiovascular involvement, PLR demonstrated a strong positive correlation with Pro-BNP levels (r = 0.86, p < 0.05), suggesting a potential link between systemic inflammation and subclinical cardiac stress. Conclusions: Although the overall diagnostic utility of inflammatory indices in predicting cardiovascular complications in DMD was limited, PLR showed a correlation with Pro-BNP in our cohort. However, given the small sample size and limited number of patients with ventricular dysfunction, this finding should be interpreted with caution. PLR may warrant further investigation as a potential marker of cardiovascular involvement in DMD, but larger prospective studies are needed to validate its clinical significance. Full article

Retinoblastoma is a rare but malignant pediatric retinal tumor, affecting 1 in 15,000–20,000 live births annually. It arises from biallelic mutations in the RB1 tumor suppressor gene (chromosome 13q14.2), leading to uncontrolled cell cycle progression. Clinically, it presents as unilateral (60%) or bilateral (40%) disease, with leukocoria and strabismus as hallmark signs. Untreated, retinoblastoma is fatal due to metastatic spread. The disease follows Knudson’s two-hit model: heritable forms (30–40% of cases) involve a germline RB1 mutation (M1) and a somatic second hit (M2), predisposing to bilateral/multifocal tumors and secondary cancers. Non-heritable cases (60–70%) result from somatic RB1 mutations or, rarely, MYCN amplification (2%). Genetic testing is critical to classify risk (H0, H1, and HX categories), guide surveillance, and inform family counseling. Bilateral cases almost always harbor germline mutations, while 15% of unilateral cases may carry germline/mosaic RB1 defects. Advanced techniques (Sanger/NGS sequencing for mutation detection, NGS for copy number alterations, and methylation assays) detect RB1 mutations, CNVs, and epigenetic silencing. Tumor DNA analysis resolves ambiguous cases. H1 patients require intensive ocular and brain MRI surveillance, while H0 cases need no follow-up. Prenatal/preimplantation genetic diagnosis (PGD) can prevent transmission in high-risk families. Emerging research explores additional genes (BCOR, CREBBP) and MYCN-amplified subtypes. Genetic counseling addresses recurrence risks, reproductive options, and long-term cancer monitoring. Integrating genetic insights into clinical practice enhances precision medicine, reducing morbidity and healthcare costs. Future directions include whole-genome sequencing and functional studies to refine therapeutic strategies. Full article

Work-related musculoskeletal disorders (WMSDs) have a significant impact on healthcare professionals. The aim of this study was to conduct an umbrella review and meta-analysis to examine the overall body area prevalence of WMSDs by continents, according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Mendeley, PubMed/Medline, Science.gov, ScienceDirect, and Google Scholar were screened without date limitation to identify relevant meta-analyses. The selection, quality appraisal, and data extraction process were performed independently by two reviewers. Ten meta-analyses were included from the 3853 unique records, for a total of 100,211 participants, including dentists, nurses, surgeons, and mixed healthcare professionals. High heterogeneity (Cochran’s Q test and I² statistic) was observed. The largest number of meta-analyses was performed among nurses. Subgroup analysis by continent revealed an imbalance in the number of works, with Asia being the most documented. The analysis of prevalence rates was complete in Asia (overall and nine body areas), and partial in Europe (neck, shoulder, wrist) and Africa (lower back only). A ranking of the most exposed areas by continent was proposed. The lower back was the most exposed area (Africa: 54.5%; Asia: 56.6%). It would be relevant in future work to consider the numerous cross-sectional studies in order to improve subgroup analyses by continent and, thus, complete and strengthen the initial results presented in this first umbrella review. Full article

The principles of least effort and the illusion of control may influence the decision-making process. It is challenging for a decision-maker to maintain complete independence when assessing the membership and non-membership degrees of indicators. However, existing neutrosophic sets and q-rung orthopair fuzzy sets assume full independence of such information. In view of this, this paper proposes a new neutrosophic set, namely the q-type semi-dependent neutrosophic set (QTSDNS), based on the classical neutrosophic set, whose membership and non-membership degrees are interrelated. QTSDNS is a generalized form of classical semi-dependent fuzzy sets, such as the intuitionistic neutrosophic set. It contains a regulatory parameter, which allows for decision-makers to flexibly adjust the model. Furthermore, a multi-attribute group decision-making (MAGDM) algorithm is proposed by integrating QTSDNS with evidence theory to solve the supplier selection problem. The algorithm first utilizes QTSDNS to represent the preference information of experts, then employs the q-TSDNWAA (or q-TSDNWGA) operator to aggregate the evaluation information of individual experts. Following the analysis of the mathematical relationship between QTSDNS and evidence theory, evidence theory is used to aggregate the evidence from each expert to obtain the group trust interval. Then, the best supplier is determined using interval number ranking methods. Finally, a numerical example is provided to demonstrate the feasibility of the proposed method. Full article

With the rapid development of the Internet of Things and 5G communication technologies, the demand for the random access of a massive number of user equipment in burst scenarios has significantly increased. Traditional fixed-frame-length mechanisms, due to their inability to dynamically adapt to fluctuations in access traffic, are prone to exacerbating channel resource competition, increasing the probability of preamble collisions, and significantly elevating access delays, thereby constraining the system performance of large-scale machine-type communications. To address these issues, this paper proposes a dynamic frame length optimization algorithm based on Q-learning. By leveraging reinforcement learning algorithms to autonomously perceive access traffic characteristics, this algorithm can dynamically adjust frame length parameters without relying on estimates of the number of user equipment. It optimizes the frame length to improve random access performance, reduces collisions among user equipment competing for preambles, and enhances the utilization ratio of preamble resources. Full article