Search Results (82)

The correct course of DNA replication is crucial to maintaining the integrity of the genome. Any abnormality in this process inevitably leads to replication stress (RS). Hydroxyurea (HU) is a replication stressor widely used to inhibit DNA biosynthesis by depleting the deoxyribonucleoside triphosphate (dNTP) pool. The aim of the study was to examine how the 24-, 48-, and 72 h exposures to 0.75 mM HU affect the localization of fibrillarin (FBL; a highly conserved nucleolar protein and the component of Cajal bodies) and the amount of rRNA transcripts (detected using 5-ethynyl uridine; 5-EU), in root meristem cells of Allium cepa. The consequence of prolonged RS was initially (after 24 h of incubation in HU) a 2-fold increase in 5-EU incorporation into the nucleolus, then (after 48- and 72 h incubations) followed by a gradual decrease in rRNA transcription to a level similar to that of the control. In interphase and in early prophase, both in the control material and during successive periods of incubation of root meristems in HU, the immunofluorescence of FBL accumulated in the fibrillar centers (FCs) of the nucleoli, in the dense fibrillar components (DFC), and in the granular components (GC). In some HU-treated metaphase cells, FBL was localized around the telomeres of the chromosomes, while in telophase, it was found in the fragmented chromosomes. In addition, an increase in the number of Cajal bodies (CBs) was observed during subsequent incubation periods with HU. After 48 and 72 h of treatment with HU, the number of CBs was found to be almost twice that observed in the control series. CBs disappeared in prophase and reappeared in interphase. These results suggest that depending on the duration of RS, changes in the level of rRNA transcription and in the abundance of CBs may correlate with the production of RNP and ribosome biogenesis. Full article

As the most commercially developed metal additive process, laser powder bed fusion (LPBF) is vital to advancing several industry sectors, enabling high-precision part production across aerospace, biomedical, and manufacturing industries. Al 7075 alloy offers low density and high-specific strength yet faces LPBF challenges such as hot cracking and porosity due to rapid solidification, thermal gradients, and a wide freezing range. To address these challenges, this study proposes an integrated computational and experimental framework to enhance the LPBF processability of Al 7xxx alloys by compositional modification. Using the Calculation of Phase Diagram approach, printable Al 7xxx compositions were designed by adding grain refiners (V and/or Ti) and a eutectic solidification enhancer (Mg) to Al 7075 alloy to enable grain refinement and eutectic solidification. Subsequent LPBF experiments and characterization tests, such as metallography (scanning electron microscopy), energy-dispersive X-ray spectroscopy, X-ray diffraction, and X-ray micro-computed tomography, confirmed the production of refined microstructures with reduced defects. This study contributes to existing approaches for producing high-quality Al 7xxx alloy parts without significant compositional deviations using an integrated computational and experimental approach. Finally, aligning with the Materials Genome Initiative, this study contributes to the development and industrial adoption of advanced materials. Full article

Cotton’s susceptibility to low temperatures makes it a crucial raw resource for the world’s textile industry, yet its cultivation in temperate regions is severely limited. Although plant growth and stress responses depend on receptor-like kinases (RLKs), the functions of the MEDOS (MDS) gene family, which includes genes that encode RLK, are still poorly understood in cotton. In this study, we conducted a genome-wide analysis to systematically investigate the distribution of MDS gene family members in four cotton species. Phylogenetic analysis identified five evolutionary clades of the MDS gene family in cotton. The role of promoter cis-acting elements in hormone signaling and abiotic stress responses was suggested by analysis. Collinearity analysis demonstrated that segmental duplication was the primary driver of family expansion. Gene expression profiling showed that GhMDS11 was significantly upregulated under cold stress. Functional validation through silencing GhMDS11 compromised cold tolerance, confirming its role in stress adaptation. Comparative transcriptome study of silenced plants demonstrated substantial enrichment in pathways associated with hormone signal transduction and fatty acid breakdown. It is speculated that the chain of “hormone synthesis → signal transduction → secondary metabolism” completely presents the transcriptional regulation network and functional response of plants after receptor kinase VIGS. Silencing the GhMDS11 gene in cotton initiates regulatory effects through hormone synthesis, which is amplified via a signal transduction cascade, ultimately affecting secondary metabolism. This comprehensive pathway clearly demonstrates the downstream transcriptional reprogramming and functional changes. This work thoroughly examined the evolutionary traits of the MDS family across four cotton species and clarified the functional and molecular processes of GhMDS11 in improving low-temperature tolerance, laying a solid foundation for further clarifying multidimensional regulatory networks and breeding cold-resistant cotton materials. Simultaneously, our findings pave the way for future research to develop molecular markers, which could potentially shorten the breeding cycle and facilitate the targeted enhancement of cold tolerance in cotton. Full article

Postharvest shiitake mushrooms (Lentinus edodes) often undergo browning under low-temperature, high-humidity storage conditions, which significantly reduces their commercial value and constrains industry development. However, the molecular mechanisms regulating this process remain unclear. In this study, we used ‘Nongxiang No. 1’ as the experimental material and observed that during storage, the L* value of caps and stipes decreased continuously, shifting from light brown to dark brown-black. Concurrently, the relative electrical conductivity increased by approximately 3.07-fold, and the membrane lipid peroxidation product malondialdehyde (MDA) content increased by approximately 7.9-fold. Superoxide dismutase (SOD) activity initially increased then declined, indicating that elevated membrane permeability accelerates senescence. Peroxidase (POD) activity exhibited a significant upward then downward trend and improved 75.83% at day 22 of postharvest storage, with LEHP1, LEHP2, and LEHP3 gene expression patterns closely aligning with these changes. Specifically, LEHP2 and LEHP3 expression was upregulated by 23.8-fold and 2.35-fold on day 22 than day 0. Cis-element analysis identified MYB binding sites in all three LEHP genes. Genome-wide screening combined with qRT-PCR revealed two MYB transcription factors, LeMYB2 and LeMYB5, whose expression synchronized with LEHP genes. Transient expression assays in tobacco leaves confirmed their nuclear localization, consistent with transcription factor characteristics. Electrophoretic Mobility Shift Assay (EMSA) and Dual-Luciferase Reporter Assay (DLR) experiments further demonstrated that LeMYB2 and LeMYB5 directly activate LEHP2 and LEHP3 promoters, highlighting their key regulatory roles in postharvest browning of shiitake mushrooms. Full article

Nitrogen is an essential nutrient for the growth and development of maize (Zea mays L.), and soil nitrogen deficiency is an important factor limiting maize yield. Although excessive application of nitrogen fertilizer can increase yield, it can also cause environmental problems. Therefore, screening low-nitrogen-tolerant (LNT) germplasm resources and analyzing their genetic mechanisms are of great significance for the development of efficient and environmentally friendly agriculture. In this study, 201 maize inbred lines were used as materials. Two levels of low nitrogen (LN) (0.05 mmol/L, N1) and normal nitrogen (4 mmol/L, N2) were set up. Phenotypic indicators such as seedling length, root length and biomass were measured, and they were classified into LNT type (18 samples), nitrogen-sensitive (NS) type (27 samples) and intermediate type (156 samples). A total of 47 significant SNP loci were detected through a genome-wide association study (GWAS), and 36 candidate genes were predicted. Transcriptome sequencing (RNA-seq) analysis revealed that the differentially expressed genes (753 upregulated and 620 downregulated) in LNT materials under low nitrogen stress (LNS) were significantly fewer than those in NS materials (2436 upregulated and 2228 downregulated). Further analysis using WGCNA identified a total of eight co-expression modules. Among them, the red module was significantly correlated with root length and underground fresh weight under LN conditions (r = 0.75), and three key genes for stress response (Zm00001d005264, Zm00001d053931, Zm00001d044292) were screened out. Combined with GWAS, RNA-seq and qRT-PCR verification, eight candidate genes closely related to LNT at the seedling stage of maize were finally determined, involving biological processes such as stress response, nitrogen metabolism and substance formation. This study initially revealed the molecular mechanism of maize tolerance to LN through multi-omics analysis, providing a theoretical basis and genetic resources for breeding new nitrogen-efficient maize varieties. Full article

Background and Objectives: Metabolic syndrome (MetS) progresses gradually as individual components accumulate. However, there is limited understanding regarding whether the sequence of component appearance influences disease progression. This study sought to determine the most frequent initial MetS component and evaluate whether this component influences the subsequent risk of developing full MetS. Materials and Methods: We examined data from 6137 participants in the Korean Genome and Epidemiology Study (KoGES), free of MetS at baseline (2001–2002), followed until 2011–2012. Participants were stratified by the first emerging MetS component: abdominal obesity, elevated blood pressure, high fasting glucose, high triglycerides, or low HDL cholesterol. The primary endpoint was progression to full MetS, defined as the development of three or more components. We also assessed transition probabilities between components and sex-specific sequence differences. Results: Abdominal obesity was the most frequent initial metabolic abnormality (31.0%), followed by elevated blood pressure (26.3%), low HDL cholesterol (15.3%), high triglycerides (13.7%), and high fasting glucose (4.9%). Over a median 8.2-year follow-up, participants with initial abdominal obesity exhibited the greatest progression rate to full MetS (44.4%), significantly higher than those with elevated blood pressure (24.8%), high triglycerides (23.0%), high fasting glucose (21.6%), or low HDL cholesterol (9.3%) (all p < 0.001). After controlling for age, sex, smoking status, and baseline BMI, initial abdominal obesity was associated with a 4.77-fold increased risk (95% CI: 3.68–6.18) of developing full MetS compared to initial low HDL cholesterol. Distinct transition patterns were observed: high triglycerides frequently transitioned to low HDL cholesterol (78.1%), while abdominal obesity most often led to elevated blood pressure (52.1%). Marked sex-related differences were also found: abdominal obesity was more common initially among women (41.7% vs. 25.2%), whereas elevated blood pressure was predominant among men (37.6% vs. 21.2%). Conclusions: The initial MetS component strongly predicts progression to full syndrome, with abdominal obesity conferring the highest risk. Early identification and targeted interventions addressing abdominal obesity may effectively prevent MetS and its subsequent complications. Full article

Background and Objectives: Over the past few years, there has been a significant shift in focus from developing better diagnostic tools to detecting Alzheimer’s disease (AD) earlier and initiating treatment interventions. This review will explore four main objectives: (a) the role of biomarkers in enhancing the diagnostic accuracy of AD, highlighting the major strides that have been made in recent years; (b) the role of neuropsychological testing in identifying biomarkers of AD, including the relationship between cognitive performance and neuroimaging biomarkers; (c) the amyloid hypothesis and possible molecular mechanisms of AD; and (d) the innovative AD therapeutics and the challenges and limitations of AD research. Materials and Methods: We have searched PubMed and Scopus databases for peer-reviewed research articles published in English (preclinical and clinical studies as well as relevant reviews and meta-analyses) investigating the molecular mechanisms, biomarkers, and treatments of AD. Results: Genome-wide association studies (GWASs) discovered 37 loci associated with AD risk. Core 1 biomarkers (α-amyloid Aβ42, phosphorylated tau, and amyloid PET) detect early AD phases, identifying both symptomatic and asymptomatic individuals, while core 2 biomarkers inform the short-term progression risk in individuals without symptoms. The recurrent failures of Aβ-targeted clinical studies undermine the amyloid cascade hypothesis and the objectives of AD medication development. The molecular mechanisms of AD include the accumulation of amyloid plaques and tau protein, vascular dysfunction, neuroinflammation, oxidative stress, and lipid metabolism dysregulation. Significant advancements in drug delivery technologies, such as focused Low-Ultrasound Stem, T cells, exosomes, nanoparticles, transferin, nicotinic and acetylcholine receptors, and glutathione transporters, are aimed at overcoming the BBB to enhance treatment efficacy for AD. Aducanumab and Lecanemab are IgG1 monoclonal antibodies that retard the progression of AD. BACE inhibitors have been explored as a therapeutic strategy for AD. Gene therapies targeting APOE using the CRISPR/Cas9 genome-editing system are another therapeutic avenue. Conclusions: Classic neurodegenerative biomarkers have emerged as powerful tools for enhancing the diagnostic accuracy of AD. Despite the supporting evidence, the amyloid hypothesis has several unresolved issues. Novel monoclonal antibodies may halt the AD course. Advances in delivery systems across the BBB are promising for the efficacy of AD treatments. Full article

Al-Mg-Si (6XXX) series aluminum alloys are widely applied in aerospace and transportation industries. However, exploring how varying compositions affect alloy properties and deformation mechanisms is often time-consuming and labor-intensive due to the complexity of the multicomponent composition space and the diversity of processing and heat treatments. This study, inspired by the Materials Genome Initiative, employs high-throughput experimentation—specifically the kinetic diffusion multiple (KDM) method—to systematically investigate how the pop-in effect, indentation size effect (ISE), and creep behavior vary with the composition of Al-Mg-Si alloys at room temperature. To this end, a 6016/Al-3Si/Al-1.2Mg/Al KDM material was designed and fabricated. After diffusion annealing at 530 °C for 72 h, two junction areas were formed with compositional and microstructural gradients extending over more than one thousand micrometers. Subsequent solution treatment (530 °C for 30 min) and artificial aging (185 °C for 20 min) were applied to simulate industrial processing conditions. Comprehensive characterization using electron probe microanalysis (EPMA), nanoindentation with continuous stiffness measurement (CSM), and nanoindentation creep tests across these gradient regions revealed key insights. The results show that increasing Mg and Si content progressively suppresses the pop-in effect. When the alloy composition exceeds 1.0 wt.%, the pop-in events are nearly eliminated due to strong interactions between solute atoms and mobile dislocations. In addition, adjustments in the ISE enabled rapid evaluation of the strengthening contributions from Mg and Si in the microscale compositional array, demonstrating that the optimum strengthening occurs when the Mg-to-Si atomic ratio is approximately 1 under a fixed total alloy content. Furthermore, analysis of the creep stress exponent and activation volume indicated that dislocation motion is the dominant creep mechanism. Overall, this enhanced KDM method proves to be an effective conceptual tool for accelerating the study of composition–deformation relationships in Al-Mg-Si alloys. Full article

The ability of a nucleic acid molecule to self-replicate is the driving force behind the evolution of cellular life and the transition from RNA to DNA as the genetic material. Thus, the physicochemical properties of genome replication, such as the requirement for a terminal hydroxyl group for de novo DNA synthesis, are conserved in all three domains of life: eukaryotes, bacteria, and archaea. Canonical DNA replication is initiated from specific chromosomal sequences termed origins. Early bacterial models of DNA replication proposed origins as regulatory points for spatiotemporal control, with replication factors acting on a single origin on the chromosome. In eukaryotes and archaea, however, replication initiation usually involves multiple origins, with complex spatiotemporal regulation in the former. An alternative replication initiation mechanism, recombination-dependent replication, is observed in every cellular domain (and viruses); DNA synthesis is initiated instead from the 3′ end of a recombination intermediate. In the domain archaea, species including Haloferax volcanii are not only capable of initiating DNA replication without origins but grow faster without them. This raises questions about the necessity and nature of origins. Why have archaea retained such an alternative DNA replication initiation mechanism? Might recombination-dependent replication be the ancestral mode of DNA synthesis that was used during evolution from the primordial RNA world? This review provides a historical overview of major advancements in the study of DNA replication, followed by a comparative analysis of replication initiation systems in the three domains of life. Our current knowledge of origin-dependent and recombination-dependent DNA replication in archaea is summarised. Full article

Background/Aim: Cervical adenocarcinoma associated with Human Papillomavirus (HPV) infection represents 85–90% of all adenocarcinomas that have poor prognostic factors and is an important health public concern. Currently, cervical adenocarcinoma molecular markers are scarce. This study searched databases and the literature regarding candidate genes to find these molecular markers, which were experimentally evaluated in fresh cervical samples. Materials and Methods: Bioinformatic analysis of 161 transcriptomic libraries of cervical tissues with or without lesions from the NCBI database was performed using the Partek Genomics Suite 6.6v software. The selected genes with a p value of >0.05, and 1.5-fold change were considered. A search of molecular marker candidates of cervical lesions that were already published in the literature was performed. To validate the selected genes, total RNA from fresh cervical adenocarcinoma and cervical normal tissues were subjected to RT-PCR experiments; HPV detection was also performed. Results: Initially, twenty-five genes were identified using bioinformatic analysis, and their expression was evaluated. The results showed that the HOXC6, HOXC8, RARβ, ELAVL2, URG4, CISD2, CA9, BCL2, Survivin, MACC1, CDKN2A, and HPV E6/E7 genes were found to be differentially expressed in CC. Among these, RARβ, MACC1, BCL2, HOXC8, and E6/E7/HPV exhibited higher statistical significance for CC samples. Conclusions: This five-gene panel could serve as a novel molecular tool for HPV-associated cervical adenocarcinoma detection. Full article

Hexaploid wheat has a large genome, making it difficult for transgenes to produce phenotypes due to gene redundancy and tight linkage among genes. Multiple gene copies typically necessitate multiple targeting events during gene editing, followed by several generations of self-crossing to achieve homozygous genotypes. The high cost of transgenesis in wheat is another issue, which hinders the easy availability of gene-edited materials in wheat. In this study, we developed a comprehensive approach to improve wheat gene editing efficiency. First, we established a protoplast-based system to evaluate the relative efficiency of gene editing targets, which enabled the rapid and effective selection of optimal sgRNAs. We then compared two transformation strategies: biolistic bombardment and Agrobacterium-mediated transformation for generating edited wheat lines. Although biolistic bombardment showed higher initial editing efficiency, Agrobacterium-mediated transformation proved more effective for obtaining homozygous mutants. Notably, we discovered that deploying the same sgRNA through different vectors enhanced editing efficiency, whereas overlapping but distinct sgRNAs exhibited interference effects. Finally, we optimized the VITF-edit (virus-induced transgene free editing) technique using BSMV delivery to establish a relatively simple and easily applied wheat gene editing method for general laboratories. Full article

Background and Objectives: Sepsis is one of the major causes of death in modern society. This study is part of the FUSE (Functional Genomics in Severe Sepsis) project under the Human Functional Genomics Romania initiative. Our aim was to assess the epidemiology of sepsis in a tertiary academic hospital in southwestern Romania. Materials and methods: The study enrolled 184 patients with severe infections between May 2017 and November 2019, following the Sepsis-2 guidelines (SIRS criteria). Results: The present cohort of community-acquired severe infections shows respiratory and urinary tract as main sites of severe infection. The demographic and clinical characteristics of this Romanian study group are in line with those of other severe infection European cohorts. However, the predominance of confirmed Clostridium difficile cases represents a strong deviation, raising significant concerns for the communities to which the patients belong. Conclusions: Sepsis, with its complex pathophysiology and clinical presentation, remains one of the most daunting global health issues. In our cohort, the high number of Clostridium difficile cases prompts high vigilance and immediate intervention. Full article

Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized probe set consisting of 149,990 probes, targeting 663 viruses associated with humans and animals. The detection performance was initially assessed using viral reference materials in a background of human nucleic acids. Compared to standard metagenomic next-generation sequencing (mNGS), our method achieved substantial read enrichment, with increases ranging from 143- to 1126-fold, and enhanced detection sensitivity by lowering the limit of detection (LoD) from 10³–10⁴ copies to as few as 10 copies based on whole genomes. This method was further validated using infectious samples from both animals and humans, including bovine rectal swabs and throat swabs from SARS-CoV-2 patients across various concentration gradients. In both sample types, our hybrid capture-based sequencing method exhibited heightened sensitivity, increased viral genome coverage, and more comprehensive viral identification and characterization. Our method bridges a critical divide between diagnostic detection and genomic surveillance. These findings illustrate that our hybrid capture-based sequencing method can effectively enhance sensitivity to as few as 10 viral copies and genome coverage to >99% in medium-to-high viral loads. This dual capability is particularly impactful for emerging pathogens like SARS-CoV-2, where early detection and genomic characterization are equally vital, thereby addressing the limitations of metagenomics in the surveillance of emerging infectious diseases in complex samples. Full article

Background and Objectives: Severe early childhood caries (S-ECC) is a chronic infectious disease with a multifactorial etiology which has not been completely elucidated. Research on the role of oxidative stress in the etiopathogenesis of oral diseases suggests that the level of local antioxidants plays an important role in determining susceptibility to caries. This study aimed to demonstrate that the host’s redox imbalance, modified by genetic polymorphisms, may influence the onset and severity of S-ECC. Materials and Methods: A total of 110 patients were included in the study (59 diagnosed with S-ECC and 51 healthy controls). Upon initial appraisal, the DMFT (decayed-missing-filled teeth) index was determined, and epithelial cells were collected using oral swabs for genomic DNA extraction. Genotyping of SOD2 (rs4880) and GPX1 (rs1050450) was performed using TaqMan SNP genotyping assays and real-time polymerase chain reaction (PCR). Results: According to the results of the present study, there was a significant difference between the frequency of the reference genotype and variants for rs4880 (p = 0.0303). Subjects carrying the AG and GG variant genotype of rs4880 were significantly associated with a high DMFT value (p = 0.0005). However, no significant difference was found between the genotypes for rs1050450, nor was there an association with the severity of S-ECC. Conclusions: The AG and GG variant genotypes of the SOD2 polymorphism (rs4880) increase the severity of caries in preschoolers and predispose patients to develop carious lesions, especially when associated with certain feeding practices and infrequent toothbrushing. This observation emphasizes that host sensitivity to caries is a crucial factor in the onset and development of carious lesions in primary dentition, despite the main contributing factors to this pathology. The rs1050450 polymorphism was not associated with the severity of S-ECC. Full article

Background and Objectives: Shift work is associated with an increased risk of acute coronary syndrome (ACS) and higher rates of smoking and alcohol consumption. This study examines how smoking and alcohol intake may influence the effect of shift work on ACS risk, indicating a complex interaction among these factors in individuals engaged in shift work. Materials and Methods: This investigation utilized data from the Korean Genome and Epidemiology Study (KoGES). Shift work was the primary exposure, and the main outcome was ACS, defined as either myocardial infarction or angina pectoris diagnosed from 2003 to 2020. Cox proportional regression analysis was employed to assess the impact of shift work, smoking, and alcohol intake on ACS incidence. Additionally, we performed an interaction analysis to examine the effects of shift work in conjunction with smoking and alcohol intake on ACS incidence. Results: Out of 10,038 participants enrolled during the study period, 3696 (36.8%) met the inclusion criteria. The incidence rate of ACS was 11.88 per 1000 person-years in the shift work group compared to 5.96 per 1000 person-years in the non-shift work group. Using Cox proportional logistic regression, shift work was found to be associated with a hazard ratio (HR) of 1.74 (95% CI, 1.20, 2.53) compared to the non-shift work group. Smoking and alcohol consumption did not exhibit a significant HR for ACS incidence, with HRs of 1.31 (95% CI, 0.98, 1.75) and 0.83 (95% CI, 0.65, 1.07), respectively. In the interaction model, after adjusting for other covariates, shift work was not significantly associated with ACS incidence in current smokers (HR 1.05, 95% CI 0.49, 2.23). However, among non-current smokers, shift work emerged as a significant risk factor for ACS incidence (HR 2.26, 95% CI 1.44, 3.55) (p for interaction < 0.01). No interaction was found between alcohol consumption and shift work in relation to ACS incidence. Conclusions: Shift work is an independent risk factor for acute coronary syndrome (ACS), particularly among non-current smokers. This finding highlights the need to address both lifestyle and occupational factors when developing strategies to mitigate ACS risk among shift workers. Employers and policymakers should consider implementing targeted workplace interventions to reduce this risk. These may include optimizing shift schedules to minimize circadian disruption, providing regular health screenings focused on cardiovascular health, and promoting healthy lifestyle habits such as balanced nutrition, regular physical activity, and stress management programs. Additionally, workplace wellness initiatives could focus on reducing other modifiable risk factors, such as providing resources for smoking cessation and limiting exposure to occupational stressors. Integrating these strategies into occupational health policies can contribute to the early detection and prevention of ACS, ultimately improving the cardiovascular health of shift workers. Full article