Search Results (13,320)

This study investigates the phenotypic characteristics, genetic diversity, and population structure of four wild cherry species collected from various regions of Kazakhstan and Uzbekistan: Prunus fruticosa Pall., Ptunus erythrocarpa (Nevski) Gilli, Prunus griffithii var. tianshanica (Pojark.) Ingram, and Prunus verrucosa (Franch.). A total of 163 accessions were characterized morphologically using standardized descriptors for plant, leaf, and fruit traits. Genetic diversity was assessed using 13 simple sequence repeat (SSR) markers. STRUCTURE analysis revealed that 87.7% of the accessions were assigned to pure species. However, hybrid accessions were identified in P. griffithii var. tianshanica (34.4%), P. erythrocarpa (18.5%), and P. verrucosa (8.0%). Identical genotypes were found across all species, with P. fruticosa showing the highest proportion (54.8%), likely due to clonal propagation via root suckers. Among the four species, P. verrucosa exhibited the highest genetic diversity, while P. fruticosa had the lowest. Analysis of molecular variance (AMOVA) showed that genetic variation within the species (81%) was substantially greater than variation among the species (19%). These findings enhance our understanding of the genetic relationships among wild cherry species in Central Asia and provide valuable data for conservation planning and breeding programs aimed at improving drought and frost tolerance in Prunus species. Full article

Ischemic stroke (IS) is the leading cause of disability and death worldwide, and its high incidence, disability and recurrence rates impose a heavy economic burden on families and society. Recent studies have shown that oxidative stress plays a key role in the pathophysiological mechanisms of ischemic stroke, not only participating in the onset and development of neuronal damage in the acute phase but also significantly influencing the long-term prognosis of ischemic stroke through molecular mechanisms, such as epigenetic modifications. However, the potential targets of oxidative stress-related genes in IS and their mechanisms of action remain to be elucidated. The aim of this study was to systematically analyse the function and significance of oxidative stress-related genes in IS. We obtained IS-related gene expression datasets from the GEO database and integrated known oxidative stress-related genes from the Genecards database for cross-analysis. Multidimensional feature screening using unsupervised consensus clustering and a series of machine learning algorithms led to the identification of the signature gene GPX7. The correlation between this gene and immune cell infiltration was assessed using MCPcounter and a potential therapeutic agent, glutathione, was identified. Binding was verified by molecular docking (MD) analysis. In addition, single-cell RNA sequencing data were analysed to further reveal expression in different cell types and its biological significance. Finally, we performed in vivo experiments using the Wistar rat middle cerebral artery occlusion (MCAO) model, and the results indicated that GPX7 plays a key role in IS, providing a new theoretical basis and potential intervention target for the precise treatment of IS. Full article

The fossil and molecular evidence suggests that the area of origin of the Hairy Armadillo Chaetophractus villosus was the central Pampas region of Argentina, with a current distribution that includes Bolivia, Paraguay and Chile. We studied the evolutionary history of peripheral individuals of C. villosus using phylogeographic approaches and potential distribution models for the Holocene. We sequenced a segment of the mitochondrial DNA control region in 22 individuals with a peripheral distribution that inhabit the western limit of its current distribution in Chile, which was compared with Argentine sequences of the central distribution. The results show that the peripheral individuals studied have less genetic polymorphism than populations in the central distribution. All Chilean sequences were grouped in the haplotype C, which is dominant in Patagonian populations of Argentina. The potential distribution model predicts that during the Holocene the areas in which the peripheral populations of Chilean C. villosus are currently distributed presented medium–high habitability conditions for the species. Our results are consistent with the center–periphery model, showing a decrease in genetic diversity in peripheral areas of the distribution of C. villosus. It is probable that the low genetic diversity of the peripheral population is related to recent population establishment by dispersion from adjacent Argentine Patagonian populations. Peripheral populations such as those studied can have small population sizes; however, they can remain stable and have high survival rates during climatic oscillations, acting as important relics for the conservation and evolutionary potential of the species. Full article

Murine double minute 2 (MDM2) is involved in various cancers and is an attractive target. The RING domain of MDM2 has been discussed as an alternative target to stabilize p53. Designing drugs to target the RING domain of MDM2 is an alternative approach to preventing MDM2-mediated deactivation of p53. In this study, we obtained a human VH single-domain antibody and revealed its regulatory effects and mechanisms. The RING domain of MDM2 was synthesized using a chemical synthesis method, and antibodies against the MDM2 RING domain were screened from a human VH single-domain antibody library and expressed intracellularly. A nuclear localization sequence was designed to ensure intrabody efficiency. The binding activity of the individually cloned antibodies was detected using ELISA. MTT and flow cytometry assays were used to detect the reactions related to intrabody in vitro. The combination and its influence on MDM2 were detected using immunoprecipitation assays, confocal microscopy, and Western blotting. The effects on apoptosis-related mitochondrial pathways downstream of p53 were examined using Western blotting. The influence on cell cycle distribution and cyclin-related proteins was detected using flow cytometry and Western blotting. A549 cell xenografts were constructed to assess the effect of intrabodies on growth in vivo. The molecular mechanisms of MDM2 and p53 were studied using Western blotting. Eight individual cloned antibodies were positive compared to the signals on the BSA-coated plates, especially intrabodies VH-HT3. In A549 and MCF-7 cell lines, VH-HT3 exhibited significant inhibitory effects on cell proliferation and apoptosis. VH-HT3 co-localized with MDM2 in the nucleus and cytoplasm. The specific combination of VH-HT3 triggered no significant effect on MDM2 activity for p53 degradation but upregulated the levels of factors downstream of p53, especially those in the mitochondrial apoptosis pathway. Moreover, VH-HT3 induced cell cycle arrest, and the expression of cyclin-related proteins was consistent with this observation. VH-HT3 also retarded the growth of A549 xenografts in vivo. Further tests suggested that VH-HT3 inhibited MDM2 function by increasing HIPK2 levels and activating p53 at the Ser46 site. VH-HT3, prepared from a human VH single-domain antibody library, inhibited p53 activity and produced a tumor-suppressive effect. The intrabody VH-HT3 is a candidate for the development of novel MDM2 inhibitors. Full article

The network regulatory mechanism governing the dynamics of plant maturity and tuber development in potatoes (Solanum tuberosum L.) has remained a major focus in potato molecular biology research. In this study, three potato cultivars with different maturity periods (‘Shishu 2’, ‘Zhongshu 3’, and ‘Zhongshu 49’) were examined. RNA sequencing was performed on samples from five tissues, including the leaves, stems, stolon (T0), sub-apical swellings (T1), and initiation stage (T2), to reveal the co-expression regulatory network involved in leaf, stem, and tuber development. StSWEET11 and StSP6A were significantly upregulated in the early-maturing cultivar ‘Shishu 2’. Differentially expressed genes were classified into 18 modules (ME) using weighted gene co-expression network analysis (WGCNA). Among these, ME1, ME3, and ME13 showed significant positive correlations with leaf tissue, ME2, ME4, and ME15 with stem tissue, and ME7, ME8, and ME14 with T1 and T2 tissues. StSP5G was identified as the core hub gene of ME4. Genes such as StCOL1, StSWEET11, and StSP6A exhibited significant co-expression in leaf-related modules. StGIGANTEA and StGIGANTEA-like played important regulatory roles in linking the expression networks of stems and tubers. Metabolism-related genes, including StSUSⅠc/StSuSy4 and StDPE1, were also found to be crucial in mediating interactions between leaf and tuber tissues. Therefore, this study provides new insights into the regulatory network governing tuberous signal transmission from leaves and stems to tubers. Full article

Malaria remains a significant public health challenge, particularly in endemic regions. The extensive genetic diversity of Plasmodium falciparum (Pf) complicates outbreak prediction and transmission control. One of its most polymorphic markers, merozoite surface protein 2 (MSP2), presents a potential target for molecular surveillance. This cross-sectional study, conducted at King Faisal Hospital Rwanda (KFHR) from October 2021 to June 2023, assessed MSP2′s utility in malaria prediction. PfMSP2 was sequenced, and selected amplicons were cloned, expressed in bacteria, and purified. These antigens were tested against sera from malaria patients and geographically diverse healthy individuals, with complementary surveys contextualizing serological findings. Of the 75 processed monoallelic clinical isolates, 3D7 strains predominated over FC27. Three MSP2-derived biomarkers were produced, eliciting significantly low IgG responses in malaria patients and Belgian controls, but a complex pattern emerged in healthy individuals, with significant differences between Rwandan and Cameroonian samples. IgG3 was the predominant subclass in individuals with high IgG responses. Notably, Rwandan individuals with weak humoral responses to the tested antigens but also other with high responses experienced malaria episodes in the subsequent year. These findings highlight MSP2 polymorphism as a valuable tool for malaria surveillance and outbreak prediction. Integrating genotyping and serology could enable precise, community-specific malaria risk assessments, strengthening control strategies. Full article

Wastewater-based epidemiology (WBE) offers valuable insight into viral circulation at the community level. In this study, we combined digital PCR (dPCR) with molecular typing to investigate the prevalence and diversity of human adenoviruses (HAdVs) in untreated wastewater samples collected throughout Italy. HAdV genomes were detected in over 93% of the 168 samples analyzed, with concentrations up to 4.5 × 10⁶ genome copies per liter. For genotypic characterization, we used nested PCR followed by Sanger and Oxford Nanopore Technologies (ONTs) long-read sequencing. While Sanger sequencing identified three dominant genotypes (HAdV-A12, HAdV-B3, and HAdV-F41), ONT sequencing provided enhanced resolution, confirming all previously identified types and revealing seven additional genotypes: HAdV-B21, HAdV-C5, HAdV-D45, HAdV-D46, HAdV-D49, HAdV-D83, and HAdV-F40. This comprehensive approach highlights the added value of ONT long-read sequencing in uncovering the genetic complexity of adenoviruses in wastewater, particularly in detecting rare or low abundance types that conventional methods may miss. Our findings highlight the value of integrating quantitative and high-resolution molecular tools in WBE to improve surveillance and better understand the epidemiology of viral pathogens circulating in the human population. Full article

In plants, the transition from the juvenile to adult stage involves physiological and anatomical changes initiated and partially controlled by evolutionarily conserved microRNAs. This process is of particular significance for the successful propagation of woody plant species that have transitioned to vegetative maturity and are recalcitrant to propagation. Conserved miRNAs differentially expressed between rejuvenated and mature Ilex paraguariensis plants were identified using high-throughput sequencing of small RNA libraries. The expression of miR156/miR157/miR528 was high in the leaves of juvenile plants and gradually decreased as the plant transitioned from juvenile to adult stages. In contrast, miR172 was predominantly expressed in adult plants. This variation confirmed that adults transitioned back to a juvenile phase after serial-rooted cuttings, allowing the plants to regain juvenile characteristics. Rejuvenation promotes the formation of adventitious roots and improves root structure, which supports the overall growth of the plant and results in greater vigour. The results will offer insights for further investigation into the molecular mechanisms regulating vegetative phase change in I. paraguariensis and other recalcitrant woody plant species. This knowledge could facilitate the earlier identification of rejuvenated material by analysing a wider range of genotypes and maturation stages, enhancing the efficiency of Ilex paraguariensis mass propagation. Full article

Cytokinins play an important role in plants and are targets of wheat breeding, particularly in terms of flowering and yield. The objective of this study was to determine relative synonymous codon usage (RSCU), molecular weight (g/mol), theoretical isoelectric point, instability index, aliphatic index, and hydrophobicity for the wheat cytokinin sequences from two different databases. The methods employed involved different formulas for calculations. The relative synonymous codon usage values were calculated as the ratio of the observed frequency to the expected frequency for the particular codon. The theoretical isoelectric point was calculated based on dissociation constant for groups of carboxylic acid and amino acids groups. The results showed that values of the relative synonymous codon usage divided amino acids of wheat into two groups. In the first group, values were above 1.6 (significant overrepresentation), such as those for phenylalanine (TTC), and Leucine (TTA). In the second group, values were below 0.6 (underrepresentation) such as those for leucine (CTA) and valine (GTT). In addition, the theoretical isoelectric point (pI) ranged from 4.81 to 6.6, and the instability index values were 34.3 and 38.16. A high degree of instability was observed at 1D and 5D of wheat genomes with values of 54.16 and 50.36, respectively. Principal component analysis (PCA) of the RSCU revealed that the main variation was attributed to PC1, accounting for a total variation of about 72.11%. The amino acids contributing to this variation included isoleucine, leucine, lysine, aspartic acid, and serine. PCA of the theoretical isoelectric point results found that the main variation was attributed to PC1, with a total variation of about 58.88%, and these chromosomes included 5D, 4D, 1A, 4B, and 3D of wheat genomes. Understanding the importance of RSCU in plant breeding helps breeders understand the mechanisms and functional aspects of wheat genomes, thereby enabling the development of wheat genomes for environmental adaptations. These results will provide a reference for nutrition and industrial applications, as well as supporting breeding programs. Full article

This study investigates the interplay between cellular senescence and inflammation in human umbilical vein endothelial cells (HUVECs). We employed RNA sequencing to analyze gene expression changes in HUVECs subjected to replicative- or radiation-stress-induced senescence, and we compared these profiles with those of cells under acute or chronic TNFα-mediated inflammation. Our findings reveal that both senescence types exhibited significant upregulation of genes associated with epithelial- (or endothelial) mesenchymal transition (EMT) and inflammatory pathways, indicating a shared molecular response. Notably, chronic inflammation led to a pronounced EMT signature, while acute inflammation primarily activated classical inflammatory responses. Experimental validation confirmed reduced proliferation and increased secretion of pro-inflammatory cytokines (IL-6 and IL-8) in senescent and chronically inflamed cells and substantiated the upregulation of EMT marker genes. Additionally, we observed impaired wound healing capacity in senescent and chronically inflamed cells, highlighting the functional consequences of these cellular states. Our study underscores the critical role of inflammation in exacerbating senescence-related changes, contributing to the understanding of age-related cardiovascular pathologies. These insights may inform future therapeutic strategies aimed at mitigating the effects of aging and inflammation on endothelial function and cardiovascular health. Full article

The ongoing threat of viral pandemics such as COVID-19 highlights the urgent need for novel antiviral therapeutics targeting conserved viral proteins. In this study, peptides of 10–30 kDa derived from the marine diatom Phaeodactylum tricornutum were identified as potential inhibitors of SARS-CoV-2 main protease (Mpro), a key enzyme in viral replication. Peptides less than 60 amino acids in length were retrieved from the UniProt database and aligned with reference antiviral sequences using the Biopython pairwise2 algorithm. Six candidates were selected for structural modeling using AlphaFold2 and Swiss-Model, followed by molecular docking using ClusPro2. LigPlot+ was used to assess molecular interactions, while NetMHCpan 4.1 and AVPpred evaluated immunogenicity and antiviral potential, respectively. Molecular dynamics simulations over 100 ns were conducted using OpenMM. These peptides demonstrated stable binding interactions with key catalytic residues of Mpro. Specifically, peptide A0A8J9SA87 interacted with Cys145 and Glu166, while peptide A0A8J9SDW0 exhibited interactions with His41 and Phe140, both of which are known to be essential for Mpro inhibition. Although peptide A0A8J9X3P8 also interacted with catalytic residues, it exhibited greater structural fluctuations during molecular dynamics simulations and achieved lower AVPpred scores, suggesting lower overall antiviral potential. Therefore, A0A8J9SA87 and A0A8J9SDW0 were identified as the most promising candidates. Molecular dynamics simulations further supported the high structural stability of these peptide-Mpro complexes over a 100 ns timescale, reinforcing their potential as effective inhibitors. These findings support P. tricornutum as a valuable source of antiviral peptides and demonstrate the feasibility of in silico pipelines for identifying therapeutic candidates against SARS-CoV-2. Full article

Background: The GhA01EP1 gene in upland cotton encodes an epidermal-specific secreted glycoprotein, whose functional characterization remains unexplored beyond our initial discovery of its water deficit resistance association. Therefore, we further designed experiments to investigate the functional role of GhA01EP1. Methods: We sequenced and analyzed the transcriptomes of wild-type (Col-0) and GhA01EP1-transgenic Arabidopsis thaliana. The differences in morphological and biochemical indicators were examined. In addition, the proteins interacting with GhA01EP1 in Arabidopsis were screened using a glutathione-S-transferase pull-down assay. Results: The GhA01EP1-transgenic Arabidopsis plants flowered earlier, produced more branches, and had a higher seed yield than Col-0. Transcriptome analysis revealed that differentially expressed genes detected in the comparison of GhA01EP1-transgenic and Col-0 Arabidopsis under the water treatment (the control) were associated especially with circadian rhythm regulation, photoperiodic flowering reaction, hormone metabolism, glyoxalase I synthesis, antioxidant pathway, branching development, and carbon-nitrogen allocation. Under water-sufficient or water-deficient treatments, the glyoxalase I activity and lignin content of GhA01EP1-transgenic Arabidopsis were significantly higher. Under water deficit stress, the malondialdehyde and starch contents were significantly lower, while peroxidase activity and protein content were significantly higher than those of Col-0. Conclusions: GhA01EP1 synergistically improved the precocity, water deficit tolerance, and seed yield of GhA01EP1-transgenic Arabidopsis. Analysis of GhA01EP1 function provides a molecular basis for breeding improved cotton varieties. Full article

Objectives: The objective of this study was to investigate the significance of molecular classification in guiding treatment decisions for patients with endometrial cancer (EC) or atypical hyperplasia (AH) undergoing fertility-sparing treatment (FST), particularly for those with non-NSMP subtypes. Methods: We conducted a retrospective cohort study involving EC/AH patients undergoing FST and molecular classification using next-generation sequencing at Peking University People’s Hospital between June 2020 and September 2023. Results: A total of 118 EC/AH patients were included, including 92 cases with NSMP, 11 with MMRd, 11 with POLEmut, and 4 with p53abn. (1) Of the 11 patients with MMRd, 6 achieved a complete response (CR) with 1 case receiving progestin, 3 cases showed insensitivity to the initial progestin before transitioning to a combined regimen of progestin and a PD-1 inhibitor, and 2 cases initially received progestin plus a PD-1 inhibitor. There were no significant differences in the cumulative CR rates between the MMRd and NSMP subgroups but a trend of a lower relapse-free-survival (RFS) rate for the MMRd subgroup (p = 0.074). (2) Of the 11 cases with POLEmut, 10 achieved CR but 4 relapsed. There was also a trend for a lower RFS rate in the POLEmut patients (p = 0.069) compared with the NSMP subgroup. (3) Three of the four patients with p53mut achieved CR after treatment with the GnRHa plus LNG-IUS regimen. Conclusion: The selection of appropriate regimens may improve FST outcomes in EC/AH patients with molecular classification of non-NSMP subtypes. Immunotherapy is an effective fertility-preserving approach for patients with MMRd. Full article

Background/Objectives: Mango, which is known as the “King of Tropical Fruits”, is an evergreen plant belonging to the Anacardiaceae family. It belongs to the genus Mangifera, which comprises 69 species of plants found in tropical and subtropical regions, including India, Indonesia, the Malay Peninsula, Thailand, and South China. However, research on the structural information of complete chloroplast genomes of Mangifera is limited. Methods: The rapid advancement of high-throughput sequencing technology enables the acquisition of the entire chloroplast (cp) genome sequence, providing a molecular foundation for phylogenetic research. This work sequenced the chloroplast genomes of six Mangifera samples, performed a comparative analysis of the cp genomes, and investigated the evolutionary relationships within the Mangifera genus. Results: All six Mangifera samples showed a single circular molecule with a quadripartite structure, ranging from 157,604 bp to 158,889 bp in length. The number of RNA editing sites ranged from 60 to 61, with ndhB exhibiting the highest number of RNA editing sites across all species. Seven genes—namely, atpB, cemA, clpP, ndhD, petB, petD, and ycf15—exhibited a Ka/Ks value > 1, suggesting they may be under positive selection. Phylogenetic analysis revealed that Mangifera siamensis showed a close relationship between Mangifera indica and Mangifera sylvatica. Conclusions: Our comprehensive analysis of the whole cp genomes of the five Mangifera species offers significant insights regarding their phylogenetic reconstruction. Moreover, it elucidates the evolutionary processes of the cp genome within the Mangifera genus. Full article

Alfalfa, as a high-quality forage resource, has high nutritional value. Due to the high phenotypic similarity among its varieties and the susceptibility to environmental influences, challenges are encountered in variety identification and breeding. In this study, 23 simple sequence repeat (SSR) markers were screened to distinguish 49 alfalfa varieties, among which 21 SSR markers showed polymorphic fragments. The results indicated that these 21 markers were highly polymorphic, with an average of 5.91 alleles per SSR marker locus and an average polymorphic information content (PIC) of 0.66, suggesting a strong discriminatory efficiency. The results of a population genetic diversity analysis showed that there was a relatively high level of genetic diversity among the tested materials. The analysis of molecular variance (AMOVA) results indicated that the genetic variation within the population of the 49 alfalfa germplasm samples was the main source of the total variation. The results of genetic distance and genetic identity analyses showed that the genetic relationship between population 1 and population 4 was the most distant, while the relationship between population 2 and population 3 was the closest. The cluster analysis results showed that samples S16 and S55 formed a separate branch; that is, there were two main genetic subgroups. These results confirm that SSR markers are effective tools for genetic characterization and precise discrimination of alfalfa varieties and have important application values in breeding, variety registration, and germplasm resource conservation. Full article