Search Results (1,013)

Ignoring the dynamic output recovery of distributed renewable energy sources (dRESs) during distribution network restoration may lead to low voltage in the initial stage, which can cause dRESs and loads to trip and even prevent the recovery of the entire distribution system. To address this issue, this paper proposes a dynamic restoration control framework for distribution networks with dRES integration. In this framework, a topology reconfiguration method is established to capture the time-varying characteristics of dRESs during the restoration process, and a double-time-section power flow calculation strategy is incorporated to verify operational constraints throughout the restoration period. The resulting optimization problem is solved by an improved hybrid Aquila Optimizer–Binary Particle Swarm Optimization algorithm, in which pre-scheme initialization and enhanced Gaussian mutation are introduced to improve convergence and solution quality. Case studies demonstrate that the proposed framework can obtain optimal schemes of topology reconfiguration for dRES-penetrated distribution networks within dozens of seconds while avoiding off-normal voltage and unsuccessful dRES reconnection, thereby enhancing the restoration capability of the distribution system. Full article

Zucchini tigre mosaic virus (ZTMV; Potyvirus pepotigris), which infects wax gourd (Benincasa hispida), was first identified in Taiwan in 2017 and designated ZTMV-TW. In this study, mild strains of ZTMV-TW were generated by modifying the pathogenicity factor HC-Pro to develop cross-protection strategies for cucurbit crops. A full-length infectious cDNA clone of ZTMV-TW was cloned in pCAMBIA1304 under the control of the CaMV 35S promoter (ZTMV-TWic). ZTMV-TWic induced typical potyvirus particles, cytoplasmic inclusion bodies, and severe symptoms in wax gourd, pumpkin, and zucchini plants. Conserved motifs of HC-Pro were mutated to generate four single mutants (F7I, R181I, F206L, and D397N) and three double mutants (F7I+F206L, R181I+D397N, and F206L+D397N). Mutants R181I and R181I+D397N caused mild or no symptoms in zucchini, while D397N and F206L+D397N were mild in wax gourd. Cross-protection assays showed that R181I and R181I+D397N provided complete protection against ZTMV-GFP in zucchini, whereas D397N and F206L+D397N conferred high protection in wax gourd. These results demonstrate the feasibility of host-specific mild strain selection for effective ZTMV cross-protection. Full article

Complex I (NADH:quinone oxidoreductase, CI) is central to cellular aerobic energy metabolism. The L-shaped structure of CI is unique, where the hydrophilic arm is responsible for the electron transfer function and the membrane arm operates proton pumping. These two functional sites are spatially far apart yet functionally connected. This basic core subunit architecture is highly conserved from bacterial to mammalian CI. Here, to gain detailed mechanistic insight into the role of the membrane subunit ND2 in the coupling mechanism, we mutated several highly conserved residues in the middle of the membrane axis of NuoN, the E. coli CI homolog of ND2. To more precisely investigate the consequences of mutational effects on highly conserved residues, we purified each mutant CI and compared the mutational effects on electron transfer and proton pumping activity using our instant membrane reconstitution method with E. coli double knockout (DKO) membrane vesicles lacking both CI and alternative NADH dehydrogenase (NDH-2). Thre results were corroborated by conventional proteoliposome reconstitution experiments. We found that Lys247 and Lys395 are absolutely essential for both electron transfer and proton pumping activities, while about 50% reduction of NADH oxidase activity but no reduction in proton pumping activity was observed in Lys217, and no significant decrease was detected in Glu133. Furthermore, unexpectedly, we were able to purify an NuoN knockout (ΔNuoN) mutant, which contained stoichiometric peripheral subunits NuoB, NuoCD, NuoE, NuoF, NuoG, and NuoI; and a substoichiometric amount of NuoH and a reduced amount of quinone. However, surprisingly, this isolated ΔNuoN CI showed CI activities (~30% of the WT) after being reconstituted into DKO membranes but not into proteoliposomes. Later, we confirmed by blue native PAGE that the wild-type CI was partially formed from ΔNuoN CI by recruiting its missing membrane subunits that existed in DKO membranes. Our data strongly suggest that ND2/NuoN plays an essential role in the coupling mechanism in CI. CI is the entry respiratory chain enzyme and is central to cellular energy metabolism. Two highly conserved lysine residues in the center of the antiporter-like membrane subunit ND2 are essential for the coupling mechanism between electron transfer and proton translocation. Full article

Background/Objectives: Acute exercise remodels many interconnected biochemical pathways in metabolically active tissues. This remodeling involves the activation of the energy-sensing AMP-activated protein kinase (AMPK) to maintain cellular energy homeostasis. Critical energy reserves of glycogen, primarily stored in liver and skeletal muscle and known to interact with AMPK, are utilized to help meet increased energy demands with exercise. However, the breadth of metabolic pathways regulated by acute exercise and AMPK’s interactive roles with glycogen remain incompletely understood. This study therefore aimed to map mouse liver and skeletal muscle metabolite responses to continuous acute exercise and disruption of AMPK-glycogen interactions. Methods: Liquid chromatography–mass spectrometry-based untargeted metabolomics was used to measure the relative abundance of liver and gastrocnemius muscle metabolites at rest and following an acute bout of continuous treadmill running in wild type (WT) and AMPK transgenic mice with double knock-in (DKI) mutations in the β subunit carbohydrate binding module that mediates glycogen binding. Results: Over 200 total metabolites were identified/annotated across liver and skeletal muscle, including 45 metabolites responsive to exercise (p < 0.05; FDR < 0.1). Exercise-regulated metabolites included known metabolic pathways and metabolites never associated or with only emerging evidence related to exercise (e.g., ergothioneine) and/or AMPK-glycogen interactions (N6,N6,N6-trimethyl-L-lysine, a precursor of L-carnitine). Conclusions: Liver and skeletal muscle metabolomic profiles displayed shifts between WT and DKI mice at rest, with shifts also detected following a continuous acute exercise bout. An interaction effect was also observed in skeletal muscle, suggesting differential muscle metabolite responses to acute exercise in DKI mice that may contribute to their functional impairments in metabolic control and exercise capacity versus WT. Collectively, these findings expand the molecular landscape of acute exercise and reveal liver and muscle metabolites underlying exercise-induced metabolic responses. Full article

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9, a genome-editing technology pioneered in 2012, enables the precise correction of deleterious mutations or disruption of disease-causing genes through targeted double-strand breaks (DSBs), offering potential for treating genetic diseases. However, CRISPR/Cas9 can cause off-target cleavage at non-specific DNA sites, leading to unintended insertions or deletions (indels), which limit its safety and applicability despite ongoing improvements in specificity. Recently, prime editing (PE), an advanced CRISPR-derived technology, has been employed with a Cas9 nickase (Cas9n) fused with a reverse transcriptase and a prime editing guide RNA (pegRNA) to enable precise insertions, deletions, and transversions without inducing DSBs, thus reducing risks of indels and chromosomal aberrations. Furthermore, ongoing optimizations, such as improved pegRNA design and enhanced editing efficiency, have expanded the applications of PE in medical therapeutics, agriculture, and fundamental research. This review summarizes recent advancements in the PE system, including optimized pegRNA designs and enzyme engineering for enhanced efficiency and specificity, alongside novel delivery methods. It also evaluates cutting-edge delivery strategies, such as adeno-associated virus (AAV) vectors, lipid nanoparticles (LNPs) and novel extracellular vesicle (EV)-based systems, and explores PE applications in vitro and in vivo, including disease modeling and therapeutic gene correction. Full article

The miRNA172–APETALA2 (AP2) regulatory module is a conserved mechanism governing floral development in plants. Disruption of the miR172 target sites in AP2 genes has been shown to be key to the domestication of double flowers in ornamental species. Camellia japonica, a woody ornamental plant with diverse floral forms, serves as an important model for studying double-flower formation. In this study, we characterized two AP2-like transcription factors, CjAP2-1 and CjAP2-2, which possess evolutionarily conserved miR172-binding sites and exhibit broad expression across floral tissues. To investigate the role of the miR172–AP2 module in C. japonica, we identified four members of the miR172 family and demonstrated that miR172 is directly involved in the cleavage of CjAP2-1 and CjAP2-2 transcripts. Through bulked amplicon sequencing of cultivars with diverse floral forms, we uncovered natural variations at the miR172-binding sites of CjAP2-1 and CjAP2-2, which can potentially disrupt miR172-mediated mRNA cleavage. We showed that two dinucleotide mutations (CjAP2-1-mut5 and CjAP2-1-mut9) significantly reduced the miR172-mediated repression of CjAP2-1 transcripts. Functional analysis in Arabidopsis revealed that overexpression of the CjAP2-1-mut5 variant caused significant floral abnormalities, including ectopic formation of reproductive organs, loss of floral determinacy, and fusion of floral organs. Further analysis of downstream genes indicated that key regulators of floral homeotic and meristem activity were markedly altered in the transgenic plants. Our findings demonstrate that perturbations in the miR172–AP2 regulatory relationship underlie the formation of double flowers in C. japonica by altering floral meristem determinacy and organ identity. Full article

JC Polyomavirus (JCPyV) is a non-enveloped virus with circular double stranded DNA responsible for the rare but fatal demyelinating disease known as progressive multifocal leukoencephalopathy (PML). In its host, this virus exists in two different forms: one found in the periphery, named archetype, and another found in the central nervous system, named prototype. This form usually harbors recombinations in the non-coding control region (NCCR), a key region that contains sequences regulating viral replication and containing binding sites for cellular transcription factors. This form also contains mutations in the capsid protein, especially VP1. Due to the diversity of the JCPyV, a natural polymorphism also exists between the different genotypes. In this review, we aimed to summarize the main features of the archetype and prototype strains in order to facilitate the interpretation of sequence data that are increasingly generated by new sequencing technologies. This will also help to distinguish mutations associated with the natural polymorphism from those specific to the prototype form. Full article

Background: Tumor-derived small extracellular vesicles (sEV), which we call TEX, carry a cargo of molecules that resembles the producer tumor cells. Circulating freely in body fluids, TEX potentially serve as a liquid tumor biopsy. TEX horizontally transfer their cargo to various recipient cells, imparting to them pro-tumor activity. Mechanisms of TEX-driven reprogramming might involve nucleic acids, especially double-stranded (ds)DNA. Methods: TEX isolated from supernatants of human tumor cells were identified as sEV, based on their size, endocytic origin and morphology. TEX treated with DNase/RNase cocktail were examined by transmission and cryo-electron microscopy and tested for biologic activity. DNA was extracted from enzyme-treated TEX, quantified by Qubit and analyzed for fragment sizes. The presence of genomic DNA in TEX was confirmed by PCR, and sequencing of the TP53 gene fragment for a mutational signature was performed. Results: Enzymatic and microscopic studies of TEX showed that nucleic acids are present in the biocorona on the outer surface. Their removal interfered with the biocorona integrity. A short TEX exposure to DNase/RNase altered their morphology without impairing vesicle functions; longer treatments induced TEX re-organization into smaller membrane-bound vesicles. The TEX lumen contained long fragments of protected genomic DNA with a mutational signature reflecting that of the tumor. Conclusions: Nucleic acids present on the TEX surface support the vesicular integrity. The TEX lumen contains membrane-protected large (ds)DNA fragments with the mutational signature of the parent tumor. The presence of surface and luminal nucleic acids in TEX, and especially their mutational signature, suggests that TEX may serve as highly promising cancer-specific biomarkers. Full article

Background/Objectives: Acute radiotherapy-induced skin toxicity is a common complication in breast cancer treatment, with marked interindividual variability not fully explained by clinical factors. This study investigated the contribution of germline mutations in DNA repair and tumor suppressor genes to acute radiodermatitis in a homogeneous cohort treated with hypofractionated intensity-modulated radiotherapy with inverse planning, with adjustment for potential lifestyle confounders. Methods: Mutations were grouped into four functional categories: homologous recombination repair (HRR), Fanconi anemia (FA), DNA damage response (DDR), and tumor suppressor (TS) genes. Ordinal logistic regression models adjusted for clinical covariates evaluated pooled and functional category-specific mutation effects. Results: Overall, any mutation significantly increased the risk of higher-grade acute radiodermatitis (OR = 2.24, p = 0.003), an effect driven primarily by HRR and FA mutations, as exclusion of these mutations rendered the association non-significant (OR = 1.785, p = 0.064). Functional category-based analyses showed that HRR (OR = 2.60, p = 0.002) and FA (OR = 2.62, p = 0.002) mutations were the strongest predictors, reflecting overlapping roles in double-strand break and interstrand crosslink repair. DDR and TS mutations showed no significant effect. Conclusions: These results highlight the key role of high-fidelity DNA repair in normal tissue radiosensitivity and demonstrate that functional genetic stratification has diagnostic value as a pre-treatment predictive biomarker framework, enabling identification of patients at increased risk of acute skin toxicity and supporting personalized radiotherapy planning. Full article

Double-haploid (DH) technology is a well-established method for speeding up the development of inbred lines in breeding programs. The major loci qhir1 and qhir8 are widely used in marker-assisted selection (MAS) to increase the haploid induction rate (HIR) in maize. However, previous studies have shown that HIR can be unstable within populations, even in the presence of these two loci. To identify novel loci associated with HIR, we performed QTL-seq analysis on 337 S₂ haploid inducers (qhir1+/qhir8+) derived from crossing K8 with BHI306. The population exhibited HIR ranging from 0% to 31.16%. We sequence-bulked DNA from 30 extremely high-HIR lines (15.72–31.16%) and 30 extremely low-HIR lines (0–3.84%), identifying candidate intervals on chromosomes 2 (qHI2), 3 (qHI3), 6 (qHI6), and 8 (qHI8). Based on the QTL-seq results, 147 high-confidence SNPs/InDels (R² > 0.3) led to the analysis of 58 genes across three QTLs. We retrieved ten missense mutation SNPs from three genes (GRMZM2G359746 (qHI2), AC198725.4 (qHI3), and GRMZM2G091276 (qHI8)), which are located on chromosomes 2, 3, and 8. Regression analysis of these SNPs showed an R² range of 0.27 to 0.72. The two most highly associated SNPs were located in exon 2 of GRMZM2G359746 (qHI2) and in exon 5 of GRMZM2G091276 (qHI8), respectively. Marker–trait association analysis revealed that lines carrying favorable alleles at both loci, together with qhir1+ and qhir8+, exhibited significantly higher average HIR (12.77%) compared to those with unfavorable alleles (6.66%). These findings provide valuable markers for enhancing maternal haploid inducer breeding programs in maize. Full article

Background/Objectives: TP53 mutation or deletion status is important for determining cellular responses to DNA-damaging drugs. Oxaliplatin (OXA) is combined with the fluoropyrimidine (FP) drug 5-fluorouracil (5-FU) in the FOLFOX regimen used to treat advanced colorectal cancer (CRC). However, the effects of TP53 deletion on 5-FU + OXA synergy are not well known. We investigated potential synergy between OXA and 5-FU and compared it with OXA synergy with a novel polymeric FP, CF10, in four cell lines harboring either wild-type (WT) or TP53-null status. Methods: Using CompuSyn and the highest single agent (HSA) models, we compared synergy between CF10 and OXA (COXA) and between 5-FU and OXA (FOXA). Cell cycle analysis was performed, as was Western blot quantification of canonical DNA damage pathway proteins. Likewise, immunofluorescent and confocal analysis allowed us to compare topoisomerase 1 cleavage complex and double-strand DNA break formation. Results: COXA synergy displayed minimal TP53 dependence with greatly improved potency compared to FOXA. COXA synergy resulted from OXA increasing: (i) Topoisomerase 1 (Top1) cleavage complex formation; (ii) DNA double-strand breaks (DSBs), and (iii) Checkpoint Kinase 1 and 2 (p-Chk1/2) phosphorylation, consistent with increased replication stress. Additionally, increased S-phase entry in TP53-null cells enhanced synergy between CF10, 5-FU, and OXA as S-phase drugs. Conclusions: Our results demonstrate that OXA synergizes with CF10 more effectively than with 5-FU through enhanced replication stress in both WT and TP53-null cells by causing greater Top1-mediated DNA double-strand breaks. Our studies provide a foundation for further testing of this combination in an orthotopic liver metastatic setting and eventual clinical development. Full article

Background/Objectives: Non-small cell lung cancer (NSCLC) is the most frequent type of lung cancer, and its main treatments include chemotherapy with genotoxic drugs and immunotherapy. Central to the cellular response to genotoxic stress is the DNA damage response (DDR) network, regulated by key kinases such as ataxia-telangiectasia mutated and Rad3-related (ATR). Herein, we tested the hypothesis that inhibition of ATR enhances the cytotoxicity of genotoxic agents and the antitumor immune response. Methods: DDR-related parameters and redox status, expressed as GSH/GSSG ratio, and apurinic/apyrimidinic lesions, were evaluated in human (A549, H1299) and murine (LLC) NSCLC cell lines after co-exposure to ATR inhibitor (AZD6738) and ultraviolet C (UVC) irradiation or cisplatin. Using a syngeneic LLC model, treatments of AZD6738 alone or in combination with cisplatin and/or anti-programmed cell death 1 antibody (anti-PD1) were examined. Results: In all cell lines, combined treatment with AZD6738 and cisplatin or UVC irradiation markedly decreased cell viability, DNA repair efficiency, and GSH/GSSG ratios; increased drug-induced DNA damage; and augmented apurinic/apyrimidinic lesions. In vivo, following treatment with AZD6738 and cisplatin, flow cytometry analysis performed in tumor cells revealed an increased infiltration of CD3⁺ and CD8⁺ T cells, with the triple combination of AZD6738, cisplatin, and anti-PD1 achieving the strongest antitumor effect. The CD3⁺CD4⁻CD8⁻ double-negative (DN) T cell population in tumor samples also emerged as a contributing factor in this context. Conclusions: These results demonstrate that ATR blockade concurrently enhances the efficacy of genotoxic agents and immune checkpoint inhibitors, thus paving the way for combination therapies in NSCLC. Full article

NKAP (NF-kappa-B-activating protein) is a ubiquitously expressed nuclear protein involved in multiple biological processes. Males with missense NKAP mutations have been reported to present with marfanoid features and behavioral and musculoskeletal abnormalities. We have previously reported that a disruptive NKAP mutation resulted in extremely skewed X chromosome inactivation (XCI), leading to phenotypic manifestation of hemophilia A (HA) in a HA carrier. In this study, with the aim of exploring the phenotypic manifestations of deleterious NKAP mutations in males, as well as their involvement in the mechanism of XCI regulation in females, we generated NKAP mutant mice using CRISPR/Cas9 technology. Gait analysis studies conducted in male mice hemizygous for mutant NKAP by the CatWalk XT system revealed significant alterations in gait parameters, consistent with hypotonia reported in human mutant NKAP patients. By breeding mutant NKAP mice with HA mice, we generated a double heterozygous mutant NKAP/HA mouse model, i.e., female mice carrying mutant NKAP with a WT F8 copy on one X chromosome, and WT NKAP with a mutant F8 copy on the other X chromosome. XCI pattern analysis using methylation-sensitive restriction enzymes demonstrated that mutant NKAP/HA females exhibited significant XCI skewing of the X chromosome bearing the mutant NKAP copy. Furthermore, these females exhibited significantly reduced F8 mRNA levels and FVIII (factor VIII) antigen levels, as demonstrated by quantitative RT-PCR and ELISA, respectively. Murine embryonic fibroblasts (MEFs) derived from a hemizygous mutant NKAP embryo exhibited markedly reduced proliferation rate and increased senescence compared to WT NKAP MEFs, suggesting that XCI skewing induced by mutant NKAP results from secondary selection against cells with an active X chromosome bearing the mutant NKAP copy. Full article

Human preimplantation embryo arrest (PREMBA) represents a significant clinical hurdle in assisted reproductive technology (ART), in which approximately 10% of in vitro fertilized (IVF) embryos arrest at the cleavage stages. Whole-exome sequencing (WES) studies have discovered numerous genetic mutations associated with preimplantation embryo arrest. These mutations often disrupt critical biological milestones such as maternal mRNA clearance (BTG4, ZFP36L2, ZAR1), subcortical maternal complex (TLE6, PADI6, OOEP, NLRP2, NLRP5, NLRP7, KHDC3L), DNA double-strand break formation and homologous recombination (REC114, TOP6BL, MEI1, MEI4, TRIP13), spindle assembly (TUBB8 and TUBA4A) and cell cycle and checkpoints (FBXO43, MOS, CHEK1, TRIP13, CDC20), as well as nuclear transport and translational regulation (KPNA7, DDOST). However, the cause of most clinical cases remains genetically unexplained. Studies investigating these unexplained arrests have uncovered widespread multi-omics abnormalities, including transcriptional arrest, DNA hypermethylation, higher chromatin accessibility, aberrant histone modification, chromosomal aneuploidy and senescent-like states. This review provides a comprehensive overview of the molecular mechanisms underlying PREMBA, categorized into those that are attributable to known genetic mutations and those with unexplained reasons. Full article

Colorectal cancer (CRC) is traditionally considered a “cold tumor” characterized by low immunogenicity and limited responsiveness to immune checkpoint inhibitors (ICIs). However, recent findings reveal that cytotoxic modalities can reprogram this immunologically inert landscape. This review integrates these evolving concepts to guide the optimization of future treatments. Radiotherapy induces extensive DNA double-strand breaks, which may generate de novo mutations through error-prone repair while simultaneously exposing cryptic antigens via increased transcriptional instability, alternative splicing, and enhanced proteasomal processing. Chemoradiation also amplifies epigenetic and epitranscriptomic sources of neoepitope diversity, including RNA editing and stress-induced splicing alterations, expanding the immunopeptidome beyond canonical mutation-driven neoantigens. These changes collectively enhance antigen presentation and facilitate T-cell priming. Chemotherapy further reduces immunosuppressive cell populations and promotes dendritic cell activation, creating a permissive milieu for subsequent immune engagement. Clinically, the VOLTAGE studies demonstrated that long-course chemoradiotherapy can sensitize even mismatch repair–proficient rectal cancers to PD-1 blockade, yielding clinically meaningful pathological responses. In contrast, mismatch repair–deficient rectal tumors may respond completely to ICIs alone. Short-course radiotherapy combined with chemotherapy and ICIs has also shown encouraging activity in the setting of total neoadjuvant therapy. Collectively, these findings support a paradigm in which radiotherapy, chemotherapy, and epigenetic/epitranscriptomic alterations—including RNA editing—act as potent modulators of tumor antigenicity. By expanding the neoantigen repertoire and reshaping the tumor microenvironment, these strategies can transform CRC from a cold tumor into one that is increasingly responsive to immunotherapy. Full article