Search Results (586)

The combination of chemotherapy and immunotherapy represents a promising approach that leverages their complementary benefits. However, the side effects resulting from off-target effects and the low efficiency of immune activation remain a significant concern. Herein, we developed a zinc-doped calcium phosphate (ZCP) nanocarrier for the delivery of the chemotherapeutic drug doxorubicin (DOX). By further encapsulating whole proteins from 4T1 breast cancer cells, we constructed a novel nanodrug delivery system named ZCPDM. This system enables specific targeting of tumor cells and undergoes intracellular degradation to release DOX, Zn²⁺, and Ca²⁺. As a chemotherapeutic agent, DOX induces apoptosis while significantly elevating intracellular reactive oxygen species (ROS), thereby enhancing cytotoxicity. This leads to DNA damage and the release of chromosomal fragments. These DNA fragments, together with Zn²⁺, activate the cGAS-STING signaling pathway and trigger pyroptosis, which promotes more efficient recognition and clearance of tumor cells by the immune system. Through these dual mechanisms, ZCPDM effectively combines chemotherapy and immunotherapy. The anti-tumor efficacy and underlying mechanisms were validated at the cellular level. Furthermore, studies in tumor-bearing mice demonstrated its robust anti-tumor performance and ability to suppress tumor recurrence, along with good biosafety. This targeted drug delivery system achieves safe and synergistic chemo-immunotherapy through homologous targeting-mediated pyroptosis and activation of the cGAS-STING pathway, offering a novel and promising strategy for cancer treatment. Full article

Cyanobacteria are increasingly recognised as photosynthetic chassis for sustainable metabolic engineering because oxygenic photosynthesis generates ATP and NADPH via the photosynthetic electron transport chain, which drive CO₂ fixation through the Calvin–Benson–Bassham cycle into carbon intermediates that can be redirected toward engineered heterologous pathways. Their genetic tractability, CO₂-fixing capacity, ecological adaptability, and relatively simple cellular organisation make them attractive platforms for developing low-carbon biotechnological processes. This review explores recent progress in engineering cyanobacteria for heterologous pathway construction, critically evaluating genetic tools including transformation methods, genome integration strategies, promoter systems, and CRISPR-based editing, with specific emphasis on challenges of direct relevance to phototrophic chassis: host–pathway metabolic compatibility, precursor supply, cofactor balancing between photosynthetic output and heterologous pathway demand, and achieving genetic stability in polyploid cyanobacterial genomes. The review also addresses key limitations with mechanistic context: metabolic burden from multi-gene pathway expression reduces growth rate and selects against producing cells; polyploidy delays complete chromosomal segregation of engineered constructs; slow photoautotrophic growth constrains volumetric productivity; native regulatory networks resist carbon flux redirection; and cultivation constraints—including light attenuation in dense cultures and mismatches between photosynthetic ATP/NADPH supply and heterologous pathway demand—further limit achievable yields. Full article

Polygonatum cyrtonema is a medicinally and edible perennial herb, yet functional studies in this species are constrained by limited knowledge of regeneration-associated developmental regulators. Here, we performed a genome-wide characterization of the WUSCHEL-related homeobox (WOX) gene family in P. cyrtonema. Eleven PcWOX genes were identified and classified into the ancient, intermediate, and modern/WUS clades. Comparative phylogenetic, syntenic, structural, and chromosomal analyses indicated that the PcWOX family retains a conserved evolutionary framework but also exhibits clear lineage-specific diversification. Tissue- and stage-specific expression profiling, promoter cis-element analysis, and subcellular localization further supported functional differentiation among PcWOX members, particularly between PcWOX5 and PcWUS. Weighted gene co-expression network analysis identified 33 co-expression modules, including six key modules strongly associated with PcWOX abundance patterns, and prioritized 49 candidate transcription factors (TFs) to construct PcWOX-centered regulatory networks. These TFs showed marked tissue- and stage-dependent heterogeneity. Heterologous assays in Nicotiana benthamiana showed that both PcWUS and PcWOX5 enhanced regeneration competence but produced distinct developmental outputs. These findings support PcWUS and PcWOX5 as promising candidate morphogenic regulators and provide a useful framework for future mechanistic studies, homologous validation, and regeneration improvement in P. cyrtonema. Full article

Background/Objectives: The Chinese porcupine (Hystrix hodgsoni) is a distinctive rodent species characterized by specialized ecological adaptations and sensory traits; however, genomic resources for this species have remained limited. This study aims to provide a reliable reference for comparative and evolutionary analyses by constructing a high-quality genome. Methods: We generated a chromosome-level genome assembly of the Chinese porcupine using long-read sequencing combined with chromatin conformation-based scaffolding, followed by comprehensive structural and functional annotation. Comparative genomic analyses across representative mammals and functional enrichment analyses were conducted to investigate lineage-specific gene family dynamics. Results: The assembled genome shows high contiguity and completeness. Comparative analyses revealed a substantial number of gene families significantly expanded along the porcupine lineage. Functional enrichment demonstrated strong overrepresentation of olfactory-related processes, including olfactory receptor activity, odorant binding, and detection of chemical stimuli. Additionally, several expanded families were associated with epidermal differentiation, keratinization, and skin development. Conclusions: Gene family expansions in the Chinese porcupine are biased toward sensory perception and epidermal functions, suggesting potential genetic bases for its enhanced environmental sensing and integumentary specialization. This assembly provides an important genomic resource for porcupine research and new insights into the molecular mechanisms underlying sensory and skin-related adaptations in rodents. Full article

Plant mitochondrial genomes are difficult to analyze because of their structural dynamism and frequent annotation errors. To address these challenges, we first constructed a high-confidence mitochondrial reference library for Rhodiola by integrating transcriptomic evidence, public sequence resources, and experimental validation. This curated resource defined 30 mitochondrial protein-coding genes (PCGs), including corrected exon–intron boundaries and validated 5′-terminal variants in ccmC, ccmFn, and nad9. Leveraging this curated dataset, we developed the RhoMitoAnnotator, which integrates three novel algorithms, EBAnno, REAnno, and NCAnno, to accurately annotate trans-splicing, RNA editing, and non-canonical start/stop codons. Using long-read sequencing guided by the RhoMitoAnnotator, we completed the mitogenomes of R. rosea, R. crenulata, and R. sacra, systematically re-annotated seven publicly available mitogenomes, revealing cross-chromosomal gene arrangement, and widespread structural misannotations. To enable scalable analysis with short-read data, we built Polypods, an integrated pipeline that successfully assembled mitochondrial PCGs from 108 samples across 39 Rhodiola species, and identified variant genes, stop codon-lacking regions in nad6, and internal stop codons in rpl16. Phylogenetic analyses based on mitochondrial and chloroplast PCGs showed a lineage pattern consistent with the hypothesis of an evolutionary transition from hermaphroditism to dioecy in Rhodiola, and consistently supported six species as monophyletic lineages. Overall, this study provides a curated mitochondrial gene atlas for Rhodiola and a reference-guided analytical framework for mitochondrial PCG annotation and recovery in this genus, with potential adaptability to other plant lineages after lineage-specific database construction and parameter optimization. Full article

Aminoglycoside resistance is commonly mediated by enzymatic modification, target alteration, or efflux mechanisms; however, acquired resistance has not been characterized in radiation-resistant Deinococcus species. Here, we investigated the occurrence and genomic context of acquired aminoglycoside resistance genes in all publicly available Deinococcus radiodurans genomes. A total of 19 genomes were screened using ResFinder and CARD, followed by comparative genomic analyses. The aadA1 gene was identified in two genomes, being located on the plasmid pSP1 in strain R1 dM1, a known shuttle vector used for genetic manipulation. In contrast, aadA1 was found on a chromosomal contig in strain DRR11, suggesting a possible assembly artifact. Additionally, the aph(3′)-Ia gene was detected in three genomes within a conserved chromosomal region that lacks this gene in reference strains. Sequence similarity analyses indicated that aph(3′)-Ia is associated with laboratory vectors, being consistent with a potential non-natural origin. Considering the high recombination capacity and genomic plasticity of D. radiodurans, these findings suggest that the detected aminoglycoside resistance genes may be derived from laboratory constructs, potentially combined with assembly inconsistencies or chromosomal integration events. Therefore, this study highlights the importance of integrating genomic context with molecular and evolutionary plausibility to avoid misinterpretation of antimicrobial resistance in extremophiles and model organisms, and underscores the importance of complementary raw-read analyses to distinguish natural acquisition from technical or laboratory-derived origins. Full article

The simultaneous improvement of fiber strength (FS) and lint percentage (LP) is a critical objective for achieving high-quality and high-yield cotton production. Identifying key genes and their regulatory networks that govern the synergistic development of FS and LP is essential for achieving their simultaneous improvement. In our previous study, a stable chromosome segment, Seg-D06-2, was identified for its ability to concurrently enhance both FS and LP with high reliability. In the present study, homozygous individuals harboring the Seg-D06-2 segment within a nearly uniform genetic background were selected to construct a large BC₆F₂ chromosome segment substitution line (CSSL) population comprising 3324 individuals. Extreme individuals characterized by simultaneous improvement in FS and LP, which shared similar genetic and phenotypic backgrounds, were subjected to comparative transcriptomic and weighted gene co-expression network analysis (WGCNA) at 0, 5, 10, 15, 20, and 25 days post-anthesis (DPA). The results highlighted the ’blue’ and ’yellow’ modules as being significantly associated with the simultaneous improvement of FS and LP. Four hub genes (GH_D06G0542, GH_D06G1609, GH_D06G0627 and GH_D06G2689) and two DEGs (GH_D06G0564 and GH_D06G0723) were identified in the ’blue’ module. Three hub genes (GH_D06G0540, GH_D06G0558 and GH_D06G0636) and one DEG (GH_D06G0527) were identified in the ’yellow’ module. These 10 key genes likely play pivotal roles in regulating the synergistic development of FS and LP, warranting further investigation. The reliability of the RNA-seq data was confirmed by qRT-PCR. This study provides a valuable resource for molecular breeding aimed at the simultaneous improvement of FS and LP and offers new insights into the molecular mechanisms governing their synergistic development. Full article

Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with leaf color using SPAD values as a phenotypic indicator. Methods: An ${\mathrm{F}}_2$ population derived from a cross between the dark green line YSG1go and the light green line Asagikei-KUJYO was used. A linkage map was constructed based on RNA-seq-derived SNP markers, and SPAD values were measured for QTL analysis. Results: The linkage map consisted of eight linkage groups with a total length of 2103.0 cM and 765 mapped markers. SPAD values showed significant differences between the parental lines, with high broad-sense heritability ($H^2$ = 0.76), indicating a strong genetic contribution to this trait. Multiple significant QTLs were detected on chromosomes 4 and 5, each explaining 27.4–38.1% of the phenotypic variance. The direction of allelic effects differed among QTLs, suggesting that favorable alleles are distributed between the parental lines. In addition, genes related to chloroplast protein translation were identified within the QTL regions. Conclusions: SPAD values are a suitable indicator for genetic analysis of leaf color in bunching onion, and the QTLs identified in this study provide valuable information for molecular breeding aimed at improving dark green leaf color. Full article

Soil salinization severely restricts rice growth and global grain production, posing a serious threat to food security. Dongxiang wild rice serves as an important genetic resource for improving salt tolerance in rice. In this study, a backcross inbred line (BIL) population derived from Dongxiang wild rice DY80 and an indica restorer line R974 were used to detect QTLs for salt tolerance at the germination and seedling stages. Four QTLs related to germination-stage salt tolerance and three QTLs for seedling-stage salt tolerance were identified, among which qSTS5 on chromosome 5 showed the largest effect with a LOD score of 8.0 and a phenotypic contribution rate of 14.8%. An F_2:3 population was further constructed to validate qSTS5, which increased its LOD value to 10.4 and phenotypic variation explanation rate to 18.5%, and the locus was finally delimited to a 2.3 Mb interval. Transcriptome analysis identified eight differentially expressed genes (DEGs) within the qSTS5 region under salt stress. Sequence comparison between the parents revealed that three DEGs had no coding-region variations, while the other five showed nucleotide polymorphisms leading to amino acid changes. Among them, Os05g0349800 encodes a LEA protein, a typical stress-responsive gene, and harbors a frameshift mutation in DY80. Combined with its induced expression pattern under salt stress, this gene was considered the most promising candidate for qSTS5. This study not only provides a stable major QTL for rice breeding for salt tolerance but also lays a foundation for dissecting the molecular mechanism of salt tolerance in Dongxiang wild rice. Full article

Ankylosing spondylitis (AS) is a chronic immune-mediated inflammatory disease affecting the axial skeleton, characterized by progressive structural damage and functional impairment. Although biologic therapies targeting tumor necrosis factor and interleukin-17 have improved clinical outcomes, a substantial proportion of patients fail to achieve sustained disease control. Emerging evidence suggests that metabolic alterations may contribute to AS pathogenesis; however, systematic characterization of metabolism-related biomarkers and their regulatory networks remains limited, and the interplay between metabolic dysfunction and immune dysregulation in AS is poorly understood. Two whole-blood GEO datasets (GSE25101, GSE73754; n = 104) were integrated as the primary analytical cohort. A third dataset (GSE11886, n = 18; monocyte-derived macrophages) was included for exploratory cross-tissue analysis. Differential expression analysis identified 847 DEGs, which were refined to 16 metabolism-related genes through weighted gene co-expression network analysis (WGCNA) and GeneCards database filtering. Eleven machine learning algorithms with 5-fold cross-validation were applied to construct diagnostic models and identify hub genes. Validation analyses included immune cell infiltration estimation using CIBERSORT, metabolic pathway activity assessment via ssGSEA, single-cell transcriptomics from GSE268839, functional enrichment through GSEA/GSVA, and chromosomal localization analysis. A competing endogenous RNA (ceRNA) regulatory network was constructed to map post-transcriptional regulation. Natural compounds from 66 AS-treating traditional Chinese medicines were screened against hub genes using deep learning-based binding prediction. Multiple machine learning algorithms achieved comparable cross-validated performance (CV AUC range 0.741–0.836; top five models: 0.805–0.836) using the six hub genes (MFN2, SLC27A3, RHOB, SMG7, AKR1B1, LCOR) identified through SHAP-based feature importance analysis of the PLS model. Leave-one-dataset-out validation between the two whole-blood cohorts showed that all algorithms exceeded an AUC of 0.77 in Round 1 (validate: GSE73754, n = 72; best AUC 0.861), while Round 2 (validate: GSE25101, n = 32) yielded more modest performance (best AUC, 0.715) reflecting the smaller validation sample. Exploratory application to GSE11886 (macrophage-derived samples) showed near-chance performance, consistent with the tissue-source discrepancy. AS patients exhibited significant downregulation of oxidative phosphorylation, TCA cycle, and glycolysis pathways (p < 0.01), accompanied by elevated glutathione metabolism (p < 0.001). Immune cell deconvolution revealed reduced CD8+ T cell proportions correlating with MFN2 downregulation, and increased neutrophil frequencies correlating with SLC27A3 upregulation. Exploratory single-cell analysis indicated that RHOB expression was relatively enriched in border-associated macrophages and fibroblasts, while AKR1B1 was more prominently expressed in vascular endothelial cells and plasmacytoid dendritic cells. The ceRNA network identified 21 miRNAs and 65 lncRNAs forming 86 regulatory interactions, with four key regulatory axes (SATB1-AS1/miR-539-5p/LCOR, FAM95B1/miR-223-3p/RHOB, LINC01106/miR-106a-5p/MFN2, AATBC/miR-185-5p/SMG7) predicted to regulate hub gene expression. Compound screening identified betaine, pyruvic acid, citric acid, etc., as top-ranking candidates, with MFN2 showing the highest binding capacity among hub genes. This study provides an integrative framework linking metabolic reprogramming with immune dysfunction in AS. The six-gene diagnostic signature showed preliminary discriminatory ability in the available datasets, while the ceRNA regulatory network and natural compound screening results prioritize candidate regulatory pathways and compounds for future validation. These findings advance our understanding of AS pathogenesis and may guide future biomarker development and targeted intervention strategies. Full article

To address the challenges of narrow genetic backgrounds and low phenotypic selection efficiency in tomato breeding, comparative genomics was applied. Based on the genomic sequences of five tomato varieties (‘Micro-Tom’, ‘Moneymaker’, ‘M82’, ‘Heinz 1706’, and ‘LA2093’), a total of 285,796 InDel loci were preliminarily identified. Based on these loci, a total of 255 pairs of molecular markers were developed. Subsequently, based on InDel length, polymorphism, and electrophoretic performance, 63 InDel markers with stable amplification, clear polymorphic bands, and coverage across all 12 chromosomes were rigorously selected. These markers were subsequently used to analyze the genetic diversity of 52 tomato germplasm resources. The polymorphism information content (PIC) values of the markers ranged from 0.074 to 0.402, with an average of 0.2804. Cluster analysis based on InDel genotyping data divided the 52 germplasm samples into four distinct groups with significant genetic differentiation, which was validated in conjunction with previously collected phenotypic data from the 52 tomato germplasm resources. Furthermore, a set of core InDel primer combinations (24 pairs) was selected to construct unique DNA fingerprint profiles for each germplasm group. Overall, the InDel markers developed in this study provide an efficient tool for evaluating genetic diversity in tomato germplasm and offer a reliable molecular basis for germplasm identification, heterosis prediction, and marker-assisted breeding, thereby facilitating the development of improved tomato cultivars. Full article

Background/Objectives: The Arabidopsis thaliana GDS1 (Growth, Development and Splicing 1) gene has recently been identified as a key regulator linking nitrate signaling to leaf senescence. However, a systematic analysis of the GDS1 gene family in maize (Zea mays L.) is lacking. This study aims to identify and characterize the ZmGDS1 gene family in maize, providing a foundation for functional studies on their roles in growth, development, and low-nitrogen-induced leaf senescence. Methods: Putative ZmGDS1 family members were identified by searching the maize B73 reference genome using BLASTP (version 2.11.0+) and HMMER (version 3.4), with the Arabidopsis GDS1 protein sequence as the query. Candidate sequences were verified for the presence of the conserved zf-CCCH domain using NCBI CD-Search and SMART. Phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, collinearity, and promoter cis elements were comprehensively analyzed using MEGA 11, TBtools (version 1.098), MEME (version 5.5.9), and PlantCARE. Phylogenetic trees were constructed using the maximum likelihood (ML) method with the LG+G+I model and 1000 bootstrap replicates. Results: Thirteen ZmGDS1 genes were identified, distributed unevenly across eight maize chromosomes. Phylogenetic analysis classified the ZmGDS1 proteins into four distinct groups (A–D), revealing a lineage-specific expansion in group D. While all members contained the conserved zf-CCCH domain, their motif compositions varied considerably; ZmGDS1.1 exhibited the most complex structure, whereas ZmGDS1.12 had the most simplified. Subcellular localization predictions indicated that most ZmGDS1 proteins are targeted to the nucleus, consistent with a potential role as transcription factors. Promoter analysis revealed an abundance of cis elements associated with light response, hormone signaling (methyl jasmonate, abscisic acid, auxin), and stress responses. Notably, phylogenetically related genes tended to share similar cis-element profiles. Conclusions: This genome-wide analysis provides the first characterization of the ZmGDS1 gene family in maize. The observed structural conservation and diversity, together with regulatory elements linked to senescence-associated signals, support the hypothesis that ZmGDS1 genes may contribute to leaf senescence, particularly under low-nitrogen conditions. These findings provide a basis for future functional validation studies. Full article

Severe southern soybean crinkle leaf disease (SSCLD) reduces soybean seed yield by approximately 40%. Identifying the genes that control SSCLD is crucial for breeding resistant varieties and elucidating the molecular mechanisms underlying SSCLD infection. In this study, recombinant inbred lines (RILs, n = 236) derived from a cross between Nannong1138-2 (NN1138-2) and Zhengxiaodou (ZXD) were used as experimental materials. A field trial employing a randomized block design was conducted in four environments across two locations, Nanning (2019–2021) and Du’an (2020) in Guangxi, to identify the disease severity grades of SSCLD in the field. QTLs controlling SSCLD were detected via a genetic map constructed using 3255 SLAF (specific locus amplified fragment) markers from the recombinant inbred lines. RT–qPCR was used to analyze candidate gene expression at major effect loci. The results revealed that eight SSCLD-associated QTLs were identified on chromosomes 3, 6, 12, and 17. Notably, the qw12-1 locus on chromosome 12 was detected across three developmental stages in three of the four environments, explaining 10.18–58.20% of the phenotypic variation. RT–qPCR analysis of 12 disease resistance-related genes within the qw12-1 interval revealed that GLYMA_12G233000 and GLYMA_12G239200 presented significantly higher expression in crinkled leaf lines than in normal leaf lines during the V5 (fifth trifoliolate stage), R2 (full bloom stage), and R6 (full seed stage) stages. These genes were prioritized as potential prime candidates for SSCLD resistance genes. This research provides foundational data for the fine mapping of qw12-1 and cloning SSCLD-related genes, advancing our understanding of the molecular mechanisms underlying SSCLD. Full article

Background/Objectives: Bacteriophage-based display has been utilized for a variety of purposes, such as to assemble protein libraries and conduct biopanning. We have created a modified lambda (λ) bacteriophage platform, ideal for the display and delivery of proteins. Our system utilizes counter-selection recombineering for versatile modification, temperature-sensitive induction for timely lysate production, and an arabinose-inducible mechanism for high-titer, stable yield. Here, we investigated the ability of this specialized λ phage display platform to stimulate highly specific antibodies in mice against the displayed cancer-variant cell-surface receptor EGFRvIII, demonstrating its potential in cancer immunotherapy and broader vaccine development. Methods: λ display immunogenicity was explored by generating fusion proteins between the λ head protein D and a 13-mer peptide from the N terminus of glioblastoma variant cell-surface receptor, EGFRvIII. The 13-mer peptide was fused to either the N or C terminus of the λD protein while λ remained a dormant lysogen in the bacterial host chromosome. Recombinant phage lysates were then generated with ~420 displayed fusion proteins per phage particle. Mice were injected with purified recombinant λ phage without an adjuvant via both intraperitoneal and intramuscular routes, and sera harvested at various timepoints were profiled for immunogenicity. Results: Analysis of serum samples by ELISA and Western blotting demonstrated the ability of the λD~EGFRvIII phage display, especially in the C-terminal fusion construction, to elicit a robust anti-EGFRvIII humoral response by either injection route. Notably, the antibody response was highly specific to EGFRvIII without exhibiting cross-reactivity to wild-type EGFR. Conclusions: The data generated in this study demonstrate the λ system’s immunotherapeutic potential as a high-titer, stable, self-adjuvanting vector for the stimulation of robust antibody titers with defined specificity. Full article

As the hybrid offspring of cattle and yak, cattle–yaks suffer from male sterility, manifesting as cascading spermatogenic failure. Despite the Y chromosome’s pivotal role in spermatogenesis, the absence of a high-quality yak Y assembly has long impeded mechanistic understandings from this perspective. Here, a near-complete 42.4 Mb yak Y chromosome is constructed through a multi-stage assembly strategy that integrates de novo assembly with pangenome graph construction and Hi-C guided refinement. By developing a rigorously standardized gene annotation pipeline for precise cross-species comparison, we find that yaks have undergone a greater expansion of Y-linked ampliconic genes than cattle. Integrating this ampliconic landscape with short-read and full-length transcriptomics further demonstrates that yaks exhibit a drastic 2-to-4-fold increase in transcriptionally active copies of spermatogenesis-related ampliconic genes (including TSPY1, ZNF280BY, HSFY and PRAMEY) relative to cattle. Given negligible homology outside the pseudoautosomal region and conservation of key meiotic proteins, we propose a ‘cis-trans regulatory mismatch’ model driven by divergent Y-linked amplification as a working hypothesis to explain the primary genetic mechanism of cattle–yak male sterility. Together, these findings offer critical insights for addressing cattle–yak male sterility and establish the Y chromosome as an active driver of reproductive isolation beyond its traditional degenerate characterization. Full article