Search Results (876)

Zinc (Zn) deficiency poses a major global health challenge, and wheat grains generally contain low Zn concentrations. In this study, the wheat cultivar ‘Zhongmai 175’ was identified as zinc-efficient. Hydroponic experiments demonstrated that Zn deficiency induced the secretion of oxalic acid and malic acid in root exudates and significantly increased total root length in ‘Zhongmai 175’. To elucidate the underlying regulatory mechanisms, transcriptome profiling via RNA sequencing was conducted under Zn-deficient conditions. A total of 2287 and 1935 differentially expressed genes (DEGs) were identified in roots and shoots, respectively. Gene Ontology enrichment analysis revealed that these DEGs were primarily associated with Zn ion transport, homeostasis, transmembrane transport, and hormone signaling. Key DEGs belonged to gene families including VIT, NAS, DMAS, ZIP, tDT, HMA, and NAAT. KEGG pathway analysis indicated that phenylpropanoid biosynthesis, particularly lignin synthesis genes, was significantly downregulated in Zn-deficient roots. In shoots, cysteine and methionine metabolism, along with plant hormone signal transduction, were the most enriched pathways. Notably, most DEGs in shoots were associated with the biosynthesis of phytosiderophores (MAs, NA) and ethylene. Overall, genes involved in Zn ion transport, phytosiderophore biosynthesis, dicarboxylate transport, and ethylene biosynthesis appear to play central roles in wheat’s adaptive response to Zn deficiency. These findings provide a valuable foundation for understanding the molecular basis of Zn efficiency in wheat and for breeding Zn-enriched varieties. Full article

Background: CCAAT/enhancer-binding protein alpha–basic leucine zipper in-frame (CEBPA^bZIP-inf) mutations are associated with favorable outcomes in acute myeloid leukemia (AML). So far, there are limited data on integrating clinical and genomic features impacting the outcomes. Methods: Clinical and genomic data from consecutive patients with CEBPA^bZIP-inf were reviewed. A Cox proportional hazards regression was used to identify the variables associated with event-free survival (EFS), relapse-free survival (RFS) and survival. Results: 224 CEBPA^bZIP-inf patients were included in this study. In the 201 patients, except for the 19 receiving the transplant in the first complete remission with no events (the transplant cohort), multivariate analyses showed that IKZF1 mutations/deletions were significantly associated with poor EFS (p = 0.001) and RFS (p < 0.001); FLT3-ITD mutations, poor RFS (p = 0.048). In addition, increasing WBC count, lower hemoglobin concentration, non-intensive induction, and MRD positivity after first consolidation predicted poor outcomes. On the basis of the number of adverse prognostic covariates for RFS, the 201 patients were classified into low-, intermediate- or high-risk subgroups, and there were significant differences in the 3-year EFS, RFS and survival rates (all p < 0.001); however, except for survival in the low-risk group, these metrics were lower than those in the transplant cohort. Conclusions: We identified a potential high-risk population with adverse prognostic factors in CEBPA^bZIP-inf AML patients for which transplantation should be considered. Full article

The bZIP gene family play a crucial role in plant growth, development, and stress responses, functioning as transcription factors. While this gene family has been studied in several plant species, its roles in the endangered woody plant Phoebe bournei remain largely unclear. This study comprehensively analyzed the PbbZIP gene family in P. bournei, identifying 71 PbbZIP genes distributed across all 12 chromosomes. The amino acid count in these genes ranged from 74 to 839, with molecular weights varying from 8813.28 Da to 88,864.94 Da. Phylogenetic analysis categorized the PbbZIP genes into 12 subfamilies (A-K, S). Interspecific collinearity analysis revealed homologous PbbZIP genes between P. bournei and Arabidopsis thaliana. A promoter cis-acting element analysis indicated that PbbZIP genes contain various elements responsive to plant hormones, stress signals, and light. Additionally, expression analysis of public RNA-seq data showed that PbbZIP genes are distributed across multiple tissues, exhibiting distinct expression patterns specific to root bark, root xylem, stem bark, stem xylem, and leaves. We also performed qRT-PCR analysis on five representative PbbZIP genes (PbbZIP14, PbbZIP26, PbbZIP32, PbbZIP67, and PbbZIP69). The results demonstrated significant differences in the expression of PbbZIP genes under various abiotic stress conditions, including salt stress, heat, and drought. Notably, PbbZIP67 and PbbZIP69 exhibited robust responses under salt or heat stress conditions. This study confirmed the roles of the PbbZIP gene family in responding to various abiotic stresses, thereby providing insights into its functions in plant growth, development, and stress adaptation. The findings lay a foundation for future research on breeding and enhancing stress resistance in P. bournei. Full article

Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response. Results: RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C. Conclusions: Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage. Full article

Background/Objectives: We examined the in vivo effects of successive treatments with the histone deacetylase (HDAC) inhibitor romidepsin in patients with cutaneous T-cell lymphoma (CTCL), using changes in gene expression in peripheral blood mononuclear cells (PBMCs). Methods: Exploiting data from a highly responsive CTCL patient through 12 months of treatment, we identified a malignant cell predictor (MCP), a gene signature associated with the diminishing numbers of circulating malignant cells. Results: The MCP was successfully validated in the patient’s relapse sample 9 months after treatment was terminated and via an independent set of CTCL patient samples. Conclusions: The MCP set of genes contained novel CTCL markers, including membrane-associated proteins not normally expressed in lymphocytes. A subclass of those markers was also detectable in residual malignant cells undetected by flow cytometry in remission samples from a patient who relapsed 10 months later. We identified a subset of transcriptional regulators, miRNAs and methylation patterns associated with the effect of progressive treatments revealing potential mechanisms of transcriptional dysregulation and functional effects in the malignant cells. We demonstrate a role for transcriptional activator HLF, over-expressed in malignant cells, and downregulated transcriptional-suppressor and immune-modulator NFIL3, as regulators of CTCL-specific genes. Full article

Tomato (Solanum lycopersicum) is a globally important crop, and enhancing its fruit quality and phenotypic traits is a key objective in modern breeding. This study investigates the role of the LEAFY-COTYLEDON1-LIKE4 (L1L4), an NF-YB subunit of the nuclear factor Y (NF-Y) transcription factor, in tomato fruit development using RNA-sequencing data from zinc-finger nuclease (ZFN)-targeted disruption lines. Differential gene expression (DEG) analyses of two independent l1l4 mutant lines compared to the wild-type line revealed significant alterations in key metabolic pathways and regulatory networks that are implicated in fruit ripening. Specifically, L1L4 disruption impacted the genes and pathways related to the fruit’s color development (carotenoid and flavonoids), texture (cell wall modification), flavor (sugar and volatile organic compound metabolism), and ripening-related hormone signaling. The analyses also revealed multiple differentially expressed histones, histone modifiers, and transcription factors (ERFs, MYBs, bHLHs, WRKYs, C2H2s, NACs, GRAS, MADs, and bZIPs), indicating that L1L4 participates in a complex regulatory network. These findings provide valuable insights into the role of L1L4 in orchestrating tomato fruit development and highlight it as a potential target for genetically improving the fruit quality. Full article

NAC (NAM, ATAF1/2, CUC1/2) is a plant-specific transcription factor (TF) family that plays important roles in various physiological and biochemical processes of plants. However, the NAC gene family in Lagerstroemia indica and its role in anthocyanin metabolism are still unexplored. In our study, a total of 167 NACs were identified in the L. indica genome via genome-wide analysis and bioinformatics techniques. Amino acid sequence analysis showed that all 167 NAC proteins contained a conserved NAM domain. This domain primarily comprised random coils, extended strands, and alpha helices. Most NACs were found on the nucleus and dispersed over 23 of the 24 plant chromosomes. Based on phylogenetic analysis, the NACs can be categorized into ten subgroups. Furthermore, the promoter homeotropic elements predicted the cis-acting elements in the promoters of these genes related to hormones, development, environmental stress response, and other related responses, demonstrating the diverse regulatory mechanisms underlying gene functions. In addition, a co-expression network was established through RNA sequencing. This network helped identify seven key LiNACs, genes related to anthocyanin expression (CHS) and transcription factors (MYB and bHLH). To identify potential anthocyanin regulatory factors present in L. indica petals, protein interaction prediction was performed, which revealed that LiNACs might participate in anthocyanin regulation by interacting with other proteins, such as MYB, ABF, ABI, bZIP, MYC, etc. Our results provided novel insights and could help in the functional identification of LiNACs in L. indica and the regulation of anthocyanin synthesis. Full article

The TGACG motif-binding factor (TGA) family is an important group of basic region/leucine zipper (bZIP) transcription factors in plants, playing crucial roles in plant development and stress responses. This study conducted a comprehensive genome-wide analysis of the TGA transcription factor (TF) family in common wheat (Triticum aestivum L.). A total of 48 wheat TGAs were identified and classified into four subgroups. Collinearity analysis of the TGAs between wheat and other species identified multiple duplicated gene pairs and highlighted the presence of highly conserved TGAs in wheat. Whole-genome and segmental duplications were identified as the primary drivers of TaTGA expansion. Expression pattern analysis indicated that TaTGAs are involved in plant development and responses to abiotic stresses, including drought, heat, and cold treatment. Among these, TaTGA16-2D was significantly upregulated under both drought and heat stresses, showing more than a five-fold increase in expression. Subcellular localization confirmed its nucleus localization. Functional validation through ectopic expression in Arabidopsis demonstrated that transgenic lines overexpressing TaTGA16-2D exhibited significantly improved stress tolerance. Under heat stress, the survival rates of transgenic lines exceeded 34%, compared to less than 18% in wild-type plants. Overall, this study provides valuable insights into the evolution and functional roles of TaTGAs and identifies TaTGA16-2D as a promising candidate to enhance abiotic stress tolerance in wheat via molecular breeding. Full article

Developing early-heading wheat cultivars is an important breeding strategy to utilize light and heat resources, facilitate multiple-cropping systems, and enhance annual grain yield. Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) possesses numerous agronomically beneficial traits for wheat improvement, such as early maturity and resistance to biotic and abiotic stresses. In this study, we found that a cytogenetically stable wheat–P. huashanica 7Ns disomic addition line showed (9–11 days) earlier heading and (8–10 days) earlier maturation than its wheat parents. Morphological observations of spike differentiation revealed that the 7Ns disomic addition line developed distinctly faster than its wheat parents from the double ridge stage. To explore the potential molecular mechanisms underlying the early heading, we performed transcriptome analysis at four different developmental stages of the 7Ns disomic addition line and its wheat parents. A total of 10,043 differentially expressed genes (DEGs) were identified during spike development. Gene Ontology (GO) enrichment analysis showed that these DEGs were linked to the carbohydrate metabolic process, photosynthesis, response to abscisic acid, and the ethylene-activated signaling pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were involved in plant hormone signal transduction (ARF, AUX/IAA, SAUR, DELLA, BRI1, and ETR), starch and sucrose metabolism (SUS1 and TPP), photosynthetic antenna proteins (Lhc), and circadian rhythm (PRR37, FT, Hd3a, COL, and CDF) pathways. In addition, several DEGs annotated as transcription factors (TFs), such as bHLH, bZIP, MADS-box, MYB, NAC, SBP, WRKY, and NF-Y, may be related to flowering time. Our findings reveal spike development-specific gene expression and critical regulatory pathways associated with early heading in the wheat–P. huashanica 7Ns addition line, and provide a new genetic resource for further dissection of the molecular mechanisms underlying the heading date in wheat. Full article

3D (three-dimensional) property volume is an important data carrier for 3D land administration by using 3D cadastral technology, which can be used to express the legal space (property rights) scope matching with physical entities such as buildings and land. A 3D property volume is represented by a dense set of 3D coordinate points arranged in a predefined order and is displayed alongside the parcel map for reference and utilization by readers. To store a 3D property volume in the database, it is essential to record the connectivity relationships among the original 3D coordinate points, the associations between points and lines for representing boundary lines, and the relationships between lines for defining surfaces. Only by preserving the data structure that represents the relationships among points, lines, and surfaces can the 3D property volume in a parcel map be fully reconstructed. This approach inevitably results in the database storage volume significantly exceeding the original size of the point set, thereby causing storage redundancy. Consequently, this paper introduces a reversible 3D property volume compression coding method (called 3DPV-CC) to address this issue. By analyzing the distribution characteristics of the coordinate points of the 3D property volume, a specific rule for sorting the coordinate points is designed, enabling the database to have the ability of data storage and recovery by merely storing a reordered point set. The experimental results show that the 3DPV-CC method has excellent support capabilities for 3D property volumes of the vertical and slopped types, and can compress and restore the coordinate point set of the 3D property volume for drawing 3D parcel maps. The compression capacity of our method in the test is between 23.66% and 38.42%, higher than the general data compression methods (ZIP/7Z/RAR: 8.37–10.32%). By means of this method, land or real estate administrators from government departments can store 3D property volume data at a lower cost. This is conducive to enhancing the informatization level of land management. Full article

Maize (Zea mays L.) is one of the most important food crops. Salt stress can hinder crop growth and development, but the molecular mechanisms underlying maize’s response to salt tolerance remain unclear. In this study, we conducted comparative transcriptome, metabolome, and physiological analyses of a salt-tolerant maize inbred line (J1285) subjected to different NaCl concentrations during the seedling stage. The results demonstrated that, with increasing salt concentration, seedling growth parameters and antioxidant enzyme activities (SOD, POD, CAT) exhibited initially increases before subsequently decreasing, peaking at 50–150 mmol/L. Transcriptome data analysis revealed that the experimental groups subjected to 50, 100, 150, and 200 mmol/L treatments had 375, 1043, 2504, and 2328 differentially expressed genes (DEGs) compared to the control group, respectively. Additionally, through GO and KEGG analysis, we found that the DEGs were primarily enriched in the MAPK signaling pathway and plant hormone signal transduction, especially the abscisic acid (ABA) signaling pathway, both of which play instrumental roles in orchestrating the maize response to salt-induced stress. Transcription factors involved in the salt stress response, including WRKY, TIFY, bZIP, and bHLH, were identified. Metabolomic data analysis revealed that the experimental groups subjected to 50, 100, 150 and 200 mmol/L treatments had 44, 335, 278, and 550 differentially expressed metabolites (DEMs) compared to the control group, respectively. The DEMs were mainly enriched in metabolic pathways and the biosynthesis of secondary metabolites. Transcriptomics and metabolomics combined analysis were performed on J1285 seedling leaves, and it was found that the co-enrichment pathways included starch and sucrose metabolism, linoleic acid metabolism, α-linolenic acid metabolism, phenylpropanoid biosynthesis pathway, etc. Collectively, these results will aid in identifying resistance genes and elucidating the molecular mechanisms underlying salt tolerance for maize. Full article

The basic leucine zipper (bZIP) transcription factors are involved in a wide range of physiological processes in plants, including hormone signaling, stress responses, and growth and development regulation. They play a key role in abscisic acid (ABA)-mediated immune regulation. However, the immune-related function of OsbZIP76 in rice remains poorly understood. In this study, we generated OsbZIP76 knockout (KO) lines using CRISPR/Cas9-mediated genome editing and examined their phenotypic responses to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the fungal pathogen Magnaporthe oryzae. The KO lines showed increased susceptibility to both pathogens compared to wild-type (WT) plants. Furthermore, qRT-PCR analysis revealed that, upon pathogen infection, the expression of pathogenesis-related genes such as PR1a, PR5, and NPR1 was significantly suppressed in the KO lines. ABA treatment experiments showed that KO lines were hypersensitive to exogenous ABA, indicating a role for OsbZIP76 in ABA perception and signaling. Notably, the expression of the OsbZIP76 gene itself was strongly induced by both ABA treatment and pathogen infection, supporting its role as a positive regulator in ABA-associated immune signaling. Overall, this study demonstrates that OsbZIP76 functions as an important immune regulator by integrating defense gene expression with ABA signaling, providing new insights into the molecular crosstalk between hormonal signaling and pathogen defense mechanisms. Full article

This study introduces Logarithmic Positional Partition Interval Encoding (LPPIE), a novel lossless compression methodology employing iterative logarithmic transformations to drastically reduce data size. While conventional dictionary-based algorithms rely on repeated sequences, LPPIE translates numeric data sequences into highly compact logarithmic representations. This achieves significant reduction in data size, especially on large integer datasets. Experimental comparisons with established compression methods—such as ZIP, Brotli, and Zstandard—demonstrate LPPIE’s exceptional effectiveness, attaining compression ratios nearly 13 times superior to established methods. However, these substantial storage savings come with elevated computational overhead due to LPPIE’s complex numerical operations. The method’s robustness across diverse datasets and minimal scalability limitations underscore its potential for specialized archival scenarios where data fidelity is paramount and processing latency is tolerable. Future enhancements, such as GPU-accelerated computations and hybrid entropy encoding integration, are proposed to further optimize performance and broaden LPPIE’s applicability. Overall, LPPIE offers a compelling alternative in lossless data compression, substantially redefining efficiency boundaries in high-volume numeric data storage. Full article

Abscisic acid (ABA), a pivotal phytohormone regulating plant growth and stress adaptation, orchestrates abiotic stress responses through the ABA-responsive element-binding factors ABF/AREB/ABI5. Nevertheless, the functional characterization of ABF/AREB/ABI5 homologs in Z. jujuba cv. Dongzao remains unexplored. In this study, we identified seven ZjABF genes distributed across five chromosomes. Domain analyses revealed high structural conservation, particularly within the basic leucine zipper (bZIP) DNA-binding domain. Subcellular localization confirmed nuclear targeting of all seven ZjABF proteins. Phylogenetic classification resolved these factors into three clades (A–C). Cis-regulatory element profiling implicated the involvement of the ZjABFs in hormone signaling, abiotic stress transduction, and photoregulatory pathways. Synteny analyses identified three segmental duplication events within the gene family. Tissue-specific expression patterns indicated critical roles for ZjABF2 and ZjABF3 in fruit maturation, and most of the ABF/AREB/ABI5 genes were highly expressed in the root. Under drought stress, four ZjABF genes exhibited differential expression, with ZjABF2 demonstrating pronounced sensitivity. These findings establish a molecular framework for understanding ZjABF-mediated abiotic stress responses in non-model woody perennials. Full article

The metalloid arsenic (As) and the metals lead (Pb) and mercury (Hg), which together we call the “Toxic Triad”, are among the pollutants of greatest global concern, harming the health of millions of people and contributing to biodiversity loss. The widespread distribution of As, Pb and Hg facilitates the exposure of humans and other species to these elements simultaneously, potentially amplifying their individual toxic effects. While As, Pb and Hg are well established as toxic elements, the mechanisms by which they interact with genetic material and impact the health of various species remain incompletely understood. This is particularly true regarding the combined effects of these three elements. In this context, the objective of this work was to perform a toxicogenomic analysis of As, Pb and Hg to highlight multiple aspects of element-gene interactions, in addition to revisiting information on the genotoxicity and carcinogenicity of the Toxic Triad. By using The Comparative Toxicogenomics Database, it was possible to identify that As interacts with 7666 genes across various species, while Pb influences 3525 genes, and Hg affects 692 genes. Removing duplicate gene names, the three elements interact with 9763 genes across multiple species. Considering the top-20 As/Pb/Hg-interacting genes, catalase (CAT), NFE2 like bZIP transcription factor 2 (NFE2L2), caspase 3 (CASP3), heme oxygenase (HMOX1), tumor necrosis factor (TNF), NAD(P)H quinone dehydrogenase 1 (NQO1) and interleukin 6 (IL6) were the most frequently observed. In total, 172 genes have the potential to interact with the three elements. Gene ontology analysis based on those genes evidenced that the Toxic Triad affects several cellular compartments and molecular functions, highlighting its effect on stimulation of toxic stress mechanisms. These 172 genes are also associated with various diseases, especially those of the urogenital tract, as well as being related to biological pathways involved in infectious diseases caused by viruses, bacteria and parasites. Arsenic was the element with the best-substantiated genotoxic and carcinogenic activity. This article details, through a toxicogenomic approach, the genetic bases that underlie the toxic effects of As, Pb and Hg. Full article