Search Results (9,999)

Soil salinization is a significant environmental stress factor, threatening global agricultural yield and ecological security. Plants must effectively cope with the adverse effects of salt stress on survival and successful reproduction. Lateral Organ Boundaries (LOB) Domain (LBD) genes, a gene family encoding plant-specific transcription factors (TFs), play important roles in plant growth and development. Here, we identified and functionally characterized the LBD family TF PtrLBD41 from Populus trichocarpa, which can be induced by various abiotic stresses, including salt, dehydration, low temperature, and Abscisic Acid (ABA). Meanwhile, transgenic plants overexpressing PtrLBD41 showed a better phenotype and higher tolerance than the wild-type (WT) plants under salt stress treatment. Transcriptome analysis found that the differentially expressed genes (DEGs) between the WT and overexpression (OE) line were enriched in the flavonoid biosynthetic process, in which chalcone synthases (CHS), naringenin 3-dioxygenase (F3H), and chalcone isomerase (CHI) were significantly up-regulated under salt stress conditions through qRT-PCR analysis. Therefore, we demonstrate that PtrLBD41 plays an important role in the tolerance to salt stress in P. trichocarpa. Full article

Background: The early exposure of nutrients during pubertal mammary gland development may reduce the risk of developing breast cancer later in life. Anticancer n-3 polyunsaturated fatty acids (n-3 PUFA) are shown to modulate pubertal mammary gland development; however, the mechanisms of action remain unclear. Prior work focused on effects at the whole tissue level, and little is known at the cellular level, such as at the level of mammary epithelial cells (MECs), which are implicated in cancer development. Methods: This pilot study examined the effects of lifelong n-3 PUFA exposure on the transcriptome by RNA-Seq in the isolated MECs of pubertal (6–8-week-old) female fat-1 transgenic mice capable of de novo n-3 PUFA synthesis. edgeR and DESeq2 were used separately for the differential expression analysis of RNA sequencing data followed by the Benjamani–Hochberg procedure for multiple testing correction. Results: Nine genes were found concordant and significantly different (p ≤ 0.05) by both the DESeq2 and edgeR methods. These genes were associated with multiple pathways, suggesting that n-3 PUFA stimulates estrogen-related signaling (Mlltl0, Galr3, and Nrip1) and a glycolytic profile (Soga1, Pdpr, and Uso1) while offering protective effects for immune and DNA damage responses (Glpd1, Garre1, and Rpa1) in MECs during puberty. Conclusions: This pilot study highlights the utility of RNA-Seq to better understanding the mechanistic effects of specific nutrients such as n-3 PUFA in a cell-specific manner. Thus, further studies are warranted to investigate the cell-specific mechanisms by which n-3 PUFA influences pubertal mammary gland development and breast cancer risk later in life. Full article

Seed germination is a fundamental process in plant reproduction, and it involves a series of complex physiological mechanisms. The germination rate of Astragalus mongholicus (AM) seeds is significantly lower under natural conditions. To investigate the key genes associated with AM seed germination, seeds from AM plants were collected at 0, 12, 24, and 48 h for a transcriptomic analysis, weighted gene co-expression network analysis (WGCNA), and machine learning (ML) analysis. The primary pathways involved in AM seed germination include plant-pathogen interactions and plant hormone signaling. Four key genes were identified through the WGCNA and ML: Cluster-28,554.0, FAS4, T10O24.10, and EPSIN2. These findings were validated using real-time quantitative reverse transcription PCR (qRT-PCR), and results from RNA sequencing demonstrated a high degree of concordance. This study reveals, for the first time, the key genes related to AM seed germination, providing potential gene targets for further research. The discovery of N4-acetylcysteine (ac4C) modification during seed germination not only enhances our understanding of plant ac4C but also offers valuable insights for future functional research and application exploration. Full article

Heavy metal pollution is one of the most devastating abiotic factors, significantly damaging crops and human health. One of the serious problems it causes is a rise in cadmium (Cd) toxicity. Cd is a highly toxic metal with a negative biological role, and it enters plants via the soil–plant system. Cd stress induces a series of disorders in plants’ morphological, physiological, and biochemical processes and initiates the inhibition of seed germination, ultimately resulting in reduced growth. Fiber crops such as kenaf, jute, hemp, cotton, and flax have high industrial importance and often face the issue of Cd toxicity. Various techniques have been introduced to counter the rising threats of Cd toxicity, including reducing Cd content in the soil, mitigating the effects of Cd stress, and genetic improvements in plant tolerance against this stress. For decades, plant breeders have been trying to develop Cd-tolerant fiber crops through the identification and transformation of novel genes. Still, the complex mechanism of Cd tolerance has hindered the progress of genetic breeding. These crops are ideal candidates for the phytoremediation of heavy metals in contaminated soils. Hence, increased Cd uptake, accumulation, and translocation in below-ground parts (roots) and above-ground parts (shoots, leaves, and stems) can help clean agricultural lands for safe use for food crops. Earlier studies indicated that reducing Cd uptake, detoxification, reducing the effects of Cd stress, and developing plant tolerance to these stresses through the identification of novel genes are fruitful approaches. This review aims to highlight the role of some conventional and molecular techniques in reducing the threats of Cd stress in some key fiber crops. Molecular techniques mainly involve QTL mapping and GWAS. However, more focus has been given to the use of transcriptome and TFs analysis to explore the potential genomic regions involved in Cd tolerance in these crops. This review will serve as a source of valuable genetic information on key fiber crops, allowing for further in-depth analyses of Cd tolerance to identify the critical genes for molecular breeding, like genetic engineering and CRISPR/Cas9. Full article

Autophagy is an important cellular response against intracellular pathogens. However, some viruses have evolved mechanisms to hijack this defensive process to provide favorable conditions for virus replication in host cells. The porcine epidemic diarrhea virus (PEDV) has been shown to alter autophagy pathways; however, it is still unknown through which receptors PEDV induces autophagy in IPEC-J2 cells, whether autophagy facilitates PEDV replication, and which functional domains of PEDV proteins are primarily responsible for inducing autophagy. Here, we found that PEDV infection induces autophagy in host cells via distinct and uncoupled molecular pathways. RNA-seq technology was used to analyze the expression patterns of intracellular genes in PEDV-infected IPEC-J2 cells using transcriptomics. The results demonstrate that PEDV triggers autophagy via the cellular pathogen receptor TLR4 and the AKT-mTOR pathway. As evidenced by autophagosome detection, PEDV infection increases autophagosomes and light chain 3 (LC3)-II as well as downregulated AKT-mTOR phosphorylation. Our study revealed that the binding of the viral protein NSP61-2C (56-151aa) to TLR4 triggers autophagy and inactivates the AKT-mTOR pathway, both of which are critical for facilitating PEDV infection. Through screening and analysis, TLR4 was found to be a key gene involved in PEDV-induced autophagy. The screening of the key functional domains of NSP6 (56-151aa) for their ability to induce autophagy in IPEC-J2 cells provided a basis for the in-depth analysis of the pathogenic mechanism of PEDV infection-induced autophagy and promotion of self-replication and also provided an important target for the study of PEDV antiviral drugs. In conclusion, we elucidated that the PEDV infection of IPEC-J2 cells could induce autophagy and found that PEDV could use autophagy to promote its own replication. Full article

Torreya grandis is a widely cultivated fruit species in China that is valued for its significant economic and agricultural importance. The molecular mechanisms underlying pigment formation and photosynthetic performance in Torreya leaf color mutants remain to be fully elucidated. In this study, we performed transcriptome sequencing and measured photosynthetic performance indicators to compare mutant and normal green leaves. The research results indicate that the identified Torreya mutant differs from previously reported mutants, exhibiting a weakened photoprotection mechanism and a significant reduction in carotenoid content of approximately 33%. Photosynthetic indicators, including the potential maximum photosynthetic capacity (F_v/F_m) and electron transport efficiency (Ψ_o, φ_Eo), decreased significantly by 32%, 52%, and 49%, respectively. While the quantum yield for energy dissipation (φ_Do) increased by 31%, this increase was not statistically significant, which may further reduce PSII activity. A transcriptome analysis revealed that the up-regulation of chlorophyll degradation-related genes—HCAR and NOL—accelerates chlorophyll breakdown in the Torreya mutant. The down-regulation of carotenoid biosynthesis genes, such as LCY1 and ZEP, is strongly associated with compromised photoprotective mechanisms and the reduced stability of Photosystem II. Additionally, the reduced expression of the photoprotective gene psbS weakened the mutant’s tolerance to photoinhibition, increasing its susceptibility to photodamage. These changes in gene expression accelerate chlorophyll degradation and reduce carotenoid synthesis, which may be the primary cause of the yellowing in Torreya. Meanwhile, the weakening of photoprotective mechanisms further impairs photosynthetic efficiency, limiting the growth and adaptability of the mutants. This study emphasizes the crucial roles of photosynthetic pigments and photosystem structures in regulating the yellowing phenotype and the environmental adaptability of Torreya. It also provides important insights into the genetic regulation of leaf color in relation to photosynthesis and breeding. Full article

Efficient RNA isolation from filamentous fungi is crucial for gene expression studies, but it poses significant technical challenges due to the robust cell walls and susceptibility of RNA to degradation by ribonucleases. This study presents the effectiveness of two RNA isolation protocols for four species of filamentous fungi: Penicillium crustosum, Penicillium rubens, Penicillium griseofulvum, and Aspergillus fumigatus. Both protocols utilized Fenzol Plus for cell lysis but varied in the mechanical disruption methods: bead-beating versus manual vortexing. The results show that the bead-beater method (Protocol 1) yielded significantly higher RNA quantities, with better purity and integrity, as demonstrated by higher A260/A280 and A260/A230 ratios. RNA concentrations ranged from 30 to 96 µg/g of dry biomass in Penicillium species and up to 52 µg/g in A. fumigatus. The use of chloroform in Protocol 1 also enhanced RNA purity, effectively separating contaminants such as DNA, proteins, and polysaccharides. This optimized protocol is highly efficient and can be applied in routine laboratories handling large numbers of fungal samples, making it a robust method for downstream applications such as cDNA synthesis and transcriptome analysis. Full article

E3 ubiquitin ligases known as plant U-box (PUB) proteins regulate a variety of aspects of plant growth, development, and stress response. However, the functions and characteristics of the PUB gene family in alfalfa remain unclear. This work involved a genome-wide examination of the alfalfa U-box E3 ubiquitin ligase gene. In total, 210 members were identified and divided into five categories according to their homology with the members of the U-box gene family in Arabidopsis thaliana. The phylogenetic analysis, conserved motifs, chromosomal localization, promoters, and regulatory networks of this gene were investigated. Chromosomal localization and covariance analyses indicated that the MsPUB genes expanded MsPUB gene family members through gene duplication events during evolution. MsPUB genes may be involved in the light response, phytohormone response, growth, and development of several biological activities, according to cis-acting element analysis of promoters. In addition, transcriptome analysis and expression analysis by qRT-PCR indicated that most MsPUB genes were significantly upregulated under cold stress, drought stress, and salt stress treatments. Among them, MsPUBS106 and MsPUBS185 were significantly and positively correlated with cold resistance in alfalfa. MsPUBS110, MsPUBS067, MsPUBS111 and MsPUB155 were comprehensively involved in drought stress, low temperature, and salt stress resistance. All things considered, these discoveries offer fresh perspectives on the composition, development, and roles of the PUB gene family in alfalfa. They also provide theoretical guidance for further investigations into the mechanisms regulating the development, evolution, and stress tolerance of MsPUB. Full article

Background: In clinical practice, various methods are used to identify ALK gene rearrangements in tumor samples, ranging from “classic” techniques, such as IHC, FISH, and RT-qPCR, to more advanced highly multiplexed approaches, such as NanoString technology and NGS panels. Each of these methods has its own advantages and disadvantages, but they share the drawback of detecting only a restricted (although sometimes quite extensive) set of preselected biomarkers. At the same time, whole transcriptome sequencing (WTS, RNAseq) can, in principle, be used to detect gene fusions while simultaneously analyzing an incomparably wide range of tumor characteristics. However, WTS is not widely used in practice due to purely analytical limitations and the high complexity of bioinformatic analysis, which requires considerable expertise. In particular, methods to detect gene fusions in RNAseq data rely on the identification of chimeric reads. However, the typically low number of true fusion reads in RNAseq limits its sensitivity. In a previous study, we observed asymmetry in the RNAseq exon coverage of the 3′ partners of some fusion transcripts. In this study, we conducted a comprehensive evaluation of the accuracy of ALK fusion detection through an analysis of differences in the coverage of its tyrosine kinase exons. Methods: A total of 906 human cancer biosamples were subjected to analysis using experimental RNAseq data, with the objective of determining the extent of asymmetry in ALK coverage. A total of 50 samples were analyzed, comprising 13 samples with predicted ALK fusions and 37 samples without predicted ALK fusions. These samples were assessed by targeted sequencing with two NGS panels that were specifically designed to detect fusion transcripts (the TruSight RNA Fusion Panel and the OncoFu Elite panel). Results: ALK fusions were confirmed in 11 out of the 13 predicted cases, with an overall accuracy of 96% (sensitivity 100%, specificity 94.9%). Two discordant cases exhibited low ALK coverage depth, which could be addressed algorithmically to enhance the accuracy of the results. It was also important to consider read strand specificity due to the presence of antisense transcripts involving parts of ALK. In a limited patient sample undergoing ALK-targeted therapy, the algorithm successfully predicted treatment efficacy. Conclusions: RNAseq exon coverage analysis can effectively detect ALK rearrangements. Full article

Dye wastewater pollution, particularly from persistent and toxic polycyclic organic pollutants, such as aniline blue, poses a significant environmental challenge. Aniline blue, a triphenylmethane dye widely used in the textile, leather, paper, and pharmaceutical industries, is notoriously difficult to treat owing to its complex structure and potential for bioaccumulation. In this study, we explored the capacity of Comamonas testosteroni (CT1) to efficiently degrade aniline blue, focusing on the underlying enzymatic mechanisms and degradation pathways. Through prokaryotic transcriptome analysis, we identified a significantly upregulated short-chain dehydrogenase (SDRz) gene (log₂FC = 2.11, p < 0.05) that plays a crucial role in the degradation process. The SDRz enzyme possessed highly conserved motifs and a typical short-chain dehydrogenase structure. Functional validation using an SDRz-knockout strain (CT-ΔSDRz) and an SDRz-expressioning strains (E-SDRz) confirmed that SDRz is essential for aniline blue degradation. The knockout strain CT-ΔSDRz exhibited a 1.27-fold reduction in the degradation efficiency, compared to CT1 strain after 12 h; while the expression strain E-SDRz showed a 1.24-fold increase compared to Escherichia coli DH5α after 12 h. Recombinant SDRz (rSDRz) was successfully produced, showing significant enzymatic activity (1.267 ± 0.04 mmol·L⁻¹·min⁻¹ protein), with kinetic parameters Vmax = 2.870 ± 0.0156 mmol·L⁻¹·min⁻¹ protein and Km = 1.805 ± 0.0128 mM·mL⁻¹. Under optimal conditions, the rSDRz achieved a degradation efficiency of 62.17% for aniline blue. Gas chromatography–mass spectrometry (GC-MS) analysis identified several intermediate metabolites in the degradation pathway, including benzeneacetaldehyde, a, a-diphenyl, 2-amino-4-methylbenzophenone, benzene, 1-dimethylamino-4-phenylmethyl, benzenesulfonic acid, methyl ester, further elucidating the biodegradation mechanism. These findings highlight SDRz as a critical enzyme in the biodegradation of aniline blue, offering valuable insights and a robust theoretical foundation for developing advanced bioremediation strategies to address dye wastewater pollution. Full article

The pathogenic mechanisms of severe aplastic anemia (SAA) in children are not completely elucidated. The insufficiency of the bone marrow microenvironment, in which mesenchymal stem cells (MSCs) are an important element, can be a potential factor associated with hematopoietic impairment in SAA. In the present study, we compared bone marrow MSCs from five children with SAA and five controls. We found a higher intensity of senescence-associated β-galactosidase activity in SAA MSCs, indicating the increased senescence in these cells. Further RNA sequencing analysis identified a distinctive profile of transcriptomes in SAA MSCs. After conducting a survey of the differentially expressed genes, we found that the up-regulated expression of TXNIP may compromise the proliferative potential of MSCs and probably relate to the pathogenesis of SAA. These results were validated by qPCR. To explore the molecular mechanism involving aberrant TXNIP regulation in SAA MSCs, the expression levels of IGF-1 and IGFBP-1 were measured. A significant increase in IGFBP-1 expression was noted in SAA MSCs despite the wide range of IGF-1 expressions. Accordingly, we postulated a novel pathogenic mechanism of SAA: a compensated increase in the expression of IGF-1 in MSCs to down-regulate TXNIP expression in the face of SAA, which is offset by the up-regulated expression of IGFBP-1. Full article

The current level of knowledge on transcriptome responses triggered by Caesalpinia sappan (CS) extract in porcine peripheral blood mononuclear cells (PBMCs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection is limited. Therefore, in the present study, we aimed to detect significant genes and pathways involved in CS extract supplementation responsiveness of PBMCs after PRRSV infection. RNA sequencing was conducted on PBMCs, which were isolated from six weaned piglets. The resultant transcriptional responses were examined by mRNA sequencing. Differential expression analysis identified 263 and 274 differentially expressed genes (DEGs) between the PRRSV and CTRL groups, and the PRRSV+CS and CTRL groups, respectively. Among these, ZNF646 and KAT5 emerged as the most promising candidate genes, potentially influencing the interaction between PRRSV-infected PBMCs and CS extract supplementation through the regulation of gene networks and cellular homeostasis during stress. Two pathways were detected to be associated with CS extract supplementation responsiveness: the cellular response to stress pathway and the NF-kB signaling pathway. Consequently, our study reveals a novel mechanism underlying cellular stress response and the NF-κB signaling pathway in PRRSV-infected PBMCs, and identifies a potential application of CS extract for activating the NF-κB signaling pathway. In conclusion, by supplementing CS extract in PBMC cells infected with PRRSV, we found that CS extract modulates PRRSV infection by inducing cellular stress, which is regulated by the NF-κB signaling pathway. This induced stress creates an adverse environment for PRRSV survival. This study contributes to a deeper understanding of the therapeutic targets and pathogenesis of PRRSV infection. Importantly, our results demonstrate that CS extract has the potential to be a candidate for modulating PRRSV infection. Full article

Nitrogen and sulfur are essential macronutrients in plant growth and development, and their interaction profoundly influences gene expression, metabolic activities, and adaptability in plants, directly affecting plant growth and yield. Garlic (Allium sativum L.) is a crop of significant economic and medicinal value. However, despite the critical role of the nitrogen–sulfur interaction in garlic’s adaptability, yield, and quality, the specific mechanisms underlying these effects remain unclear. In this study, transcriptomic and metabolomic analyses were employed to investigate the effects of combined sulfur and nitrogen application on garlic bulb tissues. The results show that the combined application of sulfur and nitrogen significantly increased the diameter and weight of garlic bulbs by 14.96% and 35.47%, respectively. The content of alliin increased by 28.48%, while the levels of abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and gibberellin (GA) increased by 15.82%, 12.94%, 32.34%, and 48.13%, respectively. Additionally, the activities of alliinase, superoxide dismutase (SOD), and catalase (CAT) were enhanced by 7.93%, 4.48%, and 19.74%, respectively. Moreover, the application of sulfur and nitrogen significantly reduced the malondialdehyde (MDA) content and peroxidase (POD) activity in garlic bulbs by 29.66% and 9.42%, respectively, thereby improving garlic’s adaptability and growth potential. Transcriptomic analysis revealed differentially expressed genes in several key pathways, including plant hormone signal transduction, RNA degradation, glutathione metabolism, amino acid biosynthesis, and glycerophospholipid metabolism. Metabolomic analysis identified 80 differentially abundant metabolites primarily consisting of amino acids, indole carboxylic acids, and fatty acids. The integrated transcriptomic and metabolomic analyses highlighted the pivotal roles of glutathione metabolism, glycerophospholipid metabolism, and amino acid biosynthesis pathways in the synergistic effects of sulfur and nitrogen. This study not only provides critical scientific evidence for understanding the mechanisms underlying the nitrogen–sulfur interaction’s impact on the yield and quality of garlic but also offers a scientific basis for optimizing nutrient management strategies to enhance garlic yield and quality. Full article

Newcastle disease virus (NDV), known as avian paramyxovirus-1, poses a significant threat to poultry production worldwide. Vaccination currently stands as the most effective strategy for Newcastle disease control. However, the mesogenic vaccine strain Mukteswar has been observed to evolve into a velogenic variant JS/7/05/Ch during poultry immunization. Here, we aimed to explore the mechanisms underlying virulence enhancement of the two viruses. Pathogenically, JS/7/05/Ch mediated stronger virulence and pathogenicity in vivo compared to Mukteswar. Comparative transcriptome analysis revealed 834 differentially expressed genes (DEGs), comprising 339 up-regulated and 495 down-regulated genes, in the spleen, and 716 DEGs, with 313 up-regulated and 403 down-regulated genes, in the thymus. Gene Ontology (GO) analysis indicated that these candidate targets primarily participated in cell and biological development, extracellular part and membrane composition, as well as receptor and binding activity. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis unveiled a substantial portion of candidate genes predominantly involved in cellular processes, environmental information processing, metabolism, and organismal systems. Additionally, five DEGs (TRAT1, JUP, LPAR4, CYB561A3, and CXCR5) were randomly identified through RNA-seq analysis and subsequently confirmed via quantitative real-time polymerase chain reaction (qRT-PCR). The findings revealed a marked up-regulation in the expression levels of these DEGs induced by JS/7/05/Ch compared to Mukteswar, with CYB561A3 and CXCR5 exhibiting significant increases. The findings corroborated the sequencing accuracy, offering promising research directions. Taken together, we comprehensively evaluated transcriptomic alterations in chicken immune organs infected by NDV strains of diverse virulence. This study establishes a basis and direction for NDV virulence research. Full article

Maize (Zea mays L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeq^TM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions. Full article