Search Results (60,568)

Rapeseed (Brassica napus L.) is an important crop for healthy edible oil and stockfeed worldwide. However, its growth and yield are severely hampered by black rot, a destructive disease caused by Xanthomonas campestris pv. campestris (Xcc). Despite the identification of several quantitative trait loci (QTLs) associated with resistance to black rot in Brassica crops, the underlying molecular mechanisms remain largely unexplored. In this study, we investigated Xcc-induced transcriptomic and metabolic changes in the leaves of two rapeseed varieties: Westar (susceptible) and ZS5 (resistant). Our findings indicated that Xcc infection elicited more pronounced overall transcriptomic and metabolic changes in Westar compared to ZS5. Transcriptomic analyses revealed that the phenylpropanoid biosynthesis, cutin, suberine and wax biosynthesis, tryptophan metabolism, and phenylalanine metabolism were enriched in both varieties. Notably, photosynthesis was down-regulated in Westar after infection, whereas this down-regulation occurred at a later stage in ZS5. Integrated analyses of transcriptome and metabolome revealed that the tryptophan metabolism pathway was enriched in both varieties. Indolic glucosinolates and indole-3-acetic acid (IAA) are two metabolites derived from tryptophan. The expression of genes involved in the indolic glucosinolate pathway and the levels of indolic glucosinolates were significantly elevated in both varieties post-infection. Additionally, exogenous application of IAA promoted the development of black rot, whereas the use of an IAA synthesis inhibitor attenuated black rot development in both resistant and susceptible rapeseed varieties. These findings provide valuable molecular insights into the interactions between rapeseed and Xcc, facilitating the advancement of black rot resistance breeding in Brassica crops. Full article

Iron stress adversely impacts plants’ growth and development. Transcription factors (TFs) receive stress signals and modulate plant tolerance by influencing the expression of related functional genes. In the present study, we investigated the role of an apple bHLH transcription factor MxbHLH30 in the tolerance to iron stresses. The expression of MxbHLH30 was induced significantly by low-iron and high-iron treatments and MxbHLH30-overexpressed Arabidopsis plants displayed iron-stress-tolerant phenotypes. A determination of physiological and biochemical indexes associated with abiotic stress responses showed that overexpression of MxbHLH30 increased the activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in Arabidopsis plants treated with iron stress, and decreased the contents of H₂O₂ and malondialdehyde (MDA), which contribute to reduce cell membrane lipid peroxidation. Meanwhile, the accumulation of proline in transgenic plant cells increased, regulating cell osmotic pressure. Furthermore, quantitative expression analysis indicated that overexpression of MxbHLH30 improved the expression levels of positive functional genes’ responses to iron stress, improving plant resistance. Interestingly, MxbHLH30 may have the ability to balance the homeostasis of iron and other metal ions for the iron homeostasis of Arabidopsis cell under low-iron environments. This research demonstrates that MxbHLH30 is a key regulator of cell iron homeostasis in Arabidopsis plants under iron deficiency, providing new knowledge for plant resistance regulation. Full article

Parasitoid elimination in Drosophila melanogaster involves special hemocytes, called lamellocytes, which encapsulate the eggs or larvae of the parasitoid wasps. The capsules are melanized, and metabolites of the melanization reaction may play a potential role in parasitoid killing. We have observed a variation in the melanization capacity of different, commonly used D. melanogaster strains, such as Canton-S, Oregon-R, and BL5905, BL6326. In this work, we aimed to clarify a possible connection between the effectiveness of capsule melanization and the success of parasitoid elimination following infection with Leptopilina parasitoid wasps. Circulating hemocytes and lamellocyte attachment were visualized by confocal and epifluorescence microscopy using indirect immunofluorescence. Expression profiles of the PPO2 and PPO3 prophenoloxidase genes, which encode key enzymes in the melanization reaction, were detected by qRT-PCR. Parasitization assays were used to analyze fly and wasp eclosion success. Active encapsulation and melanization reactions against Leptopilina boulardi were observed in the BL5905 and the BL6326 strains, though restricted to the dead supernumerary parasitoids, while fly and wasp eclosion rates were essentially the same in the four examined D. melanogaster strains. We conclude that encapsulation and melanization carried out by D. melanogaster following L. boulardi infection have no impact on survival. Full article

This study investigates the role of NIK in activating specific inflammatory genes in macrophages, focusing on the effect of a mutation in NIK found in alymphoplasia (aly/aly) mice. Mouse peritoneal macrophages from aly/aly mice showed a severe defect in the production of some pro-inflammatory cytokines, such as IL-12. This effect seemed to take place at the transcriptional level, as shown by the reduced transcription of Il12b and Il12a in aly/aly macrophages after exposure to the TLR4 agonist LPS. Immunoprecipitation studies showed that the binding of NIK to c-Rel was not efficient in RAW 264.7 cells over-expressing the aly/aly mutation. In addition, the shuttling of c-Rel to the nucleus was shown to be impaired in aly/aly macrophages in response to LPS. When looking more specifically at the regulation of the Il12b promoter, we found that c-Rel bound to the NF-kB consensus sequence in macrophages from WT mice 1 hr. after LPS challenge, whereas in aly/aly macrophages, the transcription factor bound to the promoter was p65. These findings indicate that NIK is essential for efficient c-Rel activation and proper inflammatory responses. NIK dysfunction could lead to weakened immune responses, and targeting this pathway may help in developing therapies for immune-related conditions. Full article

Objectives: The downregulation of anti-adhesive regulatory proteins and upregulation of adhesive genes are critical for the receptive endometrium. This study was designed to determine whether switching between the anti-adhesive podocalyxin (PDX) and adhesive HOXA10 receptivity modulator occurs in the endometrium of women with recurrent implantation failure (RIF). Methods: Twenty-four patients with RIF who could not conceive for three or more cycles despite good-quality embryo transfer constituted the study group. Twenty-four patients with unexplained infertility (UEI) matched for age, BMI, and infertility duration were included in the control group. Twenty women scheduled to undergo intrauterine device (IUD) placement for birth control were included in the comparative group. Endometrial tissue was collected from patients with RIF and UEI during egg retrieval after ovarian stimulation using the GnRH antagonist protocol. In the fertile group, endometrial tissues were collected during IUD insertion. HOXA10 mRNA expression was analyzed by qRT-PCR and PDX protein expression was analyzed by ELISA. The relative expression of endometrial HOXA10 mRNA was calculated using the 2^−ΔΔCt equation. Results: The relative expression of HOXA10 mRNA in the RIF group was significantly lower than that in the UEI group (p < 0.001). HOXA10 mRNA expression in the fertile group was significantly higher than that in the RIF group and was similar to that in the UEI group. PDX expression in the RIF group was significantly higher than that in the UEI group (p < 0.001). PDX expression in the fertile group was significantly lower than in the RIF and UEI groups. A negative correlation was detected between the anti-adhesive PDX protein and adhesive HOXA10 (r = −0.797, p < 0.001). Although there was a positive correlation between endometrial thickness recorded on the day of hCG administration and HOXA10 (r = 0.590, p < 0.01), endometrial thickness was negatively correlated with PDX (r = −0.529, p < 0.01). Conclusions: The failed physiological downregulation of the anti-adhesive PDX protein in patients with RIF prevented the upregulation of adhesive HOXA10 mRNA. Full article

Triple-negative breast cancer (TNBC) remains a challenging subtype due to its aggressive nature and limited treatment options. This study investigated the potential synergistic effects of Korean mistletoe lectin (Viscum album L. var. coloratum agglutinin, VCA) and cisplatin on MDA-MB-231 TNBC cells using both 2D and 3D culture models. In 2D cultures, the combination of VCA and cisplatin synergistically inhibited cell proliferation, induced apoptosis, and arrested the cell cycle at the G2/M phase. Also, the combination treatment significantly reduced cell migration and invasion. Gene expression analysis showed significant changes in specific genes related to apoptosis (Bax, Bcl-2), metastasis (MMP-2, MMP-9), and EMT (E-cadherin, N-cadherin). Three-dimensional spheroid models corroborated these findings, demonstrating enhanced cytotoxicity and reduced invasion with the combination treatment. Significantly, the 3D models exhibited differential drug sensitivity compared to 2D cultures, emphasizing the importance of utilizing physiologically relevant models in preclinical studies. The combination treatment also reduced the expression of angiogenesis-related factors VEGF-A and HIF-1α. This comprehensive study provides substantial evidence for the potential of VCA and cisplatin combination therapy in TNBC treatment and underscores the significance of integrating 2D and 3D models in preclinical cancer research. Full article

Viperin is an interferon-stimulated gene (ISG) that plays an important role in the congenital antiviral immunity of vertebrates. In this study, the common carp viperin (cc-viperin) gene is characterized, and we determine whether it has the ability to inhibit spring viremia of carp virus (SVCV) replication in EPC cells. The results showed that the full-length cDNA of the cc-viperin gene was 1044 bp and it encoded 348 amino acids. The cc-viperin sequence contained a leucine zipper in the N-terminal, a CxxxCxxC motif in the SAM domain, and a conservative C-terminus. The cc-viperin gene’s nucleotide and amino acid sequence alignment revealed that cc-viperin displayed relatively high sequence identity compared with other species. Phylogenetic analysis displayed the close relation of cc-viperin with Carassius auratus and Mylopharyngodon piceus. Subcellular localization analysis indicated that the cc-viperin protein was located in the cytoplasm. The gene expression results showed that cc-viperin was expressed in all of the tissues tested. Its expression level significantly increased in EPC cells after 24 h to 72 h compared to the control during SVCV infection. Moreover, cc-viperin significantly inhibited SVCV replication when it was overexpressed, whereas it increased SVCV replication when it had reduced expression in EPC cells, respectively. To summarize, the results obtained in this work show that cc-viperin shares similar sequence characteristics with other vertebrates, and it could inhibit SVCV replication in EPC cells, displaying an antiviral effect in common carp. Full article

There are numerous ways of portraying cancer complexity based on combining multiple types of data. A common approach involves developing signatures from gene expression profiles to highlight a few key reproducible features that provide insight into cancer risk, progression, or recurrence. Normally, a selection of such features is made through relevance or significance, given a reference context. In the case of highly metastatic cancers, numerous gene signatures have been published with varying levels of validation. Then, integrating the signatures could potentially lead to a more comprehensive view of the connection between cancer and its phenotypes by covering annotations not fully explored in individual studies. This broader understanding of disease phenotypes would improve the predictive accuracy of statistical models used to identify meaningful associations. We present an example of this approach by reconciling a great number of published signatures into meta-signatures relevant to Osteosarcoma (OS) metastasis. We generate a well-annotated and interpretable interactome network from integrated OS gene expression signatures and identify key nodes that regulate essential aspects of metastasis. While the connected signatures link diverse prognostic measurements for OS, the proposed approach is applicable to any type of cancer. Full article

Single-cell RNA sequencing (scRNA-seq) is a cutting-edge technique in molecular biology and genomics, revealing the cellular heterogeneity. However, scRNA-seq data often suffer from dropout events, meaning that certain genes exhibit very low or even zero expression levels due to technical limitations. Existing imputation methods for dropout events lack comprehensive evaluations in downstream analyses and do not demonstrate robustness across various scenarios. In response to this challenge, we propose a consensus clustering-based imputation (CCI) method. CCI performs clustering on each subset of data sampling across genes and summarizes clustering outcomes to define cellular similarities. CCI leverages the information from similar cells and employs the similarities to impute gene expression levels. Our comprehensive evaluations demonstrate that CCI not only reconstructs the original data pattern, but also improves the performance of downstream analyses. CCI outperforms existing methods for data imputation under different scenarios, exhibiting accuracy, robustness, and generalization. Full article

A circadian clock (CC) has evolved in plants that synchronizes their growth and development with daily and seasonal cycles. A properly functioning circadian clock contributes to increasing plant growth, reproduction, and competitiveness. In plants, continuous light treatment has been a successful approach for obtaining novel knowledge about the circadian clock. The olive tree (Olea europaea L.) is one of the most important crops in the Mediterranean area, and, so far, limited information is available on its CC gene network. Here, we studied the behavior of circadian rhythm genes under LD (light/darkness) and LL (light/light) conditions, the relationships in this network, and the ability of the treatments to modulate gene expression in the photoprotective pigment and lipid biosynthesis pathways. One month of LL conditions increased olive growth performance, but LL exposure also caused reductions in vegetative growth and chlorophyll accumulation. A panel was designed for a study of the transcription expression levels of the genes involved in light perception, the CC, and secondary metabolite and fatty acid biosynthesis. Our results revealed that the levels of 78% of the transcripts exhibited intraday differences under LD conditions, and most of them retained this rhythmicity after exposure to one and two months of LL conditions. Furthermore, co-regulation within a complex network among genes of photoreceptors, anthocyanidins, and fatty acids biosynthesis was orchestrated by the transcription factor HY5. This research enriches our knowledge on olive trees grown under prolonged irradiation, which may be attractive for the scientific community involved in breeding programs for the improvement of this species. Full article

Light is a vital regulator of photosynthesis, energy production, plant growth, and morphogenesis. Although these key physiological processes are well understood, the effects of light quality on the pigment content, oxidative stress, reactive oxygen species (ROS) production, antioxidant defense systems, and biomass yield of plants remain largely unexplored. In this study, we applied different light-emitting diode (LED) treatments, including white light, red light, blue light, and a red+blue (1:1) light combination, to evaluate the traits mentioned above in alfalfa (Medicago sativa L.). Fluorescence staining showed that red light significantly triggered the oxidative stress indicators compared to blue and white light, while the combined red and blue light treatment significantly reduced the ROS (O₂^•−, H₂O₂) intensity in alfalfa seedlings. Interestingly, the combined light treatment significantly boosted the seed germination rate (%), maximum photochemical quantum yield of PSII (Fv/Fm), leaf greenness (SPAD score), photosynthetic pigment levels (chlorophyll a, chlorophyll b, and carotenoids), and plant biomass yield in alfalfa seedlings. The red and/or combined (red+blue) light treatments significantly regulated antioxidant enzymes (SOD, CAT, APX, and GR) and the expression of genes related to the ascorbate–glutathione (AsA-GSH) pathway, including monodehydroascorbate reductase (MsMDHAR), dehydroascorbate reductase (MsDHAR), ascorbate peroxidase (MsAPX), and glutathione reductase (MsGR). These results indicate that light quality is crucial for regulating the morphological, physiological, and molecular traits linked to alfalfa improvement. These findings suggest a new approach to enhancing the adaptation, as well as the morphological and agronomic yield, of alfalfa and forage legumes through light-quality-mediated improvement. Full article

The Really Interesting New Gene (RING) E3 ubiquitin ligases represent the largest class of E3 ubiquitin ligases involved in protein degradation and play a pivotal role in plant growth, development, and environmental responses. Despite extensive studies in numerous plant species, the functions of RING E3 ligases in cotton remain largely unknown. In this study, we performed systematic identification, characterization, and expression analysis of RING genes in cotton. A total of 514, 509, and 914 RING genes were identified in Gossypium arboretum, G. raimondii, and G. hirsutum, respectively. Duplication analysis indicates that segmental duplication may be the primary mechanism responsible for the expansion of the cotton RING gene family. Moreover, the Ka/Ks analysis suggests that these duplicated genes have undergone purifying selection throughout the evolutionary history of cotton. Notably, 393 G. hirsutum RING genes exhibited differential expression in response to salt stress. The overexpression of the specific C3H2C3 RING gene, GhZFRG1, in Arabidopsis resulted in enhanced tolerance to salt stress. This study contributes to our understanding of the evolution of cotton RING ligases and paves the way for further functional analysis of the RING E3 ligase genes in cotton. Full article

Late embryonic developmental abundant (LEA) genes play a crucial role in the response to abiotic stress and are important target genes for research on plant stress tolerance mechanisms. Acer truncatum Bunge is a promising candidate tree species for investigating the tolerance mechanism of woody plants against abiotic stress. In our previous study, AtruLEA1 was identified as being associated with seed drought tolerance. In this study, LEA1 was cloned from A. truncatum Bunge and functionally characterized. AtruLEA1 encodes an LEA protein and is located in the nucleus. Phylogenetic tree analysis revealed a recent affinity of the AtruLEA1 protein to AT3G15760.1. Overexpression of AtruLEA1 resulted in enhanced tolerance of Arabidopsis thaliana to drought and salt stress and heightened the ABA sensitivity. Compared to wild-type (WT) plants, plants with overexpressed AtruLEA1 exhibited increased activities of antioxidant enzymes under drought stress. Meanwhile, the ROS level of transgenic Arabidopsis was significantly less than that of the WT. Additionally, the stoma density and stoma openness of AtruLEA1 Arabidopsis were higher compared to those in the WT Arabidopsis under salt and drought stress conditions, which ensures that the biomass and relative water content of transgenic Arabidopsis are significantly better than those of the WT. These results indicated that AtruLEA1 was involved in salt and drought stress tolerances by maintaining ROS homeostasis, and its expression was positively regulated by abiotic stress. These results indicate a positive role of AtruLEA1 in drought and salt stress and provide theoretical evidence in the direction of cultivating resistant plants. Full article

Microplastic exposure has become unavoidable, leading to their presence in living organisms. One area of particular concern is the genotoxicity of microplastics, which has implications for reproductive health and cancer development. This review aims to highlight the genotoxic effects of microplastics on different organisms, focusing on their impacts on chromosomes, DNA, and gene expression. More than 85 papers, primarily published in the last five years, have been reviewed. This review indicates that microplastics can cause clastogenesis and aneugenesis at the chromosome level. Clastogenesis results in chromosome damage, while aneugenesis leads to failures in chromosome segregation without causing direct damage. Additionally, microplastics can fracture and damage DNA. These effects arise from (1) the direct genotoxicity of microplastics through interactions with chromosomes, DNA, and associated proteins; and (2) their indirect genotoxicity due to the production of reactive oxygen species (ROS) by oxidative stress induced by microplastics. Microplastics can trigger the activation of genes related to oxidative stress and the inflammatory response, leading to increased ROS production. Furthermore, they may alter gene expression in other biological processes. The genotoxicity linked to microplastics can stem from the particles themselves and their associated chemicals, and it appears to be both size- and dose-dependent. Full article

Microplastics (MPs) in fish can cross the intestinal barrier and are often bioaccumulated in several tissues, causing adverse effects. While the impacts of MPs on fish are well documented, the mechanisms of their cellular internalization remain unclear. A rainbow-trout (Oncorhynchus mykiss) intestinal platform, comprising proximal and distal intestinal epithelial cells cultured on an Alvetex scaffold, was exposed to 50 mg/L of MPs (size 1–5 µm) for 2, 4, and 6 h. MP uptake was faster in RTpi-MI compared to RTdi-MI. Exposure to microplastics compromised the cellular barrier integrity by disrupting the tight-junction protein zonula occludens-1, inducing significant decreases in the transepithelial-electrical-resistance (TEER) values. Consequently, MPs were internalized by cultured epithelial cells and fibroblasts. The expression of genes related to endocytosis (cltca, cav1), macropinocytosis (rac1), and tight junctions’ formation (oclna, cldn3a, ZO-1) was analyzed. No significant differences were observed in cltca, oclna, and cldn3a expression, while an upregulation of cav1, rac1, and ZO-1 genes was detected, suggesting macropinocytosis as the route of internalization, since also cav1 and ZO-1 are indirectly related to this mechanism. The obtained results are consistent with data previously reported in vivo, confirming its validity for identifying MP internalization pathways. This could help to develop strategies to mitigate MP absorption through ingestion. Full article