Gene Expression Patterns Research Articles

Genome-Wide Identification of the Oxidative Stress 3 (OXS3) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton

Oxidative Stress 3 (OXS3) encodes a plant-specific protein that makes great contributions to a plant’s stress tolerance. However, reports on genome-wide identification and expression pattern analyses of OXS3 were only found for Arabidopsis, wheat, and rice. The genus Gossypium (cotton) serves as an ideal model for studying allopolyploidy. Therefore, two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study for a bioinformatics analysis, resulting in 12, 12, 22, and 23 OXS3 members, respectively. A phylogenetic tree was constructed using 69 cotton OXS3 genes alongside 8 Arabidopsis, 10 rice, and 9 wheat genes, which were classified into three groups (Group 1–3). A consistent evolutionary relationship with the phylogenetic tree was observed in our structural analysis of the cotton OXS3 genes and the clustering of six conserved motifs. Gene duplication analysis across the four representative Gossypium species suggested that whole-genome duplication, segmental duplication, and tandem duplication might play significant roles in the expansion of the OXS3 gene family. Some existing elements responsive to salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) were identified by cis-regulatory element analysis in the promoter regions, which could influence the expression levels of cotton OXS3 genes. Furthermore, the expression patterns of the GhOXS3 gene were examined in different tissues or organs, as well as in developing ovules and fibers, with the highest expression observed in ovules. GhOXS3 genes exhibited a more pronounced regulatory response to abiotic stresses, of which ten GhOXS3 genes showed similar expression patterns under cold, heat, salt, and drought treatments. These observations were verified by quantitative real-time PCR experiments. These findings enhance our understanding of the evolutionary relationships and expression patterns of the OXS3 gene family and provide valuable insights for the identification of vital candidate genes for trait improvement in cotton breeding.

Short-Term Exposure to 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine Induces Colonic Energy Metabolism Disorders in Rats.

2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is one of the most abundant heterocyclic aromatic amines generated in thermally processed meat products, and the toxicities of its short-term exposure in the intestines remain unclear. This study aimed to elucidate the short-term PhIP toxicity in colons through administering PhIP orally to rats for 4 weeks. The results indicated that short-term PhIP exposure induced colonic oxidative stress, a significant decrease of serum triglyceride, and a disrupted colonic gene expression pattern associated with mitochondrial electron transport chain and energy metabolism. Thirteen energy metabolites, including lactate and d-erythrose-4-phosphate, showed significant changes under short-term PhIP effects. Energy metabolism pathway analysis revealed that PhIP-induced colonic energy metabolism disorders are characterized by inhibited glycolysis and enhanced tricarboxylic acid cycle. Further investigation found that PhIP altered the energy metabolic phenotype of colon epithelial cells to increase aerobic respiration. In summary, our study provides new insights into the colon toxicity induced by a short-term PhIP exposure.

Insulin Resistance Is a Modifying Factor for Parkinson's Disease.

Parkinson's disease (PD) is the second most common, and the fastest-growing neurodegenerative disorder with unclear etiology in most cases. Therefore, the identification of non-genetic risk factors for PD pathology is crucial to develop effective preventative or therapeutic strategies. An increasing number of evidence suggests that central insulin resistance might have an essential role in PD pathology. Nevertheless, it is not clear whether insulin resistance arises from external factors/lifestyle, comorbidities such as type 2 diabetes or it can occur in a PD patient's brain independently from peripheral insulin resistance. We aimed to investigate insulin resistance and its role in GBA1mutation-associated PD pathogenesis and phenotype severity. Midbrain organoids, generated from induced pluripotent stem cells (iPSCs) of PD patients carrying the GBA1-N370S heterozygous mutation (GBA-PD) and healthy donors, were exposed to different insulin concentrations to modify insulin signaling function. Transcriptomics analysis was performed to explore insulin signaling gene expression patterns in GBA-PD and to find a potential target for GBA-PD-associated phenotype rescue. The insulin signaling pathway genes show dysregulation in GBA-PD. Particularly, we highlight that a knockdown of FOXO1 mitigates the loss of dopaminergic neurons and cellular death in GBA-PD. Additionally, our findings suggest a promising therapeutic potential of the anti-diabetic drug Pioglitazone in decreasing dopaminergic neuron loss associated with GBA-PD. Local insulin signaling dysfunction plays a substantial role in GBA-PD pathogenesis, exacerbating dopaminergic neuron death. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

The genetically programmed rhythmic alteration of diurnal gene expression in the aged Arabidopsis leaves

The circadian clock regulates the daily pattern of temporal gene expression. In Arabidopsis, aging is associated with a shortening of the endogenous period of circadian rhythms under circadian conditions. However, the functional link between the circadian clock and aging under diurnal conditions and its physiological relevance remain elusive. In this study, we investigate and characterize the effect of aging on the waveforms of rhythmic gene expression patterns under light/dark cycles. Our analysis revealed that the diurnal rhythmic patterns of core clock genes undergo significant rhythmic alteration with phase shift and change of waveforms in aged plants compared to younger plants. Transcriptomic analysis indicated that this age-dependent rhythmic alteration occurs not only in core clock genes but also globally. Due to the rhythmic alteration patterns of the diurnal rhythmic gene expression, aged plants experience subjectively a shorter day and longer night. We also observed that genetic mutants of core clock component genes exhibited broadly yet distinctively altered changes in diurnal rhythmic gene expression patterns as aging progresses. Collectively, our findings support that age-dependent rhythmic alteration of diurnal gene expression rhythms reprograms the timetable of daily gene expression, leading to the physiological changes required for plant senescence.

A powerful and versatile new fixation protocol for immunostaining and in situ hybridization that preserves delicate tissues

BackgroundUnderstanding how genes function to heal wounds and restore lost tissue is essential for studying regeneration. Whole-mount in situ hybridization (WISH) is a powerful and widely used technique to visualize the expression patterns of genes in different biological systems. Yet, existing methods to permeabilize samples for WISH can damage or destroy fragile regenerating tissues, thereby preventing such experiments.ResultsHere, we describe a new protocol for in situ hybridization (ISH) and immunostaining in the highly regenerative planarian Schmidtea mediterranea. This new Nitric Acid/Formic Acid (NAFA) protocol is compatible with both the assays and prevents degradation of the epidermis and regeneration blastema. The NAFA protocol achieves this without the use of proteinase K digestion which likely leads to better preservation of antigen epitopes. We show that the NAFA protocol successfully permits development of chromogenic and fluorescent signals in situ, while preserving the anatomy of the animal. Furthermore, the immunostaining of different proteins was compatible with the NAFA protocol following fluorescent in situ hybridization. Additionally, the tissue fixation protocol was easily adapted for regenerating killifish tail fin, which yielded better ISH signal with minimal background.ConclusionsThus, the NAFA protocol robustly preserves the delicate wounded tissues while also facilitating probe and antibody penetration into internal tissues. Furthermore, the fixation protocol is compatible for WISH on regenerating teleost fins suggesting that it will be a valuable technique for studying the processes of wounding response and regeneration in multiple species.

Identification of Sequential Molecular Mechanisms and Key Biomarkers in Early Glaucoma by Integrated Bioinformatics Analysis.

Glaucoma is a neurodegenerative disease characterized by progressive optic nerve degeneration and retinal ganglion cell (RGC) loss. In early glaucoma, before obvious axon loss, highly organized pathological processes in RGCs occur sequentially, involving axons, dendrites and synaptic terminals. The optic nerve head (ONH) is the critical structure of early glaucomatous neurodegeneration. Taking advantage of high-throughput data from the ONH and the weighted gene coexpression network analysis (WGCNA) method, the current study aims to gain insight into the full scope of pathological events in early glaucoma and define their chronological sequence. The expression profiles of GSE26299, GSE110019, and GSE139605, which measure ONH gene expression in different glaucoma models, were downloaded from the Gene Expression Omnibus (GEO) database. In GSE26299, which uses 10.5-month-old DBA/2J mice, WGCNA was utilized to construct a gene coexpression network, and the most significant modules of early (NOE), moderate (MOD) and severe (SEV) glaucoma were identified. The differentially expressed genes (DEGs) of GSE110019 and GSE139605 significantly overlapped with the correlated module of the MOD group, so the 3 gene sets were analyzed together. Pathway enrichment analysis via the GO, KEGG, and Reactome pathways was subsequently performed, followed by protein‒protein interaction (PPI) analysis to screen key genes associated with each stage. Several hub gene expression patterns were identified in a glucocorticoid-induced glaucoma (GIG) model via quantitative PCR and immunostaining. The pink module was positively correlated with the NOE group (r = 0.48, p = 4e-04) and negatively correlated with the glaucoma stage (r = -0.88, p = 3e-17). The genes in the pink module were enriched in the synaptic transmission and axonal transport pathways. The tan module was negatively correlated with the NOE group (r = -0.43, p = 0.002) and positively correlated with the glaucoma stage (r = 0.77, p = 7e-11). The genes in the tan module were associated with pathways such as tight junctions, retinol metabolism, and linoleic acid metabolism. The purple module was positively correlated with the MOD group (r = 0.64, p = 5e-07). The common genes among the purple module and the DEGs of the two other datasets were enriched in pathways related to mitotic cell division, cytokine activity, and the extracellular matrix (ECM). The hub genes identified by PPI included Nrn1, Cplx1, Timp1, and Cdk1. Quantitative PCR and immunostaining confirmed that Limk1 expression was increased in the ONH of GIG mice. In early glaucomatous neuropathy, intrinsic changes in RGCs precede the activation of glial cells and ECM remodeling. These latter events are common pathological changes observed in the ONH in both cats and mice. Our study may provide new targets for the early detection and treatment of glaucoma.

Exploring genotypic variation and gene expression associated to cadmium accumulation in bread wheat

Cadmium (Cd) contamination poses significant risks to agricultural productivity and human health, particularly through its accumulation in staple crops such as bread wheat (Triticum aestivum L.). This study evaluated Cd accumulation and tolerance among six bread wheat cultivars exposed to six Cd concentrations (0, 2.5, 5, 10, 15, 20, and 25 mg kg−1 soil). Phenotypic assessments and quantitative real-time PCR (qRT-PCR) were conducted to analyze the expression patterns of TaNRAMP and TaZIP genes in various tissues and developmental stages of wheat, which play crucial roles in Cd uptake and transport. Results demonstrated significant variability in Cd accumulation. The Barat cultivar exhibited the lowest accumulation in grain (ranging from 0.21 to 8.8 mg kg−1) and the highest tolerance. In contrast, Kavir and Pishtaz displayed elevated Cd levels in both grain and straw, while Parsi accumulated more Cd in straw at lower concentrations (56.9 mg kg−1 in Cd concentration of 10 mg kg−1 soil). The gene expression analysis revealed that most cultivars showed increased expression of TaNRAMP genes, particularly TaNRAMP2 in Cd concentration of 10 mg kg−1 soil, which facilitates Cd uptake from the soil, and TaZIP genes, such as TaZIP4 and TaZIP7, involved in transporting Cd within the plant. Notably, the expression of TaZIP1 was significantly lower in cultivars with high Cd accumulation, suggesting a potential regulatory mechanism for Cd tolerance. Furthermore, cultivars exhibiting higher Cd levels correlated with increased expression of stress-responsive genes, indicating a broader response to Cd stress. These findings highlight Barat’s potential for bread-making applications due to its low Cd accumulation, while Morvarid and Pishtaz which show reduced Cd content in the straw even under high Cd exposure are better suited for animal feed. This research underscores the genetic variability of wheat cultivars in response to Cd stress and provides essential insights into the molecular mechanisms underlying Cd accumulation, offering valuable information for breeding programs aimed at developing Cd-tolerant varieties to ensure food security in contaminated regions.

Origin, Evolution, and Diversification of the Expansin Family in Plants.

The cell wall is a crucial feature that allows ancestral streptophyte green algae to colonize land. Expansin, an extracellular protein that mediates cell wall loosening in a pH-dependent manner, could be a powerful tool for studying cell wall evolution. However, the evolutionary trajectory of the expansin family remains largely unknown. Here, we conducted a comprehensive identification of 2461 expansins across 64 sequenced species, ranging from aquatic algae to terrestrial plants. Expansins originated in chlorophyte algae and may have conferred the ability to loosen cell walls. The four expansin subfamilies originated independently: α-expansin appeared first, followed by β-expansin, and then expansin-like A and expansin-like B, reflecting the evolutionary complexity of plant expansins. Whole genome duplication/segmental duplication and tandem duplication events greatly contributed to expanding the expansin family. Despite notable changes in sequence characteristics, the intron distribution pattern remained relatively conserved among different subfamilies. Phylogenetic analysis divided all the expansins into five clades, with genes from the same subfamily tending to cluster together. Transcriptome data from 16 species across ten lineages and qRT-PCR analysis revealed varying expression patterns of expansin genes, suggesting functional conservation and diversification during evolution. This study enhances our understanding of the evolutionary conservation and dynamics of the expansin family in plants, providing insight into their roles as cell wall-loosening factors.

Development of a New Personalized Molecular Test Based on Endometrial Receptivity and Maternal-Fetal Dialogue: Adhesio.

Successful embryo implantation relies on a receptive endometrium and a maternofetal dialogue. Abnormal receptivity is a common cause of implantation failure in assisted reproductive techniques. This study aimed to develop a novel transcriptomic-based diagnostic assay, Adhesio, for assessing endometrial receptivity and guiding personalized embryo transfer. Adhesio was developed based on an initial dataset of 74 endometrial biopsies. Two types of biopsy samples were involved: 45 endometrial biopsies collected during the optimal theoretical window of implantation (WOI) and 29 endometrial biopsies which cells have been cultured with or without an autologous embryo. Microarray analysis was performed to identify differentially expressed genes associated with endometrial receptivity and selected candidate genes were assessed using quantitative real-time polymerase chain reaction (RT-qPCR) on biopsy samples. Statistical analyses were conducted to assess the performance and accuracy of Adhesio. The microarray analysis identified three distinct clusters of endometrial samples with differential gene expression patterns. Cluster 1 exhibited 1717 differentially expressed genes involved in biological processes associated with endometrial receptivity. A specific transcriptomic signature of 60 genes associated with endometrial co-culture was obtained using class prediction approach. Thereafter, an original panel of 10 genes was selected as potential biomarkers for endometrial receptivity based on their expression profiles in both endometrial biopsies and co-cultured cells. This article outlines the methodology employed to develop Adhesio, a test that assesses endometrial receptivity using an original panel of 10 genes. These genes are not only involved during the WOI but are also influenced by the maternal-fetal dialogue.

Tracing ALS Degeneration: Insights from Spinal Cord and Cortex Transcriptomes

Background/Objectives: Amyotrophic Lateral Sclerosis is a progressive neurodegenerative disorder characterized by the loss of upper and lower motor neurons. Key factors contributing to neuronal death include mitochondrial energy damage, oxidative stress, and excitotoxicity. The frontal cortex is crucial for action initiation, planning, and voluntary movements whereas the spinal cord facilitates communication with the brain, walking, and reflexes. By investigating transcriptome data from the frontal cortex and spinal cord, we aim to elucidate common pathological mechanisms and pathways involved in ALS for understanding the disease progression and identifying potential therapeutic targets. Methods: In this study, we quantified gene and transcript expression patterns, predicted variants, and assessed their functional effects using computational tools. It also includes predicting variant-associated regulatory effects, constructing functional interaction networks, and performing a gene enrichment analysis. Results: We found novel genes for the upregulation of immune response, and the downregulation of metabolic-related and defective degradation processes in both the spinal cord and frontal cortex. Additionally, we observed the dysregulation of histone regulation and blood pressure-related genes specifically in the frontal cortex. Conclusions: These results highlight the distinct and shared molecular disruptions in ALS, emphasizing the critical roles of immune response and metabolic dysfunction in neuronal degeneration. Targeting these pathways may provide new therapeutic avenues to combat neurodegeneration and preserve neuronal health.

Multiple NADPH-cytochrome P450 reductases from Lycoris radiata involved in Amaryllidaceae alkaloids biosynthesis.

Amaryllidaceae alkaloids (AAs), such as galanthamine and lycorine, are natural products of Lycoris radiata possessing various pharmacological activities including anti-acetylcholinesterase, anti-inflammatory, and antitumour activities. Elucidating the biosynthesis of these special AAs is crucial for understanding their production and potential modification for improved clinical application, of which cytochrome P450 enzymes catalyse the formation of key alkaloid skeletons and subsequent modification processes, with the NAPDH cytochrome P450 reductases (CPRs) serving as essential redox partners. This study identified three CPRs, LrCPR1, LrCPR2, and LrCPR3, encoding 700, 697 and 695 amino acids, respectively, which belong to Class II CPRs. The LrCPRs reduced cytochrome c and ferricyanide in an NADPH-dependent manner, and their activities all followed the typical Michaelis-Menten curve. In yeast, the co-expression of LrCPRs and CYP96T6 produced the galantamine-like alkaloid namely N-demethylnarwedine, suggesting that they support the catalytic activity of CYP96T6. Quantitative analysis of the transcriptional expression profiles showed that LrCPRs were expressed in all the examined tissues of L. radiata, and their gene expression patterns are consistent with other genes that may be involved in the biosynthetic pathway of AAs, including cinnamate 4-hydroxylase and phenylalanine ammonia-lyase. Our study firstly provides the functional characterization of LrCPRs in L. radiata, which will contribute to the discovery of biosynthetic pathways and heterologous production of AAs.

Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum.

Mammalian spermatogenesis is a highly stereotyped and conserved developmental process that is essential for fitness. At the same time, gene expression in spermatogenic cells is rapidly evolving. This combination of features has been suggested to drive rapid fixation of new gene expression patterns. Using a high-resolution dataset comprising bulk and single-cell data from juvenile and adult testes of the opossum Monodelphis domestica, a model marsupial, we define the developmental timing of the spermatogenic first wave in opossum and delineate conserved and divergent gene expression programs across the placental-marsupial split by comparison to equivalent data from mouse, a model placental mammal. Epigenomic data confirmed divergent regulation at the level of transcription, and comparison to data from four additional amniote species identified hundreds of genes with evidence of rapid fixation of expression. This gene set encompasses known and previously undescribed regulators of spermatogenic development.

Metabolome and transcriptome reveal the biosynthesis of flavonoids and amino acids in Isatis indigotica fruit during development.

Isatis indigotica Fort. is a famous medicinal plant that is also used as a natural dye and functional vegetable. The characteristics of the I. indigotica fruit during development are largely unknown, information that is essential for the exploitation and seedlings cultivation of I. indigotica. In this study, the biochemical, metabolite characteristics and gene expression profiling of I. indigotica at four developmental stages were investigated. A total of 428 metabolites were detected and categorized into 17 categories. High contents of anthocyanins, especially cyanidin 3-glucoside, might contribute to the purple colouration of I. indigotica fruits. Moreover, dozens of flavonoid components, including taxifolin, quercetin, astragalin and isovitexin 2″-O-beta-D-glucoside, and several other active components were also up-regulated in mature fruits. The abundance of antioxidants might endow a significantly stronger antioxidant activity of mature I. indigotica fruits compared to many other reported species. Enrichment analyses revealed that flavonoid and anthocyanin biosynthesis genes were mostly enriched in up-regulated gene sets during fruit development. The up-regulated structural genes, including IiCHS, IiCHI, IiF3H, IiDFR, IiANS, IiFLS, IiUGT, and transcription factors such as IiMYBs, IibHLHs and IiNACs were identified as candidate regulators of flavonoid and anthocyanin biosynthetic pathway. Furthermore, biosynthesis of amino acids was enriched in all pairwise comparisons of metabolites in fruits at four developmental stages. The differential accumulation of amino acids might result from the differentially expressed genes involved in amino acid biosynthesis. Taken together, these findings provide a comprehensive understanding of metabolite profiling and gene expression patterns in I. indigotica fruit during maturity, which is useful for pharmaceutical extractions and seedling cultivation of I. indigotica.

Transcriptional evidence of HPA axis dysregulation in adolescent females: Unique contributions of chronic early-life stressor exposure and maternal depression history

BackgroundDepression risk increases dramatically for adolescent females following the pubertal transition. Although chronic early-life stressor exposure and a maternal history of depression are established risk factors for depression onset in this population, we know little about the biological mechanisms underlying these associations. MethodTo investigate, we examined how chronic early-life stressor exposure and maternal depression history were associated with stress-related gene expression patterns, using a high-risk family design in 48 psychiatrically healthy adolescent females, 20 of whom had a mother with a lifetime history of depression. Lifetime chronic stressor exposure was assessed using the STRAIN and gene expression patterns were estimated using transcriptional profiling of whole blood. ResultsConsistent with hypotheses, we found that adolescent females with greater chronic stressor exposure had higher NR3C1 expression levels compared to those with less chronic stressor exposure. Additionally, youth with a depressed mother had lower levels of FKBP5 expression compared to those without a depressed mother. Levels of FKBP5 expression, in turn, interacted with chronic stressor exposure to predict NR3C1 expression. Specifically, for those with low chronic stressor exposure, levels of FKBP5 and NR3C1 expression were strongly interrelated, whereas for those with high chronic stressor exposure, NR3C1 expression was high regardless of levels of FKBP5 expression. LimitationsThis study was correlational, the sample size was limited, and additional research is needed to elucidate the underlying mechanisms and predict who subsequently develops depression. ConclusionsNotwithstanding these limitations, these data indicate that having low FKBP5 expression, alongside high NR3C1 expression, may be a potential preclinical marker of depression risk in adolescent females that warrants additional investigation.

Water fluxes and nutrient absorption along the midgut of three hemipterans, Mahanarva fimbriolata, Dysdercus peruvianus, and Rhodnius prolixus

Hemiptera Order comprises insect species adapted to different diets regarding water and nutrient content and availability, thus suggesting different combinations of proteins to ensure their absorption. To find out whether hemipterans use the same or distinct set of proteins and whether these differences are related to the phylogeny or the diet, RNAseq analyses were conducted in gut sections of three hemipterans, M. fimbriolata, D. peruvianus, and R. prolixus, with remarkable distinct diet. Since only a few of the selected proteins were functionally characterized, the coded putative proteins were manually curated by bioinformatics to infer their physiological function. The results suggest a relationship between gene expression patterns and water and nutrient dietary content and availability. In contrast, putative gene expansions and deletions are related to phylogeny, corresponding to evolutionary adaptations of ancestral forms to feed on xylem, cotton seeds, and blood, resulting in more resemblances between D. peruvianus and R. prolixus than M. fimbriolata. M. fimbriolata absorbs water through aquaporins Drip and Prip in the filtration chamber by passive diffusion, with a higher contribution of water-selective Drip. D. peruvianus water absorption involves Drip and Prip, but Prip contribution appears to be higher, and they probably cooperate with water-ion cotransporters in the posterior midgut. R. prolixus absorbs water in the anterior midgut involving a sodium transporter and a putative water-urea Prip. Sugars, amino acids, and lipids might be absorbed along the midgut in the three species, with a higher contribution of the posterior midgut for amino acid and lipid absorption in M. fimbriolata and D. peruvianus and the middle midgut in R. prolixus.

Inoculation with multifunctional Bacillus sp. NEAU-DCB1-2 mitigates chromium toxicity in pakchoi (Brassica rapa ssp. chinensis) through a multi-level mechanism

Soil chromium (Cr) accumulation is escalating, severely hindering plant growth and development. Plant growth-promoting bacteria (PGPB) have shown potential in enhancing plant tolerance to heavy metals. However, the role and mechanisms of Cr(VI)-reducing PGPB strains in improving the growth of pakchoi under Cr toxicity remain unclear. This study aimed to isolate a Cr(VI)-reducing PGPB strain from Cr-contaminated soil, evaluate its effect on pakchoi growth under Cr(VI) stress, and investigate the mechanisms involved. Our findings showed that Bacillus sp. NEAU-DCB1-2 effectively reduce Cr(VI) to Cr(III) and produced indole-3-acetic acid and siderophores. Under Cr(VI) stress, inoculation with NEAU-DC1-2 significantly promoted seed germination and early growth of pakchoi. In pot experiments, NEAU-DCB1-2 significantly increased biomass accumulation, plant height, and root length of Cr(VI)-treated pakchoi seedlings, while reducing the Cr(VI) content in root, shoot and soil. Moreover, NEAU-DCB1-2 greatly increased catalase, superoxide dismutase, peroxidase, and ascorbate peroxidase activities in seedlings under Cr(VI) stress, thereby reducing malondialdehyde content. Transcriptome analysis indicated substantial alterations in gene expression patterns after inoculation with NEAU-DCB1-2 under Cr(VI) stress. Further analyses revealed that NEAU-DCB1-2 mainly affected the responses of antioxidant system, metal chelation and transport, together with auxin, abscisic acid, and jasmonic acid signaling to Cr(VI) stress. Conclusively, the Cr(VI)-reducing PGPB strain NEAU-DCB1-2 significantly enhances the growth and Cr tolerance of pakchoi through multiple mechanisms, offering a valuable microbial resource for mitigating the adverse effects of heavy metal contamination in agricultural soils on the yield and safety of vegetable crops.

Characterization of Human Melanoma Skin Cancer Models: A step towards Model-Based Melanoma Research.

Advancing 3D in vitro human tissue models is crucial for biomedical research and drug development to address the ethical and biological limitations of animal testing. Recently, 3D skin models have proven to be effective for studying serious skin conditions, such as melanoma. For these advanced models to be applicable in preclinical studies, thorough characterization is essential to understand their applicability and limitations. In this study, we used bioimaging and RNA sequencing to assess the architecture and transcriptomic profiles of skin models, including models with melanoma. Our results indicated that these models closely mimicked skin morphology and gene expression patterns. The full-thickness (FT) model shows a superior resemblance to the human skin, particularly in basement membrane formation and cellular interactions. The integrity of the skin-like properties and gene expression signatures of both skin and melanoma cells were preserved upon the integration of melanoma cells, establishing these models as robust platforms for cancer research. The responsiveness of the FT melanoma models to vemurafenib treatment was successfully monitored, demonstrating their validity as a reliable, reproducible, and humane tool for pharmacological testing and drug development. Furthermore, the transcriptomic data showed that skin models with cancer spheroids had upregulated genes linked to aggressive and resilient cancer behavior compared to spheroids alone. This emphasizes the importance of the microenvironment in cancer progression and suggests that 3D skin models can serve to uncover mechanisms and therapeutic targets that are not detectable in simpler systems. STATEMENT OF SIGNIFICANCE: This study introduces advanced, ethically sound skin and melanoma models as alternatives to animal testing in drug discovery. By thoroughly characterizing these models using bioimaging and RNA sequencing, we demonstrate their close resemblance to human skin, particularly in full-thickness models. These models not only replicate the complex cellular interactions and gene expression patterns of human tissue but also maintain robustness after melanoma integration. Our findings highlight the potential of these models in revealing cancer mechanisms and therapeutic targets, offering a significant impact on melanoma research and preclinical testing.

Systematic identification and prediction of sex-specific MADS-box genes in Zanthoxylum armatum during flower development

Zanthoxylum armatum, as a vital economic tree species serving both as a food source and medicinal plant, it stands as one of the key industries supporting rural revitalization in southwestern China, offered significant economic, ecological, and social benefits. In recent years, there has been a significant increase in the occurrence of male flowers being sterile, which has greatly impeded the industrial development of Z. armatum. In this study, we investigated the MADS-box gene as a pivotal transcription factor (TFs) influencing flower development. To gain a comprehensive understanding of the evolutionary dynamics of MADS-box genes in Z. armatum and establish a solid foundation for future research on this significant gene family, we conducted a genome-wide investigation and analyzed the expression patterns of MADS-box genes. The present study identified a total of 72 MADS-box genes (ZaMADS1–72) from Z. armatum and proposed that the ZaMADS41 gene is pivotal candidate gene influencing the female-to-male transformation. Phylogenetic analysis revealed that these genes can be categorized into two types: Type I (29 genes) and Type II (43 genes), with the latter exhibiting more complex protein domains and motifs compared to the former. Protein-protein interactions were observed among members of the ZaMADS-box gene family, while their promoter regions contained cis-acting elements associated with light response, hormone response, and plant growth and development. Expression profiling during different stages of male and female flower development demonstrated distinct high expression patterns for certain genes specifically in mature male or female flowers. Furthermore, the determination of endogenous hormone content indicated a potential correlation between iP9G and MEJA with sex transformation, while iP9G exhibited a significantly negative association with ZaMADS33 expression. This comprehensive study on MADS-box genes in Z. armatum combined with changes in endogenous hormone levels during male and female flower development, provides a solid theoretical foundation for investigating bud differentiation mechanisms and regulatory techniques in this species.

Genome-wide analyses of Ariadne family genes reveal their involvement in abiotic stress responses in apple

E3 ligases are essential for ubiquitination and play a role in regulating various aspects of eukaryotic life. Ariadne (ARI) proteins, a subfamily of RBR (RING-between-RING) proteins, have been recognized as a new class of RING-finger E3 ligases. Recent research has shed light on their potential involvement in plants’ responses to abiotic stress. However, comprehensive studies on ARI genes in apple (Malus domestica) are still lacking. This study identified ten MdARI genes in the apple genome, and examined intraspecific and interspecific collinearity to explore the evolutionary relationships of ARI family members. Phylogenetic analyses classified MdARIs into two subfamilies (A and B), and by integrating gene structure, conserved motifs, and sequence comparison results, subfamily B was further divided into two subgroups (I and II). Tissue expression analyses revealed varied expression patterns of MdARI genes in different tissues, and subcellular localization showed that MdARI1-1, MdARI1-2, and MdARI9-1 were located in the nucleus, while the other seven MdARIs were distributed throughout the cell. Analyses of promoter cis-elements and expression patterns under cold, salt, and drought treatments indicated the involvement of MdARIs in abiotic stress responses. Several proteins crucial to the plant stress response were predicted to be potential MdARIs-interacting proteins based on the protein interaction network. Additionally, the interaction between UBC11 (E2) and MdARI7-2 was confirmed by a yeast two-hybrid (Y2H) experiment, suggesting that MdARI7-2 may function as an E3. These findings will greatly benefit future research on the role and mechanisms of ARI proteins in apple stress response.

Molecular characterization, spatio-temporal expression patterns of crtc2 gene and its immune roles in yellow catfish (Pelteobagrus fulvidraco)

cAMP response element binding (CREB) protein 2 (CRTC2) is a transcriptional coactivator of CREB and plays an important role in the immune system. Thus far, the physiological roles of Crtc2 in teleost are still poorly understood. In this study, the crtc2 gene was identified and characterized from yellow catfish (Pelteobagrus fulvidraco; therefore, the gene is termed as pfcrtc2), and its evolutionary and molecular characteristics as well as potential immunity-related roles were investigated. Our results showed that the open reading frame of pfcrtc2 was 2,346 bp in length, encoding a protein with 781 amino acids. Gene structure analysis revealed its existence of 14 exons and 13 introns. A phylogenetic analysis proved that the tree of crtc2 was clustered into five groups, exhibiting a similar evolutionary topology with species evolution. Multiple protein sequence alignment demonstrated high conservation of the crtc2 in various vertebrates with similar structure. Syntenic and gene structural comparisons further established that crtc2 was highly conserved, implying its similar roles in diverse vertebrates. Tissue distribution pattern detected by quantitative real-time PCR showed that the pfcrtc2 gene was almost expressed in all detected tissues except for eyes, with the highest expression levels in the gonad, indicating that Crtc2 may play important roles in various tissues. In addition, pfcrtc2 was transcribed at all developmental stages in yellow catfish, showing the highest expression levels at 12 h after fertilization. Finally, the transcriptional profiles of crtc2 were significantly increased in yellow catfishes injected with Aeromonas hydrophila or Poly I:C, which shared a consistent change pattern with four immune-related genes including IL-17A, IL-10, MAPKp38, and NF-κBp65, suggesting pfCrtc2 may play critical roles in preventing both exogenous bacteria and virus invasion. Anyway, our findings lay a solid foundation for further studies on the functions of pfcrtc2, and provide novel genetic loci for developing new strategies to control disease outbreak in teleost.