Search Results (9,776)

In this study, we report the draft genome sequence of Pseudomonas aeruginosa strain ASK-80, a multidrug-resistant bacterium isolated from municipal wastewater in Baddi, district Solan, Himachal Pradesh, India. The whole genome was sequenced through Illumina MiSeq sequencing (150 bp paired-end). The size of the assembled genome was 6,261,345 bp, and the genome annotation revealed 5834 genes, including 5778 CDSs, 5748 protein-coding genes, 56 RNA genes and 30 pseudo genes. Genomic characterization revealed the occurrence of multiple antibiotic resistance genes (bla_OXA-396, bla_OXA-486, bla_OXA-494, bla_PAO, bla_PDC-8, aph(3′)-IIb, catB7, fosA and others), virulence genes (algB, chpA, clpV1, exsA, flgA, pilB, pvcA, toxA, tse1, and waaA), insertion sequences, transposable elements and phage sequences. This genome data may serve as a valuable resource for comparative genomics of P. aeruginosa and research on the antibiotic resistance surveillance of wastewater. Full article

The retina is a complex sensory neural tissue composed of six major types of neurons and one type of glial cell. The cell fate specification of retinal cells is tightly governed by intrinsic factors and extrinsic microenvironmental cues. Among the key regulators directing retinal cell fate differentiation is a group of bHLH family transcription factors (TFs). Our previous work demonstrated that the bHLH TF Ngn3 exhibits robust potential to induce retinogenesis in both distantly related fibroblasts in vitro and late retinal progenitor cells (RPCs) in vivo. However, the underlying molecular mechanisms remain largely elusive. In this study, we combined immunohistological examination and RNA-seq and ATAC-seq analyses to investigate the cellular and molecular mechanisms governing Ngn3-driven retinogenesis in late RPCs. Our results revealed that Ngn3 overexpression promotes premature cell cycle exit in late RPCs and remodels their transcriptomic and epigenomic landscape towards a state favoring rod photoreceptor and RGC differentiation. Furthermore, cross-comparison with Ngn3-overexpressing fibroblasts in vitro revealed cell-type-specific mechanisms underlying Ngn3-mediated neuronal fate reprogramming. These findings advance our understanding of Ngn family-mediated retinal cell fate regulation and provide a mechanistic framework for optimizing Ngn3-based retinal regeneration strategies for the treatment of retinal degeneration diseases. Full article

Background: Glioblastoma (GBM) exhibits marked cellular heterogeneity and resistance to therapy. Calcium (Ca²⁺) signaling at endoplasmic reticulum (ER)–mitochondria contact sites has emerged as a key regulator of mitochondrial function and cell fate; however, its lineage-specific role and therapeutic relevance in GBM remain unclear. Methods: ITPR1 expression was analyzed using single-cell and bulk RNA sequencing (RNA-seq) datasets and validated by immunohistochemistry and survival analyses. Functional studies were conducted using genetic silencing or CRISPR-mediated activation of ITPR1, combined with DRP1 knockdown, Ca²⁺ imaging, transmission electron microscopy, co-immunoprecipitation, mitochondrial fractionation, and mitochondrial functional assays. Therapeutic efficacy was evaluated in orthotopic GBM xenograft models treated with 2-aminoethoxydiphenyl borate (2-APB), temozolomide (TMZ), or their combination. Results: ITPR1 was enriched in mesenchymal-like malignant cell states and associated with higher tumor grade, recurrence, and poor prognosis. ITPR1 knockdown suppressed GBM cell proliferation and tumor growth while promoting intrinsic apoptosis. Mechanistically, loss of ITPR1 impaired ER-to-mitochondria Ca²⁺ transfer, disrupted ER–mitochondria contacts, and altered mitochondrial ultrastructure. This was accompanied by reduced DRP1 Ser616 phosphorylation and mitochondrial recruitment, as well as decreased autophagy and mitophagy activity. Consequently, ITPR1 knockdown led to mitochondrial depolarization, increased mitochondrial reactive oxygen species (ROS) accumulation, and activation of mitochondria-dependent apoptosis. Conversely, DRP1 knockdown attenuated the mitochondrial and pro-survival effects induced by ITPR1 overexpression. In vivo, combined treatment with 2-APB and TMZ resulted in greater tumor suppression and prolonged survival compared with either treatment alone, accompanied by increased apoptosis and reduced proliferation in tumor tissues. Conclusions: ITPR1 promotes GBM progression by sustaining ER–mitochondria Ca²⁺ coupling and DRP1-dependent mitochondrial quality control, thereby maintaining mitochondrial homeostasis and cell survival. Targeting inositol 1,4,5-trisphosphate receptor (IP₃R)-mediated Ca²⁺ signaling with 2-APB enhances the therapeutic efficacy of TMZ, suggesting that ITPR1-centered Ca²⁺ signaling may represent a potential therapeutic vulnerability in aggressive GBM. Full article

RNA–protein interactions (RPIs), mediated primarily by RNA-binding proteins (RBPs), are central to post-transcriptional gene regulation and govern RNA splicing, transport, localization, translation, and decay. Dysregulation of RBPs and their associated RNA networks contributes to diverse pathologies, including cancer, neurodegenerative disorders, and viral infections. However, profiling RPIs remains a challenge due to their inherent transience, low binding affinity, and shifting spatial dynamics. This review provides a comprehensive and systematic overview of current methodologies for investigating RPIs. We discuss RNA-centric and protein-centric strategies. In addition, imaging-based approaches are evaluated for their capacity to resolve spatial and temporal dynamics of RBP–RNA interactions in situ. We compare these methodologies in terms of resolution, sensitivity, specificity, and biological applicability, emphasizing the importance of integrative strategies for constructing high-resolution, context-dependent RPI maps in physiological and disease settings. Full article

Serine protease-like proteases (SBTs) constitute a distinct class of serine proteases exclusive to plants. Despite the recognized importance of SBTs in various plants, knowledge concerning the evolution and function of SBT genes in Brassica napus is limited. In this study, a total of 140, 63, and 71 SBT genes were identified in B. napus, B. oleracea, and B. rapa, respectively. Phylogenetic analysis classified these 330 identified SBTs into five subfamilies, and collinearity analyses further indicated that gene redundancy and gene loss were strongly associated with polyploidization in Brassicaceae plants. Additionally, analyses of gene structure and conserved motifs suggested that evolutionary changes in exon-intron structures may contribute to the differentiation of coding regions, expression patterns, and even functions within the BnSBT family. Analysis of promoter cis-regulatory elements revealed their predominant association with hormonal responses, abiotic stress, and processes related to plant growth and development. Furthermore, eight differentially expressed genes (DEGs) were identified through a comparative analysis of RNA-Seq data from high- and low-yielding cultivars. qRT-PCR verification also revealed that these eight DEGs (BnSBT1.4b, BnSBT1.4c, BnSBT1.4d, BnSBT1.5c, BnSBT1.6b, BnSBT1.8a, BnSBT3.14a, and BnSBT3.14b) were significantly differentially expressed in the pericarp and seeds. They could be categorized into two distinct groups: BnSBT1.4b, BnSBT1.4c, BnSBT1.4d, BnSBT1.5c, and BnSBT1.8a were highly expressed in high-SPSI material, whereas BnSBT1.6b, BnSBT3.14a, and BnSBT3.14b were highly expressed in low-SPSI material. These results suggest that BnSBTs have diverse potential functions in regulating yield traits in Brassica napus. These findings offer key insights into Brassicaceae SBT genes and highlight the importance of BnSBTs in achieving high yields in Brassica napus. Full article

Grape (Vitis vinifera L.) is an important fruit crop, but its production is severely threatened by ripe rot, a fungal disease caused by Colletotrichum gloeosporioides. However, V. pseudoreticulata ‘Dongan-1’ has been reported to have significant resistance to ripe rot. To investigate the molecular basis of this resistance, we employed RNA-Seq to profile transcriptome changes in the leaves and berry skins of ‘Dongan-1’ following infection. Gene Ontology (GO) enrichment analysis suggested that differentially expressed genes (DEGs) were mainly linked to stress response, cellular processes, and metabolic processes. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs in both tissues were predominantly enriched in the plant MAPK signaling pathway, peroxisome pathway, plant–pathogen interaction pathway, and plant hormone signal transduction pathway. Notably, VpCML41 was identified as a highly induced gene. Functional characterization through heterologous overexpression in Arabidopsis thaliana and transient expression in ‘Thompson Seedless’ grape leaves demonstrated that VpCML41 enhances resistance to C. gloeosporioides. This enhanced resistance involves the coordinated regulation of salicylic acid and jasmonic acid signaling cascades. Our findings provide valuable genetic resources for understanding ripe rot resistance and offer a foundation for developing resistant grape varieties. Full article

Chronic pain, a complex multidimensional disorder, remains a major healthcare issue and a therapeutic challenge. Neuropathic pain is a chronic pain condition that results from damage or dysfunction in the nervous system. While mechanisms of neuropathic pain at the peripheral and spinal cord level have been extensively studied, pain mechanisms in the brain remain underexplored. The amygdala, a limbic brain region, has emerged as a critical brain area for the emotional–affective dimension of pain and pain modulation. Amygdala neuroplasticity has been associated with pain states, but the exact molecular and cellular mechanisms underlying these states and the transition from acute to chronic pain are not well understood. Here, we used the spinal nerve ligation (SNL) model of neuropathic pain in male rats to investigate changes in gene expression in the amygdala at the chronic pain stage using RNA sequencing (RNA-Seq). Two amygdala nuclei, the basolateral (BLA) and central (CeA), were investigated in a hemisphere-dependent manner. We used an integrative approach that focuses on functional significance and cell-type specificity of differentially expressed genes (DEGs) to nominate mechanistic targets for central regulation of chronic pain. Our integrative transcriptomic and bioinformatic analyses identified individual genes (e.g., Cxcl10, Cxcl12, Mbp, Plp1, Mag, Mog, Slc17a6, Gad1, and Sst), molecular pathways (e.g., cytokine-mediated signaling pathway), biological processes (e.g., myelination, synaptic transmission), and specific cell types (e.g., oligodendrocytes, glutamatergic, and GABAergic neurons) affected by chronic pain. Our results also provide some evidence for the emerging concept of hemispheric lateralization of pain processing in the amygdala. Overall, our study proposes oligodendrocyte dysfunction in the amygdala, neuroimmune signaling in the CeA, and glutamatergic neurotransmission in the BLA as key processes and potential therapeutic targets for the management of chronic neuropathic pain. Full article

Background/Objectives: Zebrafish fin regeneration serves as a classic model for investigating vertebrate tissue regeneration, yet the core regulatory networks and their crosstalk with the immune microenvironment remain incompletely characterized. This study aimed to identify hub genes, and elucidate the underlying molecular mechanisms and immune microenvironment dynamics during zebrafish fin regeneration. Methods: We integrated multiple bulk RNA-seq datasets of zebrafish fin regeneration from the GEO database, followed by data standardization with batch effect removal. Hub genes were screened via differential expression analysis, weighted gene co-expression network analysis (WGCNA), and predictive models constructed with 13 classic machine learning algorithms. Functional enrichment, time-ordered gene co-expression network (TO-GCN) method, immune infiltration analyses and RT-qPCR validation were further performed. Results: We identified upregulated differentially expressed genes, regeneration-correlated gene modules and their overlapping genes, including 82 candidate genes and 10 hub genes enriched in cytoskeleton remodeling, extracellular matrix organization, and focal adhesion. Temporal analysis uncovered hierarchical gene regulation and functional switching during regeneration. Hub gene expression was significantly correlated with the infiltration of B cells, M1/M2 macrophages and CD8+ T cells, revealing a stage-specific immune microenvironment. RT-qPCR validation showed high consistency with the multi-omics data. Conclusions: This study provides potential gene targets for understanding zebrafish fin regeneration, and offers a valuable reference for investigating the crosstalk between regulatory networks and the immune microenvironment in vertebrate tissue regeneration. Full article

Background: Fertility preservation aims to maintain reproductive potential in patients undergoing potentially gonadotoxic treatments, increasingly relying on centralized cryobanks requiring ovarian tissue transport. Ovarian tissue cryopreservation is a widely implemented, evidence-based procedure for young women (age 18–35) with a regular ovarian reserve. The ovaries of patients are typically transported overnight to a centralized cryobank for freezing and storage, using a certified hypothermic organ preservation solution such as histidine-tryptophan-ketoglutarate (HTK) at 4–8 °C. The molecular effects of transport on ovarian tissue remain unclear. Methods: In this prospective study of 36 breast cancer patients, we compared whole-transcriptome RNA (RNA-seq) expression in 18 frozen–thawed ovarian biopsies after overnight hypothermic transport followed by slow-freezing versus 18 direct slow-freezing within ≤2 h under FertiPROTEKT-standard conditions. Results: The RNA-seq analysis identified 6 significantly upregulated genes (Bonferroni < 0.05, fold change > 1.5), including histone H2B and mitochondrial NADH dehydrogenase subunit 6 (MT-ND6). The small number of differentially expressed genes suggests only limited transcriptional changes between the two transport conditions. H2B upregulation was confirmed by qPCR, while MT-ND6 showed only moderate levels in RNA-seq but remained stable in qPCR. Immunohistochemical analysis confirmed protein presence and localization in formalin-fixed tissue from four samples, constituting, to our knowledge, the first report of MT-ND6 protein expression in human ovarian tissue. Conclusions: Overall, these results are consistent with subtle changes in chromatin organization and mitochondrial energy metabolism. Since RNA-seq revealed only modest differences in gene expression, with no appreciable up- or downregulation of apoptosis- or damage-related genes after ≤24 h, this indicates tissue stability under the studied combined conditions (transport + cryopreservation). These findings are consistent with the feasibility of the workflow under the studied conditions of centralized ovarian tissue cryobanking combined with overnight transportation and hypothermic HTK solution. Full article

Background: Most patients with hepatocellular carcinoma (HCC) present with advanced disease and have limited systemic treatment options. Oxaliplatin shows clinical activity in HCC but its effectiveness is frequently curtailed by intrinsic and acquired resistance. We sought to systematically identify genetic vulnerabilities that increase oxaliplatin sensitivity in HCC. Methods: Genome-scale negative-selection CRISPR–Cas9 screens were conducted in two genetically distinct HCC cell lines (Hep3B and MHCC-97H) under low-dose oxaliplatin to discover conserved determinants of sensitivity. Selected DNA damage response (DDR) hits were validated. An oxaliplatin-resistant MHCC-97H subline was generated for transcriptomic profiling to characterize resistance-associated programs. Screen results were integrated with TCGA-LIHC expression and survival data to evaluate clinical relevance. Additionally, we analyzed bulk RNA-seq data from biopsy specimens collected from 36 HCC patients prior to initiation of hepatic arterial infusion chemotherapy (HAIC), comparing expression levels of the DDR genes between patients with objective response and non-responders. Results: Screens in both cell lines converged on DDR pathways, particularly nucleotide excision repair (NER) and the Fanconi anemia/interstrand crosslink repair network; shared sensitizers included ERCC4 (XPF), FANCE and SLX4. Validation experiments showed that disruption of representative DDR factors (POLH and XPA) synergistically increased oxaliplatin efficacy at concentrations as low as 0.5 μM. Transcriptomic analysis of the resistant MHCC-97H subline revealed coordinated upregulation of DNA repair programs, G2/M checkpoint and E2F target signatures, and epithelial–mesenchymal transition features. Integration with TCGA-LIHC data demonstrated frequent overexpression of many screen-identified DDR genes in primary HCC and an association between higher expression of selected factors and poorer patient survival. In the HAIC cohort, several DDR genes, including ATR, BRCA2, CDK7, MUS81, MUTYH, PARG, POLH, POLK and XPA, were significantly lower in the objective response group. Conclusions: DDR components represent candidate biomarkers and therapeutic targets whose inhibition may enhance oxaliplatin efficacy in HCC. Full article

Background/Objectives: Although clinically distinct, bipolar disorder (BP), schizophrenia (SZ), major depressive disorder (MDD), and social anxiety disorder (SAD) share fundamental biology. We mapped these transdiagnostic systemic mechanisms. Methods: Weighted Gene Co-Expression Network Analysis (WGCNA) of peripheral blood RNA-Seq datasets evaluated module preservation, hub gene disruption, and microRNA (miRNA) networks. Results: Seven modules showed robust cross-disease preservation. Overall, 56 of 105 candidate hub genes exhibited altered expression, with 22 passing the false discovery rate (FDR) correction. Hubs like IL1B, TLR2, and MMP9 dominated networks linked to altered inflammatory signaling and structural remodeling. Downregulated ribosomal hubs characterized systemic metabolic stress. Discussion: These signatures capture extensive systemic dysregulation. Inflammation and metabolic shifts correlate strongly with pathways regulating chronic neuroinflammation, epigenetic control, and dendritic pruning. Computational models suggest these cascades evade miRNA controls, potentially compromising structural neural plasticity. Conclusions: This shared transcriptomic architecture challenges rigid diagnostic boundaries. Identifying systemic immune dysregulation and translational alterations as core pathogenic denominators provides a rationale for transdiagnostic therapies targeting upstream systemic networks to mitigate neural vulnerabilities. Full article

The aim of this study was to evaluate the nephrotoxicity and molecular mechanism of Evodiamine (EVO). We combined RNA sequencing (RNA-seq) and network toxicology (NT) screening of potential target genes and signaling pathways, used molecular docking to validate core targets, and detected the mRNA expression of the key genes through quantitative real-time polymerase chain reaction (qRT-PCR). After exposure to EVO, body weight of mice decreased significantly, and the levels of renal index, Blood Urea Nitrogen (BUN) and Creatinine (Cr) were significantly increased, with varying degrees of pathological damage to the kidneys. NT identified 125 intersecting targets of EVO exposure related to kidney injury, including AKT1, TNF, TP53, etc. Among the 2888 differentially expressed genes obtained from RNA-seq, 504 genes were up-regulated and 2384 genes were down-regulated. By integrating NT and RNA-seq, 24 intersecting targets were identified. Among them, TRPV1, NOS3, HSP90AA1, and PPARG were selected for molecular docking validation. The results indicated that EVO had the highest affinity for PPARG (−8.07 kcal/mol). The qRT-PCR results indicated that the expression of the Pparg and Hsp90aa1 genes was significantly down-regulated, and the expression of the Nos3 and Trpv1 genes was significantly up-regulated. Immunohistochemistry further confirmed that EVO inhibited the expression of HSP90AA1 and PPARG, while enhancing that of TRPV1 and NOS3. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested that EVO-induced nephrotoxicity is related to signaling pathways such as inflammatory mediator regulation of TRP channels, the PPAR signaling pathway, and the Apelin signaling pathway. In summary, the nephrotoxic effect of EVO may be related to the inhibition of the PPARG signaling pathway, the activation of the TRPV1 channel, the reduction in HSP90AA1 expression, and the imbalance of the Apelin-NOS3 pathway. This study provides a theoretical reference for clarifying the potential mechanism of renal injury caused by EVO and guiding its safe use. Full article

Background/Objectives: Hepatocellular carcinoma (HCC) remains a major malignancy with high incidence and mortality, in part due to its diverse etiology and intratumoral heterogeneity, which contributes to drug resistance and frequent recurrence. SALL1 (Spalt-Like Transcription Factor 1), a zinc-finger transcription factor, was reported to function as a tumor suppressor in several cancers, including breast cancer and glioma, and accumulating evidence support its involvement in tumor biology. In this study, the role of SALL1 in HCC was examined. Methods: Public RNA and protein databases derived from human HCC were interrogated. Western blotting quantification of clinical HCC for SALL1 levels was carried out. Cell culture and xenograft studies were performed using genetically modified HCC tumor cells. Results: As revealed by pubic RNA and protein database analysis and further western blotting quantification of clinical samples of HCC, SALL1 is decreased in human HCC. The effect of reduced SALL1 expression on the tumorigenic properties and transcriptional regulation in HCC was then examined. Knockdown of SALL1 in the HCC cell lines Huh7 and Hep3B, enhanced cell proliferation in vitro and accelerated tumor growth in a xenograft mouse model, suggesting that lower SALL1 expression increases cell proliferation and tumorigenesis in HCC. RNA-seq and ChIP analyses further identified three novel candidate target genes (SLC6A14, GABRG1, and AKR1B10), suggesting that SALL1 may exert a tumor-suppressive effect, at least in part, through negative regulation of these genes. Conclusions: These findings establish SALL1 as a possible tumor suppressor and provide new insights into the biological significance of SALL1 downregulation in HCC. SALL1 could be a candidate prognostic marker and a potential therapeutic target. Full article

Chalcones, a subclass of flavonoid-derived phenolic compounds, have demonstrated promising anthelmintic activity against parasitic nematodes. This study aimed to obtain insights into the biological effects a cis/trans mixture of chalcone and its geometric isomer, trans-chalcone, using RNA sequencing in the model organism Caenorhabditis elegans. Fourth-stage larvae (L4) were exposed to cis/trans-chalcone or trans-chalcone for 3 h, and total RNA was extracted for high-throughput sequencing. Transcriptomic analysis revealed that exposure to cis/trans-chalcone and trans-chalcone induced pronounced modulation of genes involved in lipid metabolism and repression of collagen and structural genes, potentially leading to defective extracellular matrix maintenance, thereby suggesting these combined effects as potential mechanisms underlying their anthelmintic activity. Also, metabolic and stress response pathways, with several genes implicated in detoxification and cellular defense, were markedly upregulated. These findings provide new insights into the molecular mechanisms affected by chalcones, advancing our understanding of their anthelmintic potential and supporting future drug development efforts. Full article

With the rapid progression of global industrialization and urbanization, heavy metal contamination has emerged as a major global threat, especially cadmium pollution. Consequently, optimizing remediation measures has become a pivotal means to solve cadmium contamination. Compared to traditional physical and chemical remediation methods, microbial remediation has great potential in addressing cadmium pollution. In this study, a novel bacterial strain, Chryseobacterium sp. HGX-24, exhibiting high cadmium resistance was successfully isolated and screened from cadmium-contaminated environments. A preliminary discussion of the response mechanisms of this strain under cadmium stress is provided. Additionally, preliminarily explored the synergistic remediation of microbial-plant in cadmium-contaminated soil. Under conditions of high cadmium concentration, cadmium ions were effectively adsorbed by strain HGX-24 through extracellular polymers and functional groups on the cell wall surface, including −COOH, −CONH−, −NH, −OH, and >C=O. Extracellular proteins and polysaccharides were secreted by strain HGX-24 to regulate the adverse effects of heavy-metal cadmium ions on bacterial growth. Furthermore, the expression of genes such as antioxidant defense and ROS scavenging (katG, fabG, ybjT), Fe-S cluster assembly (sufB, sufD), sulfur metabolism (cysAU), amino acid metabolism (hisA, cysD, aspC), phenylacetic acid catabolism (paaC), and ribosomal proteins (rplC, rpsC, rpsL, rplA, rplY, rpmC) was regulated, affecting the synthesis and metabolism of membrane transporters (ABC transporters and efflux RND transporters), antioxidant enzymes (SOD, COT, POD), Fe-S clusters, thioredoxin family proteins, and ribosomal proteins, thereby enhancing resistance to cadmium toxicity. Moreover, strain HGX-24 was found to regulate the activities of redox enzymes in Zea mays L., thereby alleviating oxidative stress and reducing the negative feedback effects of reactive oxygen species in Z. mays. Full article