Search Results (6,383)

Early environmental conditions play a critical role in shaping fish physiology and behaviour, with tank colour emerging as a relevant yet often overlooked factor in aquaculture and experimental research. This study investigated how rearing tank colour affects larval performance in the cichlid fish Cichlasoma dimerus. Larvae were reared in white, light-blue, or grey tanks, and survival, growth, pigmentation, sex ratio, skeletal development, and the endocrine responses of somatolactin (Sl) and growth hormone (Gh) were evaluated. Survival was significantly lower in white tanks. Conversely, larvae reared in white tanks reached a higher final body weight, while total length showed a similar but non-significant trend. Gh-immunoreactive cells exhibited significantly larger nuclear areas in larvae reared in white tanks and a tendency toward smaller cytoplasmic areas compared with those from light-blue tanks. Melanophore number did not differ among treatments, whereas larvae from grey tanks showed a higher number of Sl-immunoreactive cells. Sex ratios tended to be female-biased in white tanks. Skeletal development did not differ among tank colours and followed the expected chondrogenesis and ossification sequence. Overall, tank colour influenced multiple aspects of larval development, particularly survival, growth, and endocrine responses, underscoring its relevance in fish rearing and experimental design. Full article

Intracellular transport is essential for cellular organization and function. This process is driven by molecular motors that ferry cargo along microtubules, but is characterized by intermittent motility, where cargoes switch between directed runs and prolonged pauses. The fundamental nature of these pauses has remained a mystery, specifically whether they are periods of motor detachment and passive drifting or states of active motor engagement. By combining single-particle tracking with large-scale motion analysis, we discovered that pauses are not passive. Instead, they are active, motor-driven states. We uncovered a unifying quantitative law: the diffusivity of a vesicle during a pause scales with the square of its velocity during a run. This parabolic relationship, D_eff ∝ v², holds true for both kinesin and dynein motors, different cargo types, and a variety of cellular perturbations. We show that this coupling arises because the number of engaged motors governs motility in both states. When we reduce motor engagement, vesicles move more slowly and become trapped in longer, less mobile pauses, collectively causing them to fail to reach their destination. Our work redefines transport pauses as an essential, motor-driven part of microtubule-based cargo delivery, revealing a quantitative principle that contributes to robust cargo transport through the crowded cellular environment. Full article

Cancer metastasis, the spread of tumour cells from the primary site to distant organs, is responsible for over 90% of cancer deaths, yet effective treatments remain elusive due to incomplete understanding of the molecular drivers involved. Podocalyxin (PODXL), a protein overexpressed in many aggressive cancers, links the cell membrane to the internal skeleton through its interaction with Ezrin, an actin cytoskeleton cross-linker. Despite its therapeutic relevance, the PODXL–Ezrin interface remains structurally uncharacterised and pharmacologically intractable. Here, we employed an integrated computational approach combining protein–protein docking, molecular dynamics (MD) simulations, and virtual screening to investigate the structural basis of the PODXL–Ezrin interaction. Using AlphaFold-predicted structures, we modelled PODXL and Ezrin complexes, revealing that PODXL’s cytoplasmic domain stabilises upon Ezrin binding, with Arg495 mediating temporally distinct electrostatic interactions essential for initial complex assembly. Particularly, we characterised the R495W missense mutation in PODXL’s Ezrin-binding domain, demonstrating that substitution of arginine with bulky, hydrophobic tryptophan may allosterically destabilise Ezrin’s dormant conformation. This mutation slightly increases the intramolecular distance between the F3 subdomain and C-terminal domain from 2.59 Å to 3.40 Å, thus leading to potential partial unmasking of the Thr567 phosphorylation site that could plausibly prime Ezrin for activation. Molecular dynamics simulations in the WT state with a total simulation time of 100 ns revealed enhanced structural rigidity and reduced radius of gyration fluctuations in the mutant complex, consistent with a potential “locked,” activation-prone state that amplifies oncogenic signalling. Through virtual screening, we identified NSC305787 as a selective destabiliser of the R495W mutant complex by disrupting key Trp495–pre-C-terminal loop Ezrin interactions and causing steric hindrance to PIP2 recruitment. Our findings identified mutation-dependent changes in drug binding that can guide the development and repurposing of compounds for targeting PODXL-related cancers and improve patient outcomes in PODXL-altered malignancies. Full article

The Japanese beetle (Popillia japonica Newman) is a highly invasive, polyphagous scarab causing significant agricultural and ecological damage across invaded regions. While molecular studies are gaining traction, the unavailability of P. japonica cell lines has constrained in vitro investigations. To overcome these limitations and provide a platform for controlled biological investigation, we developed the first cell culture derived from P. japonica larvae. Fat bodies from field-collected third-instar larvae were dissected and cultured. Cells initially formed floating spheroids before transitioning to adherent monolayers. Cultures remained stable over several splits, whereas a marked reduction in cell number was observed at the eighth split due to the onset of contamination. Fluorescence microscopy confirmed nuclear integrity, while transmission electron microscopy at split 5 revealed cytoplasmic features consistent with insect fat body cells, including lipid droplets. The cell culture predominantly contained trophocyte-like cells, consistent with the known cellular composition of insect fat bodies. Transcriptomic analyses comparing fresh fat bodies and cultured cells revealed moderate transcriptional divergence, with limited upregulation of genes associated with iron homeostasis and stress response, consistent with adaptive responses to in vitro conditions. While not immortalized, this cell culture offers a short-term model for studying P. japonica physiology, toxicology, host–pathogen interactions, and potential gene-targeting strategies under controlled conditions. This work represents a first step toward enabling molecular and cellular research in this economically important pest species. Full article

Background/Objectives: This research covers both tumoral and non-tumoral (adjacent normal) tissues. Non-tumoral tissue samples were obtained from surgical resection margins located at least 5 cm from the tumor edge, with histological confirmation of the absence of tumor involvement. Methods: These samples, varying from 0 weeks to 1 week, were systematically evaluated. The assessment encompassed critical histological aspects such as tissue architecture, nuclear morphology, cytoplasmic features, and membrane characteristics. A scoring system comprising three categories (good, fair, and bad) was employed to gauge the extent of morphological alterations observed in tissue specimens. Statistical analyses were conducted using the “IBM SPSS Statistics 26.0” software. Results: Our findings unveiled a statistically significant association between tissue type and morphological degradations, highlighting the impact of prolonged cold ischemia time and fixation time on cellular swelling, cellular integrity loss, and tissue architecture disruption. The correlation between normal and tumor tissue was statistically significant for pre-analytical parameters evaluated with a strong influence on tumor tissue in cold ischemia time with a p = 0.046, p = 0.020, p = 0.029. For fixation times, the impact was significant for most of the morphological parameters, p = 0.021, p = 0.005, p = 0.023. Conclusions: These observations underscore the critical importance of minimizing cold ischemia time and refining fixation protocols to uphold tissue morphology, protein and molecular integrity. Such endeavors are pivotal in ensuring accurate histopathological evaluation and facilitating precise molecular analyses in the context of digestive cancer research. Full article

This review provides a thorough survey of long noncoding RNAs that bear the RNA modification N6-methyladenosine (m6A) and current work to understand the resulting mechanistic and biological consequences. We give an overview of lncRNA and m6A biology first, describing the writers, erasers, and readers of m6A and their targeting of lncRNAs. Next, we give an in-depth review of the field of nuclear lncRNAs that regulate chromatin and their regulation via m6A. We then describe the growing appreciation of liquid–liquid phase separation properties in lncRNA and m6A biology. Finally, we cover examples of cytoplasmic lncRNAs regulated by m6A. Overall, this review aims to emphasize how epitranscriptomics influences noncoding RNA mechanisms to provide additional layers of regulation, integrated into downstream biological processes. Full article

Cyclic di-GMP (bis-(3′ → 5′) cyclic dimeric guanosine monophosphate) is a ubiquitous bacterial second messenger that regulates a wide range of cellular processes, including biofilm formation, motility, virulence, and environmental adaptation. Its intracellular levels are dynamically controlled by diguanylate cyclases (DGCs), which synthesize c-di-GMP from GTP, and phosphodiesterases (PDEs), which degrade it into linear pGpG or GMP. The functional effects of cytoplasmic c-di-GMP are mediated through diverse effector proteins, including PilZ domain-containing receptors, transcription factors, and riboswitches. In Leptospira interrogans, a major pathogenic species responsible for leptospirosis, the regulatory roles of c-di-GMP remain poorly understood. Here, we performed a comprehensive bioinformatics and structural analysis of all predicted c-di-GMP related proteins in L. interrogans serovar Copenhageni strain Fiocruz L1-130, a serovar generally associated with severe manifestations of leptospirosis in humans. Our analysis identified seventeen proteins containing GGDEF domain, five proteins containing both GGDEF and EAL domains, four proteins containing EAL domain, five proteins containing HD-GYP domain, twelve proteins containing PilZ domain, and one protein containing an MshEN domain. Comparative analysis with well-characterized bacterial homologs suggests that L. interrogans possess a complex c-di-GMP signaling network, likely involved in modulating biofilm formation, host–pathogen interactions, and environmental survival. These findings provide new insights into the c-di-GMP regulatory network and on signal transduction in Leptospira and lay the foundation for future functional studies aimed at understanding its roles in physiology, virulence, and persistence. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) exhibits poor clinical response to gemcitabine, largely due to intrinsic and acquired mechanisms of chemoresistance. Identifying agents capable of enhancing gemcitabine efficacy without increasing cytotoxicity remains an unmet therapeutic need. Here, we characterise a small drug sensitiser molecule, B12, and evaluate its potential to sensitise PDAC cells to gemcitabine. Methods: Gemcitabine’s dose–response was assessed by MTT assay to determine IC₅₀ values and dose-modifying factor (DMF). Phenotypic consequences of co-treatment were examined using colony formation and wound scratch assays. Mitochondrial membrane potential (JC-1) and apoptosis (Annexin V/PI) were measured using flow cytometry. Transcriptomic profiling was performed using mRNA-seq with differential expression analysis and pathway enrichment (KEGG/GSEA). NF-κB activity was assessed by nuclear and cytoplasmic fractionation of p65, and RT-qPCR validation of NF-κB associated target genes. Results: B12 alone displayed minimal cytotoxicity in the PANC-1 cell line and normal pancreatic ductal HPDE cells, yet shifted the gemcitabine dose–response curve in PANC-1 cells, reducing the IC₅₀ and yielding a dose-modifying factor of 1.39. Functionally, B12 enhanced gemcitabine-induced suppression of colony formation and reduced wound closure relative to gemcitabine alone. The co-treatment also increased both mitochondrial depolarisation and apoptotic cell populations, with increased cell proliferation inhibition over time. Transcriptomic profiling identified a set of B12-associated genes downregulated both in B12-treated and B12 + gemcitabine conditions, including factors linked to growth, survival, inflammation, metabolism, and drug inactivation. Gene set enrichment analysis revealed negative enrichment of NF-κB associated pathways during B12 co-treatment. Consistently, nuclear-cytoplasmic fractionation showed that B12 reduced gemcitabine-induced nuclear accumulation of p65, accompanied by decreased expression of NF-κB associated targets such as BCL2L1, CCL20, SLC2A1, and MAP3K14. Conclusions: In PDAC cell models, B12 enhances gemcitabine cytotoxic response while displaying minimal intrinsic toxicity under the conditions tested. The sensitising phenotype is accompanied by increased apoptotic susceptibility and is associated with reduced NF-κB signalling at the pathway, transcript, and p65 nuclear localisation levels. However, to establish causality, the lack of sensitisation in HPDE cells will require further validation. Full article

Neurodegenerative diseases (NDs) are the most prevalent age-associated disorders, characterized by progressive neuronal loss and cognitive decline. Mitochondrial dysfunction is strictly associated with NDs and represent one of the hallmarks of these disorders, with neurological syndromes frequently representing the primary clinical manifestations of mitochondrial abnormalities. As central regulators of cellular bioenergetics, mitochondria play a pivotal role in both the physiological maintenance and pathogenesis of disease by different regulatory approaches. One of these, microRNAs (miRNAs), a class of small non-coding RNAs, are well-established regulators of gene expression across different biological pathways. These miRNAs were usually investigated within the cytoplasmic context, but recent discoveries have revealed the presence of these miRNAs in different parts of mitochondria, where they contribute to the regulation of gene expression and metabolic activity. These mitochondrial-localized miRNAs, termed mito-MiRNA, may originate from either nuclear or mitochondrial genomes and have been shown to modulate the translational machinery of the cells. Despite extensive research on cytoplasmic miRNAs, the functional roles of mito-MiRNA remain poorly understood, particularly in the context of neurodegenerative disorders. Based on these findings, this review aims to synthesize emerging evidence on the involvement of mito-MiRNA in in one of most prevalent neurodegenerative diseases—Parkinson’s disease (PD). Full article

Mitochondria play a crucial role in metabolism and energy production by generating adenosine triphosphate (ATP) through oxidative phosphorylation. They also help maintain intracellular calcium levels, facilitate communication between the nucleus and cytoplasm, detoxify reactive oxygen species (ROS), and regulate apoptosis. Reversible acetylation of mitochondrial proteins is a key post-translational modification influencing these processes, with the NAD⁺-dependent deacetylase SIRT3 being a major regulator. While SIRT3 has been described as a tumor suppressor in some contexts and as a tumor promoter in others, its role appears to be tissue- and metabolism-specific. Here, we compared the proteomic and acetylomic responses of lung adenocarcinoma (A549) and breast adenocarcinoma (MCF7) cell lines to SIRT3 inhibition by 3-TYP. The two lines were selected based on distinct metabolic phenotypes and reported differences in basal SIRT3 abundance. Total proteome and mitochondrial-enriched fractions were analyzed separately for each cell line to avoid cross-line normalization bias. We identified 6457 proteins and 4199 acetylated peptides, revealing distinct pathway enrichments and acetylation changes after SIRT3 inhibition. A549 cells showed increased oxidative metabolism, while MCF7 cells exhibited metabolic reprogramming. These results indicate that the proteomic impact of SIRT3 modulation is strongly influenced by cellular metabolic context. All raw mass spectrometry data are publicly available in PXD063181. Full article

Although large-scale studies and potential pathways of genes on intramuscular fat (IMF) in livestock have been reported, research on circRNAs in yaks—a unique, low-IMF-content animal species that is native to the Qinghai–Tibetan Plateau—is still lacking. Based on previous high-throughput sequencing results on longissimus dorsi with different IMF content, a novel circRNA encoded by the VPS13C gene (designated as circVPS13C) was found to exhibit significant differential expression. Here, we systematically characterized the function and mechanism of circVPS13C on IMF deposition in yaks by adopting a series of experiments. Sequencing, RNase R processing, and nucleoplasmic separation experiments confirmed the circular structure feature of circVPS13C, and it was predominantly distributed in the cytoplasm. Furthermore, these experiments demonstrated that circVPS13C was mainly distributed in the cytoplasm. The circVPS13C/miR-5606-x/ECHDC3 axis was constructed through ceRNA network analysis and validated by dual-luciferase reporter and rescue experiments. Furthermore, the function of these three potential regulators during IMF deposition was investigated through CCK-8, BODIPY, Oil Red O staining, and qRT-PCR analyses, and results showed that both circVPS13C and miR-5606-x promoted the differentiation and inhibited the proliferation of yak intramuscular preadipocytes, while the function of ECHDC3 was the opposite. In conclusion, circVPS13C could act as a competitive endogenous RNA (ceRNA) sponge to sequester miR-5606-x, thereby relieving the inhibitory effect of miR-5606-x on ECHDC3. Full article

Myosin XI-K plays an important role in cell expansion and polarized growth, acting as a motor protein that drives organelle trafficking and cytoplasmic streaming. To elucidate the molecular mechanisms of myosin XI-K’s role in the polarized growth of cotton fiber, we investigated the interactions between GhXI-K and Rab GTPases in cotton (Gossypium hirsutum). Protein docking analyses based on AlphaFold3 predicted that GhXI-K interacted with eight Rab GTPases. A total of 37 interaction residues were identified in GhXI-K, of which 5 crucial contact residues were located in the globular tail domain (GTD) and 2 were located in the motor domain. Key interaction residues in the Rab GTPases were also found to be located in conserved regions: switch-I and switch-II. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays confirmed the predictions and showed that these interactions occur primarily in the GTD and the motor domain. Our findings reveal that GhXI-K interacts with Rab GTPases through both the motor and tail domains, suggesting a synergistic mechanism that facilitates polarized vesicle trafficking in cotton fiber cells. Full article

Background/Objectives: The emergence of immune-evasive SARS-CoV-2 variants highlights the need for adaptable vaccine strategies. Trimeric receptor-binding domain (tRBD) antigens offer structural and immunological advantages over monomeric RBDs, but DNA vaccine efficacy has been limited by inefficient antigen expression, particularly in non-dividing antigen-presenting cells. Although cytoplasmic transcription–based DNA platforms have been developed to overcome nuclear entry barriers, their utility for antigen structure–function optimization remains underexplored. This study evaluated whether integrating a rationally designed trimeric RBD with a T7-driven cytoplasmic transcription system could enhance immunogenic performance. Methods: A DNA vaccine encoding a tandem trimeric SARS-CoV-2 RBD was delivered using a T7 RNA polymerase-driven cytoplasmic transcription system. In vitro antigen expression was assessed following Lipofectamine 3000-mediated transfection. In vivo, mice were immunized with the SM-102-based Rpol/tRBD/LNP formulation, and immunogenicity was assessed by antigen-specific antibody titers, serum neutralizing activity, and T-cell response profiling, together with basic safety/tolerability evaluations. Results: The T7-driven cytoplasmic transcription system markedly increased antigen mRNA and protein expression compared with conventional plasmid delivery. Rpol/tRBD vaccination induced higher anti-RBD IgG titers, enhanced neutralizing antibody activity, and robust CD8⁺ T cell responses relative to monomeric RBD and plasmid-based trimeric RBD vaccines. Immune responses were Th1-skewed and accompanied by germinal center activation without excessive inflammatory cytokine induction, body-weight loss, or hepatic and renal toxicity. Conclusions: This study demonstrates that integrating rational trimeric antigen engineering with direct cytoplasmic transcription enables balanced and well-tolerated immune activation in a DNA vaccine context. The T7 autogene-based platform provides a flexible framework for antigen structure–function optimization and supports the development of next-generation DNA vaccines targeting rapidly evolving viral pathogens. Full article

Although cytoplasmic male sterility (CMS) is well established in eggplant, CMS-based interspecific hybrids with allied species have not yet been reported or studied. In this study, five previously developed CMS-based interspecific F₁ hybrids between eggplant and Solanum aethiopicum Group Aculeatum (=S. integrifolium) and Group Gilo (=S. gilo), together with their parental lines, were morphologically evaluated for 67 seedling, vegetative, floral, and fruit traits, and their heterosis for vegetative growth was studied. Male fertility was assessed based on anther morphology and pollen viability, while female fertility was evaluated through backcrosses to both parents. The hybrids exhibited predominantly intermediate phenotypes and clustered distinctly from parental lines as confirmed by principal component analysis. Remarkable heterosis was observed for most growth-related traits, indicating favorable nuclear–cytoplasmic interactions despite the use of CMS eggplant lines as maternal parents. All hybrids showed complete male sterility, characterized by non-viable pollen and pronounced anther homeotic alterations, the latter indicating CMS-related effects on male fertility. Female fertility was severely reduced, likely due to meiotic irregularities, as evidenced by the failure of most attempted backcrosses. However, successful recovery of BC₁ progeny after backcrossing one CMS-based F₁ hybrid to S. gilo demonstrates partial reproductive compatibility and provides a genetic bridge for CMS introgression into S. gilo. These results indicate that CMS systems are suitable for eggplant interspecific crosses aimed at vigorous rootstock production and CMS cytoplasm introgression into allied germplasm. Full article