Search Results (196)

Background/Objectives: Lower-grade gliomas, particularly IDH-mutant astrocytomas, represent a distinct molecular subtype with unique therapeutic challenges. Whole-genome sequencing (WGS) plays a crucial role in uncovering genetic alterations that drive glioma pathogenesis and therapeutic resistance. This study identifies and evaluates a novel GATA2 p.Arg396Trp mutation in a clinical sample of lower-grade glioma, assessing its structural impact and implications for drug binding. Methods: A WHO Grade II astrocytoma specimen from a 33-year-old female patient was analyzed using WGS with Oxford Nanopore sequencing, followed by comprehensive bioinformatics processing to identify genomic variants. The GATA2 p.Arg396Trp mutation was evaluated using protein modeling, structural analysis, and pathogenicity prediction tools. Drug affinity analysis was conducted using molecular docking simulations to assess the computational impact of the mutation on drug binding. Results: The GATA2 p.Arg396Trp mutation was identified as a computationally predicted pathogenic variant, potentially disrupting protein interactions within critical functional domains. Structural analysis revealed altered binding dynamics with key anti-neoplastic agents, suggesting potential implications for therapeutic response. These findings represent computational predictions requiring experimental validation. Conclusions: Our preliminary findings suggest a potential role of the GATA2 p.Arg396Trp mutation in lower-grade glioma pathogenesis. The mutation predicted impact on transcriptional regulation and drug affinity suggests GATA2 as a possible biomarker candidate. Extensive experimental validation in larger patient cohorts is needed to establish clinical relevance and explore targeted therapeutic strategies. Full article

Background: Metabolic stress from amino acid (AA) insufficiency is increasingly linked to pathological angiogenesis, but specific essential AA (EAA) roles remain undefined. Neovascular age-related macular degeneration (AMD), a major cause of blindness driven by aberrant ocular neovascularization, has limited efficacy with current VEGFA-targeting therapies. We sought to identify specific EAAs that regulate pathological angiogenesis and dissect their mechanisms to propose new therapeutic strategies. Methods: Human retinal microvascular endothelial cells (HRMVECs) were used to identify angiogenesis-regulating amino acids through systematic EAA screening. The molecular mechanism was investigated using shRNA-mediated knockdown of key stress response regulators (HRI, PKR, PERK, GCN2) and ATF4. Angiogenesis was assessed via tubule formation and migration assays. Therapeutic potential was examined in a laser-induced choroidal neovascularization (CNV) mouse model, evaluated by fluorescein angiography and histomorphometry. Results: Deprivation of methionine, lysine, and threonine potently induced capillary-like tube formation (p < 0.01). Mechanistically, restriction of these three EAAs activated HRI and GCN2 kinases, converging on eIF2α phosphorylation to induce ATF4 and its target VEGFA. Dual, but not single, knockdown of HRI and GCN2 abolished eIF2α-ATF4 signaling and angiogenic responses. Restricting these EAAs exacerbated CNV area in mice. Conclusions: Our findings reveal a coordinated HRI/GCN2-ATF4-VEGFA axis linking EAA scarcity to vascular remodeling, establishing proof-of-concept for targeting this pathway in CNV. This work highlights the therapeutic potential of modulating specific AA availability or targeting the HRI/GCN2-ATF4 axis to treat CNV. Full article

APOBEC3B (A3B) has been implicated in host–virus interactions, but its role in SARS-CoV-2 infection is unclear. Here, we demonstrate that A3B is overexpressed in bronchoalveolar lavage fluid (BALF) cells from severe COVID-19 patients compared to those with mild disease. A3B knockdown in Caco-2 cells significantly reduces SARS-CoV-2 infectivity, likely through attenuation of the PKR-mediated integrated stress response, a pathway proposed to promote SARS-CoV-2. Single-cell RNA sequencing (scRNA-seq) data suggest that BALF cells from severe COVID-19 patients exhibit a repressed state for cellular translation, potentially mediated by eIF2α phosphorylation. However, in A549-ACE2 cells, SARS-CoV-2 does not activate PKR, but A3B knockdown still reduces SARS-CoV-2 infectivity, suggesting an alternative mechanism of action in different cellular contexts. To further investigate A3B’s role in severe COVID-19, we employed Geneformer, a transformer-based machine learning model, which predicted that A3B knockout would perturb AMPD2 (adenosine monophosphate deaminase 2), a key enzyme in purine metabolism and immune regulation. We validated this prediction using bulk RNA-seq and clinical scRNA-seq data, confirming that AMPD2 expression is downregulated in severe COVID-19 but restored upon A3B knockdown. Together, these findings suggest that A3B plays a proviral role in SARS-CoV-2 infection by modulating translational control and immune regulatory networks, warranting further studies to elucidate the underlying mechanistic details. Full article

Background: Protein kinase R (PKR) inhibits general mRNA translation by phosphorylating the alpha subunit of eukaryotic translation initiation factor 2 (eIF2). PKR also modulates NF-κB signaling during viral infections, but comparative studies of PKR-mediated NF-κB responses across mammalian species and their regulation by viral inhibitors remain largely unexplored. This study aimed to characterize the conserved antiviral and inflammatory roles of mammalian PKR orthologs and investigate their modulation by poxviral inhibitors. Methods: Using reporter gene assays and quantitative RT-PCR, we assessed the impact of 17 mammalian PKR orthologs on general translation inhibition, stress-responsive translation, and NF-κB-dependent induction of target genes. Congenic human and rabbit cell lines infected with a myxoma virus strain lacking PKR inhibitors were used to compare the effects of human and rabbit PKR on viral replication and inflammatory responses. Site-directed mutagenesis was employed to determine key residues responsible for differential sensitivity to the viral inhibitor M156. Results: All 17 mammalian PKR orthologs significantly inhibited general translation, strongly activated stress-responsive ATF4 translation, and robustly induced NF-κB target genes. Inhibition of these responses was specifically mediated by poxviral K3 orthologs that effectively suppressed PKR activation. Comparative analyses showed human and rabbit PKRs similarly inhibited virus replication and induced cytokine transcripts. Amino acid swaps between rabbit PKRs reversed their sensitivity to viral inhibitor M156 and NF-κB activation. Conclusions: Our data show that the tested PKR orthologs exhibit conserved dual antiviral and inflammatory regulatory roles, which can be antagonized by poxviral K3 orthologs that exploit eIF2α mimicry to modulate the PKR-NF-κB axis. Full article

Early embryonic loss is a major cause of reproductive inefficiency in cattle, primarily due to premature luteolysis. Interferon tau (IFN-τ), secreted by the trophoblast, plays a critical role in maternal recognition of pregnancy by maintaining corpus luteum function. However, its practical application has been limited by its rapid degradation and short half-life in vivo. Here, we developed a novel formulation of recombinant bovine IFN-τ, combining chitosan-based microencapsulation with starch–chitosan hydrogel delivery, enabling sustained intrauterine release. This dual-delivery strategy offers a significant improvement over conventional IFN-τ administration methods that rely on repeated intrauterine infusions of soluble protein. The rbIFN-τ was expressed in Pichia pastoris, purified to 90.1% homogeneity, and structurally validated via homology modeling and molecular docking, confirming its interaction with type I interferon receptors. The encapsulated formulation retained antiviral activity, stimulated transcription of interferon-stimulated genes (PKR, OAS1, OAS2), and showed sustained release in vitro for up to 26 days. In vivo evaluation demonstrated safety and biological efficacy, with treated cattle showing inhibited luteolysis, sustained serum progesterone levels, and preserved corpus luteum integrity. This formulation represents a promising biotechnological approach to improve reproductive efficiency through a long-acting, species-specific IFN-τ delivery system. Full article

Stress granules (SG), dynamic cytoplasmic condensates formed via liquid-liquid phase separation (LLPS), serve as a critical hub for cellular stress adaptation and antiviral defense. By halting non-essential translation and sequestering viral RNA, SG restrict viral replication through multiple mechanisms, including PKR-eIF2α signaling, recruitment of antiviral proteins, and spatial isolation of viral components. However, viruses have evolved sophisticated strategies to subvert SG-mediated defenses, including proteolytic cleavage of SG nucleators, sequestration of core proteins into viral replication complexes, and modulation of stress-responsive pathways. This review highlights the dual roles of SG as both antiviral sentinels and targets of viral manipulation, emphasizing their interplay with innate immunity, autophagy, and apoptosis. Furthermore, viruses exploit SG heterogeneity and crosstalk with RNA granules like processing bodies (P-bodies, PB) to evade host defenses, while viral inclusion bodies (IBs) recruit SG components to create proviral microenvironments. Future research directions include elucidating spatiotemporal SG dynamics in vivo, dissecting compositional heterogeneity, and leveraging advanced technologies to unravel context-specific host-pathogen conflicts. This review about viruses and SG formation helps better understand the virus-host interaction and game process to develop new drug targets. Understanding these mechanisms not only advances virology but also informs innovative strategies to address immune escape mechanisms in viral infections. Full article

Fish red blood cells (RBCs) are nucleated, transcriptionally active, and key players in both gas transport and immune responses. They are the primary targets of Orthoreovirus piscis (PRV), the etiological agent of heart and skeletal muscle inflammation (HSMI), which includes three genotypes (PRV-1, PRV-2, and PRV-3), linked to circulatory disorders in farmed salmon. In Chile, PRV-3 affects the coho salmon (Oncorhynchus kisutch), but host–pathogen interactions remain poorly characterized. This study compared the interactions of PRV-3 in coho salmon and PRV-1 in Atlantic salmon (Salmo salar) using RBC infection models. RBCs were isolated from healthy juvenile salmon (n = 3) inoculated with either PRV-1 (Ct = 18.87) or PRV-3 (Ct = 21.86). Poly I:C (50 µg/mL) was used as a positive control for the antiviral response. Cells were monitored for up to 14 days post-infection (dpi). PRV-3 infection in coho salmon RBCs caused significant metabolic disruption, apoptosis from 7 dpi, and correlated with increasing viral loads. In contrast, PRV-1 infection in Atlantic salmon RBCs showed limited apoptosis and maintained cell viability. Coho salmon RBCs upregulated rig-i, mx, and pkr transcripts, indicating activation of the type I interferon pathway, whereas Atlantic salmon RBCs exhibited a more attenuated response. PRV-3 induced notable morphological changes in coho salmon RBCs, although neither PRV-3 nor PRV-1 caused hemolysis. These findings highlight species-specific differences in RBC responses to PRV infection and provide new insights into the pathogenesis of PRV-3 and PRV-1. Full article

As a prevalent metabolic disorder, the increasing incidence of diabetes imposes a significant burden on global healthcare. Flavonoids in natural phytochemical products exhibit notable hypoglycemic properties, making them potential alternatives for diabetes treatment. This article summarizes the hypoglycemic properties of flavonoid subcategories studied in recent years, including flavones, isoflavones, flavonols, flavanols, and others. The relevant targets and signal pathways, such as α-amylase, α-glucosidase, insulin receptor substrate (IRS)/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT), PKR-like endoplasmic reticulum kinase (PERK)/eukaryotic initiation factor 2α (eIF2α)/activation transcription factor 4 (ATF4)/C/EBP homologous protein (CHOP), etc., are also elaborated. Additionally, flavonoids have also been demonstrated to modulate the gut microbiota and its metabolites. Through the aforementioned mechanisms, flavonoids mainly suppress carbohydrate metabolism and gluconeogenesis; facilitate glucose uptake, glycogenesis, and insulin secretion; and mitigate insulin resistance, oxidative stress, inflammation, etc. Notably, several studies have indicated that certain flavonoids displayed synergistic hypoglycemic effects. In conclusion, this article provides a comprehensive review of the hypoglycemic effects of the flavonoids investigated in recent years, aiming to offer theoretical insights for their further exploration. Full article

This study explores the integration of Building Information Modeling (BIM) and Geographic Information Systems (GISs) to enhance sustainable energy efficiency and flood resilience in residential buildings, with a case study from Quetta, Pakistan. The research leverages BIM to optimize energy performance through scenario-based energy consumption assessments, thermal efficiency, material properties, and groundwater considerations, ensuring structural integrity against water infiltration. Enhanced insulation and double-glazed windows reduced energy use by 11.78% and 5.8%, respectively, with monthly energy cost savings of up to 48.2%. GIS tools were employed for high-resolution flood risk analysis, utilizing Digital Elevation Models (DEMs) and hydrological data to simulate flood scenarios with depths of up to 2 m, identifying vulnerabilities and estimating non-structural damage costs at PKR 250,000 (~10% of total building costs). Groundwater data were also incorporated to evaluate their impact on foundation stability, ensuring the building’s resilience to surface and subsurface water challenges. A novel BIM-GIS integration framework provided precise 2D and 3D visualizations of flood impacts, facilitating accurate damage assessments and cost-effective resilience planning. The findings demonstrated that incorporating flood-resistant materials and design modifications could reduce repair costs by 30–50%, highlighting the cost-efficiency of sustainable resilience strategies. This research advances sustainable and resilient construction practices by showcasing the dual potential of BIM-GIS integration to address energy efficiency and groundwater-related structural vulnerabilities alongside hazard mitigation challenges. Future applications include automating workflows, integrating renewable energy systems, and validating models across diverse climatic regions to promote the global adoption of innovative urban planning solutions. Full article

Human–wildlife conflict poses significant ecological and socio-economic challenges, particularly in rural communities where agriculture and livestock rearing form the backbone of livelihoods. Despite the growing importance of this issue, District Lakki Marwat remains an unexplored area of northwest Pakistan. This study aims to fill this gap by systematically assessing the status, economic impacts, and community perceptions of five wildlife species: wild boar (Sus scrofa), grey wolf (Canis lupus), golden jackal (Canis aureus), striped hyena (Hyaena hyaena), and red fox (Vulpes vulpes). Using semi-structured surveys with 117 respondents, we analyzed species prevalence, perceived danger levels, crop damage patterns, and predation impacts on livestock and poultry. The findings revealed that wild boars were identified as the primary contributors to agricultural damage, with total annual crop losses surpassing the economic impacts attributed to the studied carnivores. On average, each surveyed household experienced an annual loss of PKR 4510.38. For the 39% of households reporting crop damage, the annual loss per reported household was PKR 11,727, which was higher than the average annual loss across all households, underscoring the severity of the impact on those specifically affected by the wild boar-related crop damage. Notably, community attitudes were most negative toward wild boars, a pattern driven by the economic burden of crop losses, challenging the conventional focus on carnivores as the primary conflict species. A Pearson’s $X^2$ test confirmed strong associations between species and perceived danger levels, while regression analysis demonstrated an association between crop damage and negative attitudes. Traditional deterrents like thorn fences were found ineffective against wild boars. More advanced methods, including game-proof fencing, trenches, bio-fencing, crop rotation, audio and visual deterrents, taste and order repellents, and watchtowers combined with group vigilance, are recommended to reduce crop damage. Integrating these approaches with community-based education, habitat management, and government-supported compensation schemes can mitigate wild boar impacts. This study contributes new insights into multi-species HWC dynamics, demonstrating that community perceptions are primarily shaped by the economic impact of a species, regardless of whether it is a carnivore or an omnivore. The attitudes of local communities are driven by the financial losses incurred, rather than the species' behavior or ecological role. This study underscores the need for collaborative efforts to reduce human–wildlife conflict, foster coexistence, and ensure ecological balance in vulnerable rural areas. Full article

The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) has caused huge economic losses to the pig industry in China. This study evaluated the damage to peripheral immune tissues in the early infection of HP-PRRSV, including the hilar lymph nodes, mandibulares lymph nodes, inguinales superficials lymph nodes, spleens, and tonsils. HP-PRRSV infection led to a reduction in CD4⁺ and CD8⁺ T cells, as well as CD19⁺ B cells, in the tonsils. Additionally, CD163⁺ macrophages and CD56⁺ NK cells increased in all peripheral lymphoid organs, with NK cells migrating toward the lymphoid follicles. However, no significant changes were observed in CD11c⁺ dendritic cells. RNA-seq analysis showed the down-regulation of T and B cell functions, while macrophage and NK cell functions were enhanced. Gene Ontology (GO) and KEGG pathway analysis indicated the up-regulation of necroptosis processes. Western blotting and immunofluorescence confirmed that HP-PRRSV induced PKR-mediated necroptosis in immunocytes. This study provides new insights into the effects of early HP-PRRSV infection on peripheral immune organs, highlighting dynamic shifts in immune cell populations, virus-induced immunosuppression, and the role of PKR-mediated necroptosis. These findings improve our understanding of the immunomodulation induced by PRRSV infection. Full article

The betacoronavirus genus contains five of the seven human coronaviruses, making it a particularly critical area of research to prepare for future viral emergence. We utilized three human betacoronaviruses, one from each subgenus—HCoV-OC43 (embecovirus), SARS-CoV-2 (sarbecovirus), and MERS-CoV (merbecovirus)—, to study betacoronavirus interactions with the PKR-like ER kinase (PERK) pathway of the integrated stress response (ISR)/unfolded protein response (UPR). The PERK pathway becomes activated by an abundance of unfolded proteins within the endoplasmic reticulum (ER), leading to phosphorylation of eIF2α and translational attenuation. We demonstrate that MERS-CoV, HCoV-OC43, and SARS-CoV-2 all activate PERK and induce responses downstream of p-eIF2α, while only SARS-CoV-2 induces detectable p-eIF2α during infection. Using a small molecule inhibitor of eIF2α dephosphorylation, we provide evidence that MERS-CoV and HCoV-OC43 maximize viral replication through p-eIF2α dephosphorylation. Interestingly, genetic ablation of growth arrest and DNA damage-inducible protein (GADD34) expression, an inducible protein phosphatase 1 (PP1)-interacting partner targeting eIF2α for dephosphorylation, did not significantly alter HCoV-OC43 or SARS-CoV-2 replication, while siRNA knockdown of the constitutive PP1 partner, constitutive repressor of eIF2α phosphorylation (CReP), dramatically reduced HCoV-OC43 replication. Combining GADD34 knockout with CReP knockdown had the maximum impact on HCoV-OC43 replication, while SARS-CoV-2 replication was unaffected. Overall, we conclude that eIF2α dephosphorylation is critical for efficient protein production and replication during MERS-CoV and HCoV-OC43 infection. SARS-CoV-2, however, appears to be insensitive to p-eIF2α and, during infection, may even downregulate dephosphorylation to limit host translation. Full article

Agroforestry improves the stability and productivity of agro-ecosystems and reduces environmental pressures, making it extremely flexible and useful in a variety of physical and social contexts. This practice is crucial to farmers’ livelihoods on both an ecological and economical level. Using an interview schedule, data were gathered from 170 heads of rural families who were chosen at random. Of the responders, the majority (77.5%) were young (25 to 40 years old). Of those who had completed more than five years of schooling, only 46.7% were literate, while a sizable majority (53.3%) were illiterate. For the vast majority of responders (62.4%), farming was their primary source of income. Given that over 54% of the respondents only owned up to five acres of land, small farming was extremely common. The majority (61.3%) were considered poor with a monthly income of less than PKR 18,000. “good source of fuel wood” was placed at the top (mean = 3.1%) when it came to the effect of agroforestry on the food security of rural households. One of the main obstacles was having a small land holding (mean = 2.52). The majority of respondents believed that the primary benefit of agroforestry was a reduction in soil loss. The amount of land held, income source, and educational attainment all significantly correlated with the perception of poverty. The study found that the best way of sustainably assuring food security in the study area and satisfying rural residents’ needs for food for extended periods of time is to incorporate agroforestry into the current farming system. Full article

This study evaluates the oncolytic potential of the Moscow strain of reovirus against human metastatic melanoma and glioblastoma cells. The Moscow strain effectively infects and replicates within human melanoma cell lines and primary glioblastoma cells, while sparing non-malignant human cells. Infection leads to the selective destruction of neoplastic cells, mediated by functional viral replication. A positive correlation was identified between viral RNA accumulation and tumor cell death, with no replication observed in non-malignant cells. This study highlights the critical roles of cathepsins B, L, and S as mediators of the oncolytic process. The pharmacological inhibition of these enzymes significantly attenuated reovirus-induced cytotoxicity in melanoma and glioblastoma cells. Conversely, PKR production analysis revealed minimal activation in reovirus-infected tumor cells, suggesting that the hyperactivation of the RAS-signaling pathway and subsequent PKR inhibition do not directly contribute to the selective efficacy of reovirus. Moreover, infected tumor cells exhibited features of both apoptotic and non-apoptotic death, emphasizing the intricate mechanisms of reovirus-mediated oncolysis. These findings underscore the therapeutic promise of the Moscow strain of reovirus as a selective and potent oncolytic agent for targeting melanoma and glioblastoma cells. Full article

This review concerns nc886, a 101-nucleotide non-coding RNA (ncRNA). Because nc886 is transcribed by RNA polymerase III (Pol III) and contains a CpG island in its promoter region, its expression is regulated by several transcription factors and the DNA methylation status. These features drive nc886 expression in two opposing directions during tumorigenesis. The known function of nc886 is to bind to and modulate the activity of target proteins such as PKR, Dicer, and OAS1. By being differentially expressed during tumorigenesis and interacting with these proteins, nc886 plays a role in tumor surveillance, promotes or suppresses tumorigenesis, and influences the efficacy of cancer therapy. The multiple roles of nc886 have been well-documented in the literature. In this review, we have summarized this literature and critically discussed the roles and mechanisms of action of nc886 in various cancers. Full article