Search Results (3,083)

Background: Chronic kidney disease (CKD) associated vascular calcification (VC) is a leading cause of cardiovascular mortality, partially driven by osteogenic transdifferentiation of vascular smooth muscle cells (VSMCs). Chaperone-mediated autophagy (CMA) is a selective lysosomal degradation cellular process. However, the precise role and mechanism of CMA in CKD-associated vascular calcification remain unknown. Methods: We studied calcified arteries from CKD patients and rats fed on a high-phosphate diet using histological and ultrastructural methods. VSMCs' calcification was induced by a calcification medium containing high phosphate and calcium. CMA activity was measured by a KFERQ reporter and lysosomal staining. The expression of LAMP2a and HSP90AA1 was knocked down by siRNA, overexpressed by plasmid, and activated by QX77.1. Bioinformatic analysis, protein interaction studies, immunofluorescence and co-immunoprecipitation were performed to investigate the potential mechanism of CMA in VC. Results: The expression of LAMP2a was increased in human calcified radial artery tissues (n = 3, p < 0.05) and rats' calcified aortic tissues (n = 3, p < 0.01), accompanied by lysosomal abnormalities. The activity of CMA was increased during the osteogenic transdifferentiation of VSMCs, as indicated by increased expression of RUNX2 and reduced expression of SM22α (p < 0.05). LAMP2a knockdown attenuated VSMCs’ calcification (p < 0.05), whereas pharmacological activation of CMA aggravated calcification in VSMCs (p < 0.01). Bioinformatic screening identified HSP90AA1 as a candidate involved in CMA in vascular calcification. Elevated HSP90AA1 expression was observed in human calcified radial artery tissues (n = 3, p < 0.01) and rat calcified aortic tissues (n = 3, p < 0.01), which promoted osteogenic transdifferentiation of VSMCs (p < 0.05). HSP90AA1 interacted with LAMP2a and positively regulated its expression (p < 0.01). Conclusions: These findings support an association between CMA activation and CKD vascular calcification. It suggests that HSP90AA1 facilitates vascular calcification in chronic kidney disease involving chaperone-mediated autophagy. Full article

The novel strain TD-94 with higher ammonia degradation efficiency was isolated from the activated sludge of SINOPEC and belongs to the family of Alcaligenes faecalis (A. faecalis) based on its 16sRNA sequence and physio-biochemical characteristics. It is a Gram-negative, highly heterotrophic aerobic ammoxidation bacterium that is capable of effectively treating ammonia-nitrogen wastewater. The genome size of strain TD-94 was 4,361,949 bp with a GC content of 56.47% and a total of 4101 genes, which accounted for 89.54% of the total genome length. Analysis of various databases showed that 649 genes were annotated in the GO database; a total of 2712, 4095 and 12 genes were annotated in the KEGG, COG, and ADRB databases, respectively; and there were 24 types of cytochrome P450, 477 signal peptides, and eight secondary metabolites. All these data provide a theoretical basis for the mechanism of action of the strain TD-94. Based on the whole-genome sequencing results, functional genes related to nitrogen metabolism in A. faecalis TD-94, including aerobic ammonia oxidation (AOB), hydroxylamine oxidoreductase (HAO), and pyruvic oxime dioxygenase (POD) were identified. Through growth curve analysis and the identification of functional genes, the nitrogen metabolism pathway of A. faecalis TD-94 was proposed, demonstrating that the strain TD-94 has good denitrification capabilities and a novel degradative pathway. Full article

Oxidation of RNA has gained interest from the community due, in part, to a link in the progression/development of disease as well as other biological processes such as apoptosis, ageing, hibernation, and signalling, amongst others. Different types of RNA with varying functions and size have been shown to be oxidized in vivo, including ribosomal RNA (rRNA), transfer RNA (tRNA), microRNA (miRNA), messenger RNA (mRNA), and mitochondrial RNA (mtRNA). This process occurs from reactions between reactive oxygen species (ROS) and all biopolymers, including RNA, from endogenous as well as exogenous sources. As a consequence, mechanisms that handle oxidized RNA are important, and enzymatic degradation is the most commonly studied process to date. This review focuses on the ribonucleases that have been shown to play a role in the degradation of oxidized RNA. While emphasis is placed on, arguably, the most common oxidatively generated chemical modification, 8-oxo-7,8-dihydroguanosine (8-oxoG), the products that arise from the oxidation of other canonical nucleosides as well as naturally occurring modifications are also discussed in the context of RNA oxidation. Processing of oxidized RNA via its enzymatic degradation is likely the main route, but a potential role of other proteins involved in the handling of oxidized RNA is hypothesized, e.g., helicases, export proteins, and extracellular environments. We postulate that this is an area with great potential for discovery. Full article

The coordinated development of achenes and receptacles in strawberry is critical for seed dispersal and fruit quality, yet the underlying molecular mechanisms remain poorly characterized. Utilizing RNA-seq analysis during the ripening transition stage, we identified pronounced transcriptomic divergence between achenes and receptacles, with receptacles exhibiting more dynamic gene expression shifts. Intriguingly, a substantial subset of differentially expressed genes (DEGs) displayed antagonistic expression patterns between these tissues, including the cytokinin degradation gene cytokinin oxidase/dehydrogenase 1 (FvCKX1), which was highly expressed in both tissues but with opposing temporal trends. Functional interrogation via transient silencing and overexpression revealed a tissue-specific regulatory role for FvCKX1. RNA interference (RNAi) suppression of FvCKX1 significantly enhanced receptacle expansion but delayed achene maturation, whereas overexpression inhibited receptacle growth while accelerating achene ripening. Abscisic acid (ABA), which positively regulates fruit enlargement, was elevated in FvCKX1 RNAi receptacles and notably reduced in overexpression fruits, indicating that FvCKX1 might negatively modulate ABA synthesis during strawberry fruit development. Our results demonstrate that FvCKX1 may function as a key regulator mediating the coordinated development between achenes and receptacles in strawberry. Full article

Leaf-color variation in plants should be associated with chlorophyll metabolism and chloroplast development. Here, we characterized a low-temperature-sensitive pakchoi DH line, 1197, which exhibited green leaves at 25 °C, but showed yellowing at 4 °C. Low temperature significantly reduced chlorophyll accumulation and disrupted chloroplast ultrastructure. After transfer from 4 °C to 25 °C for 7 days, yellow leaves partially regreened, and chlorophyll a content increased by 366.67%. RNA-seq analysis identified 3058 core DEGs associated with the yellowing–regreening transition, which were significantly enriched in photosynthesis–antenna proteins, photosynthesis, and porphyrin metabolism pathways. Leaf yellowing was characterized by repression of chlorophyll biosynthesis genes (e.g., CHLD, CHLM, PORC) and induction of degradation genes (SGR1, SGR2, NYC1, PAO), together with widespread downregulation of chloroplast function-related genes. In addition, GLK2, HBI1, NAC047, and NAC029 were identified as candidate regulators of temperature-dependent leaf-color conversion. This study provides candidate molecular insights into low-temperature-induced yellowing and regreening in pakchoi and offers candidate genes for future functional validation and Brassica breeding. Full article

Temperature and nutrient availability are pivotal drivers of coastal phytoplankton dynamics; however, how they regulate the interplay between community assembly and ecological network stability remains less explored. In this study, we integrated 18S rRNA high-throughput sequencing with molecular ecological network analysis and the iCAMP model to investigate the seasonal succession and driving mechanisms of phytoplankton in a coastal region (Qiongdong) of the South China Sea. Our results suggest that water temperature is a key factor influencing community succession. However, rather than following a linear response to temperature rise, the molecular ecological network exhibited a significant network contraction in spring, characterized by minimized complexity and peak vulnerability. This structural shift coincided with a transition in nutrient limitation (from phosphorus to nitrogen) induced by spring upwelling. Assembly process analysis revealed that while stochastic processes dominated overall community construction, a notable increase in dispersal limitation occurred in spring. The intensification of dispersal limitation driven by changes in the nutritional structure may be the main cause of network simplification and reduced stability. In conclusion, our findings highlight that while temperature affects the seasonal replacement of phytoplankton species, nutrient-induced shifts in assembly mechanisms degrade ecological network integrity in coastal environments. Full article

Regulated cardiomyocyte death is a central contributor to myocardial infarction (MI)-associated injury. Mixed lineage kinase domain-like protein (MLKL), a key effector of necroptosis, has been implicated in cardiovascular disease; however, its role in MI remains incompletely defined. MLKL expression was evaluated in hypoxia-treated cardiomyocytes, infarcted murine hearts, and human cardiac tissue. MLKL function was investigated using siRNA-mediated knockdown in neonatal mouse cardiomyocytes and genetic deletion in mice subjected to left anterior descending (LAD) coronary artery ligation. Apoptosis- and pyroptosis-related signaling were assessed by immunoblotting and immunostaining. RIP3 expression and regulation were examined at both protein and mRNA levels, and the RIP3 inhibitor GSK’872 was used to assess pathway dependence. MLKL expression was increased in hypoxic cardiomyocytes, infarcted mouse hearts, and human failing cardiac tissue. Unexpectedly, MLKL deficiency was associated with aggravated myocardial injury, impaired cardiac function, and increased fibrosis following MI. Mechanistically, MLKL deficiency was associated with increased RIP3 protein abundance without a corresponding increase in RIP3 mRNA, consistent with post-transcriptional regulation. Further analyses indicated that MLKL deficiency reduced RIP3 ubiquitination and impaired proteasome-mediated degradation, resulting in RIP3 stabilization. Elevated RIP3 levels were accompanied by increased expression of apoptosis- and pyroptosis-related proteins, particularly at early time points after MI. Pharmacological inhibition of RIP3 with GSK’872 was associated with reduced apoptosis- and pyroptosis-related signaling and improved cardiac function. MLKL deficiency is associated with stabilization of RIP3 and enhanced activation of apoptosis- and pyroptosis-related signaling following MI, contributing to aggravated myocardial injury. These findings support a regulatory role for the MLKL–RIP3 axis in cardiomyocyte death and suggest that targeting RIP3 may represent a potential therapeutic strategy in myocardial infarction. Full article

The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway serves as a central innate immune signaling axis in host defense against DNA virus infections, and RNA viruses have also evolved diverse strategies to counteract this pathway. Encephalomyocarditis virus (EMCV), a zoonotic RNA virus, utilizes its 2C protein to antagonize RIG-I-like receptor-mediated type I interferon signaling and induce autophagic degradation of calcium binding and coiled-coil domain 2, thereby evading host antiviral immunity. However, the precise molecular mechanism by which EMCV 2C protein modulates the cGAS-STING pathway remains incompletely understood. Herein, we show that EMCV infection reduces the expression of cGAS and STING proteins, and its 2C protein significantly suppresses the production of IFN-β triggered by poly(dA:dT) or viral infection, as well as the mRNA expression of interferon-stimulated genes. Mechanistically, 2C protein binds to STING via its ATPase domain and facilitates K48-linked polyubiquitination and proteasomal degradation of STING, while dominantly interfering STING translocation to the Golgi apparatus and the formation of STING-TBK1-IRF3 complex, thereby blocking STING-mediated IFN-β signal transduction at multiple levels. This study reveals a novel mechanism by which the EMCV 2C protein suppresses the host antiviral response by targeting STING and promoting its ubiquitination and degradation. This finding deepens understanding of the immune evasion mechanism of EMCV and provides a theoretical foundation for the development of antiviral therapies targeting the 2C protein of picornaviruses. Full article

Anaerobic digestion (AD) of animal manures for biogas production faces challenges including nutritional imbalance, foaming, and process instability. This study evaluated bioaugmentation with surfactant-degrading microbial consortia and cell-free extracts derived from well-characterized oil-contaminated soils during cow and pig manure digestion. These previously analyzed soils contained distinct microbial communities dominated by Pseudomonas in acidic, high-PAH soils and Bacillus in neutral-pH soils with genetic potential for hydrocarbon degradation. Over 30 days, six treatments were assessed using the Automatic Methane Potential Test System (AMPTS II), with pH monitoring, foaming analysis, and 16S rRNA sequencing coupled with PICRUSt2 functional prediction. Supplementation with microbial consortia and extract markedly increased cumulative biogas outputs (cow manure: 407.76 to 603.28 mL/gVS and pig manure: 403.82 to 627.5 mL/gVS), biomethane by 30–50%, reduced digestion time by 5–6 days, and improved pH stability. Foaming reduction was substrate-specific: extracts reduced foam by up to 60% in pig manure, while consortia reduced it by up to 65% in cow manure. Microbial analysis revealed enrichment of fermentative and syntrophic taxa (Clostridium sensu stricto and Paludibacter) and upregulation of methanogenesis pathways (tetrahydromethanopterin S-methyltransferase). This study illustrates that tailored bioaugmentation utilizing consortia from hydrocarbon-contaminated soils provides an environmentally sustainable method to enhance methane yields, improve stability, and control foaming in manure AD, with outcomes significantly affected by the type of manure and amendment strategy employed. Full article

Maize (Zea mays L.) cultivation is severely affected by Fusarium verticillioides, a highly adaptable systemic pathogen that causes serious yield losses, reduces grain quality, and produces toxic fumonisin, posing significant health risks to humans and livestock. A biological control approach to combating it was investigated. Streptomyces sp. BPTC-684 showed strong inhibitory activity (53.11%) against F. verticillioides BNGO-16, isolated from a diseased tissue sample. Based on physiological and biochemical characteristics, 16S rRNA gene sequencing, average nucleotide identity, and digital DNA–DNA hybridization, strain BPTC-684 is considered a candidate new species belonging to the genus Streptomyces. In silico analysis of Streptomyces sp. BPTC-684 showed that it expresses diverse biosynthetic gene clusters encoding potential bioactive compounds, notably antibiotics (kinamycin, antimycin, fuelimycins A-C, hangtaimycin, and deoxyhangtaimycin) and siderophores (desferrioxamines B and E). In addition, plant growth-promoting behaviors, such as indole-3-acetic acid production; phosphate solubilization; and the production of extracellular lytic enzymes that degrade cellulose, chitin, proteins, amylose, and xylan, were also discovered in Streptomyces sp. BPTC-684. The pot experiments demonstrated that plant height, fresh weight, and dry root weight were increased in strain BPTC-684 by 37.88%, 132.50%, and 223.81%, respectively, compared to F. verticillioides BNGO-16 on the 15th day of infection. These findings suggest that Streptomyces sp. BPTC-684 is a promising biological control agent for inhibiting fungal diseases and promoting maize growth. Full article

Bitter taste receptors (TAS2Rs) are G protein-coupled receptors best known for detecting bitter compounds in the oral cavity. However, their expression patterns and physiological roles in the liver remain largely unexplored. Here, we employed molecular and immunohistochemical approaches to demonstrate that multiple TAS2Rs are expressed in human Hep3B cells and mouse primary hepatocytes (MPHs) and co-localized with β-adrenergic receptors (βARs) at the bile canaliculi. Bioluminescence resonance energy transfer (BRET), cAMP assays, and Western blot analyses revealed that certain TAS2Rs exhibit ligand-dependent coupling preferences for the G protein subunits Gαi1, Gαi2, and Gαi3. This coupling leads to inhibition of cAMP production and a reduction in protein kinase A (PKA) substrate phosphorylation. Biochemical assays further showed that TAS2R activation significantly attenuates βAR-mediated lipolysis, as well as the production of glycerol and free fatty acid in both Hep3B cells and MPHs. These effects were partially reversed by small interfering RNA (siRNA)-mediated knockdown of TAS2Rs. Moreover, studies using a steatotic mouse model demonstrated that bitter compounds inhibit lipid droplet degradation, resulting in hepatic triacylglycerol accumulation. Collectively, these findings reveal a role for TAS2Rs in modulating hepatic lipid metabolism and highlight their potential as therapeutic targets for the prevention and treatment of liver diseases. Full article

Salt stress severely restricts grape (Vitis vinifera L.) production. Serine/arginine-rich (SR) proteins, as a class of RNA-binding proteins, play important roles in plant growth, development and stress responses. However, the function and regulatory mechanism of VvSR34a in grape salt tolerance remain unclear. In this study, grape callus and cutting seedlings were used as materials to explore the role and molecular mechanism of VvSR34a in grape salt stress response. The results showed that, under 100 mM NaCl treatment, the relative level of VvSR34a in grape callus exhibited a ‘first increase and then decrease’ pattern, reaching a peak at 2 h, and the gene was localized in the nucleus. Transgenic experiments confirmed that the overexpression of VvSR34a significantly enhanced salt tolerance in grape callus and cuttings, as evidenced by better growth status, higher chlorophyll content and root activity, as well as lower electrolyte leakage and malondialdehyde (MDA) content under salt stress. In contrast, the silencing of VvSR34a significantly increased salt sensitivity in grapes. Y2H and LCI assays verified that VvSR34a physically interacts with VvCOP9. VvCOP9 may play a negative regulatory role in the salt stress response of the grapevine, and through the loss of the high salt-tolerant phenotype in the VvSR34a/VvCOP9-RNAi lines, it demonstrated that VvCOP9 is genetically upstream of VvSR34a. Furthermore, the ubiquitination and degradation assay demonstrated that VvCOP9 can significantly promote the degradation of VvSR34a. RNA-seq analysis showed that a total of 2834 differentially expressed genes and 202 alternative splicing events were detected in VvSR34a overexpression lines. These differentially expressed genes were significantly enriched in ATPase activity, redox and hormone signaling pathways. This study demonstrates that VvSR34a positively regulates salt tolerance in grapes, providing an important theoretical basis for molecular breeding of salt-tolerant grapevines. Full article

The excessive use of chemical fertilizers in rice cultivation has contributed to soil degradation, creating a need for sustainable biological alternatives. This study examined the functional diversity of three indigenous nostocalean cyanobacterial strains (UP1, UP2, and UP3) isolated from forest and paddy field ecosystems by comparing the effects of their cellular biomass and extracellular polymeric substances (EPS) on rice seedling growth and soil properties. Morphological observations and partial 16S rRNA sequence analysis indicated that strains UP1 and UP2 were affiliated with the genus Ahomia, whereas UP3 was placed within the genus Nostoc. Together, these results placed all three isolates within the heterocystous cyanobacterial order Nostocales. The strains were further characterized based on EPS production and its degree of polymerization. Seed germination and seedling vigor assays were conducted to select the most effective biomass and EPS treatments, which were subsequently evaluated in 21-day pot experiments. Fresh biomass from strain UP2 most effectively enhanced rice growth, whereas EPS from strain UP3 promoted root development. EPS application from strain UP3 significantly increased root elongation to 13.44 cm, while high biomass levels of UP2 increased total sugar and free amino acid contents, indicating distinct plant response patterns. Soil analyses revealed differential responses between biomass- and EPS-based applications, with biomass generally producing stronger effects. Biomass from all strains was associated with higher physical soil function index (PSFI) values (up to 1.35). In contrast, improvements in chemical soil function index (CSFI) were observed across treatments, with variable responses and relatively higher values recorded in biomass from strain UP3 (up to 1.24). These findings suggest strain- and form-dependent response patterns of nostocalean cyanobacteria with potential for enhancing rice growth and improving soil functionality under the controlled conditions. Full article

In ruminant nutrition, the lignocellulosic complex is a primary constraint limiting the utilization of dietary fiber. The objective of this study was to evaluate the effects of inoculating lignin-degrading bacteria (LDB) isolated from the ruminant rectum on in vitro rumen fermentation characteristics. Rectal fecal samples were collected from healthy beef cattle, dairy cattle, buffaloes, and goats (n = 4 per species) using the grab sampling technique. Twenty-eight bacterial colonies were isolated through enrichment and screening on media containing sodium lignosulfonate. Lignin degradation efficiency was assessed spectrophotometrically, while laccase activity was determined using a 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) oxidation assay. Seven isolates exhibiting ligninolytic activity (1.4–5.6% degradation efficiency) were selected to evaluate their effects on in vitro rumen fermentation using a completely randomized design with four replicates. LDB treatments were standardized to a concentration of 2.4 × 10⁵ colony-forming units/mL of rumen fluid medium, while the control received an equal volume of a 0.85% sterile NaCl solution. A rice straw-based total mixed ration served as the substrate, with rumen fluid collected from beef cattle. All treatments were incubated for 48 h. Notably, isolate BC3 consistently enhanced in vitro dry matter digestibility (23.1%), total gas production (18.6%), and total volatile fatty acid concentrations (13.2%) relative to the control and other LDB isolates (p < 0.01). All seven LDB isolates were identified as Gram-negative, rod-shaped, facultative anaerobic bacteria that exhibit catalase activity and tolerate moderately acidic conditions. Phylogenetic tree analysis based on 16S rRNA gene sequencing identified isolate BC3 as being closely related to Escherichia coli strains. These findings demonstrate that the ruminant hindgut is a promising source of LDB with the functional potential to enhance feed digestibility and fermentation end-products in the rumen. Future research should prioritize in vivo trials to evaluate the safety and efficacy of LDB as a direct-fed microbial, specifically focusing on its impact on animal performance and health. Full article

Acute kidney injury (AKI) is a major complication of lupus nephritis and kidney transplantation, inevitably causing ischemia–reperfusion (I/R) injury. We previously confirmed that high-dose voclosporin induces drug nephropathy through aberrant peroxisome accumulation. The latter induces increased renal indole-3-aceticT acid (IAA) production due to the decreased expression of the IAA-degrading enzyme indolethylamine N-methyltransferase (INMT). Conversely, INMT overexpression prevents this nephropathy, suggesting that high-dose voclosporin could enable a novel therapeutic approach. This prompted us to test whether INMT overexpression with high-dose voclosporin could avert nephrotoxicity and protect against I/R injury. Inmt-overexpressing mice treated with high-dose voclosporin exhibited absence of peroxisomal abnormalities and resistance to I/R injury. RNA sequencing revealed the downregulation of tubular injury markers NGAL (Lcn2) and KIM-1 (Havcr1) concurrent with significant cytokine suppression. Mechanistic analysis revealed the robust induction of Regnase-2, an mRNA decay factor, which directly targeted stem–loop structures within the 3′ untranslated region of Lcn2 and Havcr1, thereby promoting their degradation in proximal tubular cells. Importantly, Regnase-2 knockdown mice showed Lcn2 upregulation, mitochondrial dysfunction, and peroxisomal abnormalities culminating in AKI, underscoring its renal protective effects. High-dose voclosporin under Inmt overexpression promoted Regnase-2-mediated mRNA decay to suppress tubular injury. This protective effect extended beyond I/R to rhabdomyolysis- and lipopolysaccharide-induced AKI to prevent nephropathy. Our findings demonstrate the potential transformative therapeutic approach of administering high-dose voclosporin to promote the prophylactic effect of Regnase-2 augmentation against AKI in both native and transplanted human kidneys. Full article