Search Results (71)

Cadmium (Cd) pollution poses a serious threat to freshwater ecosystems. The freshwater mussel Anodonta woodiana is increasingly used as a bioindicator for monitoring Cd pollution in aquatic environments. However, the primary routes of Cd accumulation in A. woodiana remain unclear, and the molecular regulatory mechanisms underlying Cd accumulation are poorly understood. To address these gaps, this study employed a novel stable isotope dual-tracer technique to trace Cd from water (waterborne ¹¹²Cd) and the green alga Chlorella vulgaris (dietary ¹¹³Cd) during the simultaneous exposure experiment. Comparative transcriptomic analysis was then conducted to characterize molecular responses in A. woodiana following Cd exposure. The results showed that although newly accumulated ¹¹²Cd and ¹¹³Cd increased with exposure concentration and duration, the relative importance of ¹¹²Cd (91.6 ± 2.8%) was significantly higher than that of ¹¹³Cd (8.4 ± 2.8%) (p < 0.05). Cd exposure induced differentially expressed genes primarily enriched in the metabolic processes, cellular processes, and/or the ubiquitin-mediated proteolysis pathway. Within the ubiquitin-mediated proteolysis pathway, TRIP12 (E3 ubiquitin-protein ligase TRIP12) and Cul5 (cullin-5) were significantly upregulated. The findings will provide critical insights for interpreting Cd biomonitoring data in freshwater environments using mussels as bioindicators. Full article

Recent advances have highlighted the multifaceted roles of the lymphatic vasculature in immune cell trafficking, immunomodulation, nutrient transport, and fluid homeostasis. Beyond these physiological functions, lymphatic vessels are critically involved in pathologies such as cancer metastasis and lymphedema, rendering their structural and functional regulation of major interest. Emerging evidence suggests that limited proteolysis is a key regulatory mechanism for lymphatic vascular function. In dyslipidemic conditions, dysregulated calpain activity impairs lymphatic trafficking and destabilizes regulatory T cells, partly via the limited proteolysis of mitogen-activated kinase kinase kinase 1 and inhibitor of κBα. In addition, a disintegrin and metalloprotease with thrombospondin motifs-3-mediated proteolytic activation of vascular endothelial growth factor-C has been implicated in both developmental and tumor-associated lymphangiogenesis. Proteolytic shedding of lymphatic vessel endothelial hyaluronan receptor-1 by a disintegrin and metalloprotease 17 promotes lymphangiogenesis, whereas cleavage by membrane-type 1 matrix metalloproteinase inhibits it. This review is structured around two core aspects—lymphatic inflammation and lymphangiogenesis—and highlights recent findings on how limited proteolysis regulates each of these processes. It also discusses the therapeutic potential of targeting these proteolytic machineries and currently unexplored research questions, such as how intercellular junctions of lymphatic endothelial cells are controlled. Full article

This study aimed to verify, under real operating conditions, the effectiveness of protective lactic acid bacteria (LAB) culture in counteracting the development of late blowing defects in Valtellina Casera PDO cheese and its impact on product sensory characteristics. Thirty-four LAB isolated from Bitto and Valtellina Casera PDO cheeses were screened for anti-Clostridium activity. Lacticaseibacillus casei VC201 was able to inhibit all the indicator strains through organic acid production. Valtellina Casera PDO cheese-making was performed twice in three dairy farms using a commercial autochthonous starter culture with and without the addition of the protective culture VC201. Cheese was ripened both at 8 °C and 12 °C and analyzed after 70 and 180 days for LAB population, proteolysis, and lipolysis evolution as well as sensory impact. Cheeses with the addition of the VC201 strain showed higher contents of rod-shaped LAB throughout the ripening at both temperatures. The protective culture decreased the production of butyric acid at 70 days, especially at 8 °C (−15.4%), while butyric fermentation was occasionally lightly observed at 12 °C. The sensory profile was favorably impacted by the higher relative proportion of short-chain fatty acids (SCFFAs, C2–C8), which was especially pronounced at 8 °C and persisted for 180-day ripening (23.91% vs. 18.84% at 70 days and 23.84 vs. 21.71 at 180 days of ripening). The temperature and time of ripening had a significant effect on the free fatty acid content of the cheese samples in all three classes (SCFFA, MCFFA, and LCFFA). The cheese made with Lcb. casei VC201 was preferred, according to the sensory evaluation, being perceived as less acidic, less bitter, tastier, and with more intense flavor. Protective cultures can represent a practical way to reduce late blowing defects in Valtellina Casera cheese production while maintaining adherence to its PDO regulatory requirements. Full article

Circular RNAs (circRNAs), a class of covalently closed non-coding RNAs, are pivotal regulators of gene expression and contributors to disease pathogenesis. This study elucidated the biogenesis, functional significance, and regulatory network of circRNA_4083, a novel exon-derived circRNA originating from exons 22 and 23 of the MSH3 gene in chicken. Through comprehensive molecular characterization—including Sanger sequencing, RNase R digestion assays, and subcellular localization—we confirmed the robust stability and predominant cytoplasmic localization of circRNA_4083 across diverse chicken tissues. Mechanistic investigations revealed that reverse complementary sequences within flanking intronic regions are indispensable for its circularization, as demonstrated by overexpression plasmids (#1–#4) in DF-1 cells. Functional analyses demonstrated that circRNA_4083 significantly inhibited cell apoptosis and increased cellular viability. Integrative bioinformatics approaches predicted a competing endogenous RNA (ceRNA) network comprising 12 miRNAs and 2132 target genes (FDR < 0.05), with significant enrichment in pathways critical to genomic stability, including non-homologous end joining (NHEJ) and ubiquitin-mediated proteolysis. These findings position circRNA_4083 as a key modulator of cellular viability and genomic integrity, with potential implications for avian leukosis virus-J (ALV-J) pathogenesis and resistance breeding strategies. This work advances our understanding of circRNA-driven regulatory mechanisms in avian species and underscores their relevance in poultry health. Full article

The growing threat of antimicrobial resistance has intensified the search for alternative strategies to conventional antibiotics and preservatives. Casein-derived antimicrobial peptides (CDAMPs), generated through proteolysis, exhibit potent activity against a broad spectrum of pathogens, including antibiotic-resistant strains, revealing strong potential as natural preservatives and therapeutic agents in food and medical applications. Furthermore, casein can be an ideal source for peptide production in these sectors due to its abundance, disordered structure, which enhances enzymatic cleavage, and its amino acid profile, which favors bioactivity. Nonetheless, there is limited literature addressing real-life applications in veterinary medicine, food safety, and public health. This review provides a structured synthesis of current knowledge on the antibacterial properties of CDPs. We classify the main types of these peptides, describe their production methods, and summarize their mechanisms of action against Gram-positive and Gram-negative bacteria. Furthermore, we examine their potential applications in clinical, veterinary, and food-related contexts, and discuss key aspects related to delivery systems, safety, and regulatory considerations. Overall, our findings highlight the potential of CDPs in addressing antimicrobial resistance, reducing antibiotic use in livestock and humans, and contributing to sustainable food safety and functional food production. Full article

Acid rain has many negative effects on the ecological environment and poses serious abiotic stress onto plants, resulting in substantial ecological and economic impairments annually. Ilex chinensis, a well-known medicinal plant, is sensitive to acid rain, but its response mechanisms are unclear. In this study, we simulated sulfuric acid rain (SAR), mixed acid rain (MIX), and nitric acid rain (NAR) at different pH values to investigate their effects on growth condition, photosynthesis, antioxidants, and nitrogen metabolites. We also explored the metabolic pathways and key genes involved in the response of I. chinensis to acid rain through transcriptome analysis. Physiological analysis showed that I. chinensis suffered the most significant inhibition at pH 3.0, which is manifested in the decrease in height growth rate, specific leaf weight, photosynthetic pigments content, net photosynthetic rate, stomatal conductance, and transpiration rate; the increase in MDA content and SOD activity; and the reduction in glutamine synthetase activity, nitrogen content, and proline content. Transcriptome analysis isolated 314 and 21 shared differentially expressed genes (DEGs) from I. chinensis treated with acid rain at pH 3.0 for 5 d and 15 d, respectively. KEGG enrichment analysis found that different types of acid rain caused changes in multiple metabolic pathways of I. chinensis, and the shared DEGs in 5 d treatment were mainly enriched in ribosomes, oxidative phosphorylation, and glycolysis/glycolysis, etc. The shared DEGs in 115 d treatment were mainly enriched in sulfur metabolism, RNA polymerase, cysteine and methionine metabolism, etc. Further research on gene regulatory networks at the two time points showed that the key pathways of I. chinensis, in response to acid rain stress, include plant–pathogen interaction, MAPK signaling pathway-plant, protein processing in the endoplasmic reticulum, ubiquitin mediated proteolysis, etc., in which 6 hub genes were identified, including TRINITY_DN13584_c0_g1, TRINITY_DN164_c0_g4, TRINITY_DN654_c0_g1, TRINITY_DN13611_c1_g2, TRINITY_DN21290_c0_g2, TRINITY_DN44216_c0_g1. Our findings provide a basis for exploring the regulatory mechanisms of I. chinensis in response to acid rain at the physiological and molecular levels, and for identifying candidate genes with acid tolerance potential. Full article

Cry j 7 is a 7 kDa cysteine-rich gibberellin regulatory protein (GRP) with six disulfide bonds. It was isolated from Japanese cedar as the pollen allergen in this study. It exhibits cross-reactivity with food allergens such as Pru p 7 from peach and causes pollen-food allergy syndrome (PFAS). In this work, recombinant Cry j 7 and Pru p 7 were successfully overexpressed using Pichia pastoris in a high-cell-density fermentation culture, and pure proteins were purified by reverse-phase HPLC. The characterization of Cry j 7 and Pru p 7 were performed by MS, CD, and ¹H-NMR experiments to confirm the correct native conformation of Cry j 7 as well as Pru p 7. When compared, the results showed that Cry j 7 exhibits excellent stability in disulfide linkages and preserves its original structure up to 90 °C in various pH buffers in comparison to Pru p 7. Notably, NMR analyses indicated the greater mobility in the α-helix and loop regions of S38-C47 in Pru p 7 compared to those of Cry j 7. Furthermore, our results showed that the sensitivity of Cry j 7 to enzyme digestion differed from that of Pru p 7: Cry j 7 was more susceptible to proteolysis, while Pru p 7 displayed better resistance in the gastrointestinal tract. These variations in structural stability and sensitivity to proteolysis provide valuable insights into the allergenicity within the GRP family. Full article

Ascosphaera apis is a fungal pathogen that specifically infects bee larvae, causing an outbreak of chalkbrood disease in the bee colony and a decline in the number of bee colonies. The role of miRNA regulation in honeybees in response to A. apis infection is unclear. In this study, based on small RNA-seq, we identified the differentially expressed miRNAs (DEmiRNAs) and their regulatory networks and functions in the gut of Apis cerana cerana on the first day (AcT1), the second day (AcT2) and the third day (AcT3) after A. apis infection, and analyzed the immune response mechanism of A. apis through the miRNAs-mRNA regulation network of A. apis infection. A total of 537 miRNAs were obtained, and 10, 27, and 54 DEmiRNAs were screened in the AcT1, AcT2, and AcT3 groups, respectively. The number of DEmiRNAs gradually increased with the infection time. Stem-loop RT-PCR results showed that most of the DEmiRNAs were truly expressed, and the expression trend of DEmiRNAs was consistent with the results of sRNA-seq. The top five GO terms of DEmiRNA-targeted mRNA were binding, cellular process, catalytic activity, metabolic process, and single-organism process. The main pathways enriched by KEGG were endocytosis, ubiquitin-mediated proteolysis, phagosome, and the JAK-STAT immune-related signaling pathways. The number of DEmiRNAs and target mRNAs of these related pathway genes increased with infection time. The miRNA-mRNA regulatory network analysis showed that ace-miR-539-y was the core miRNA of the early immune response in the gut of larvae infected with A. apis in the JAK-STAT pathway and phagosome, and ace-miR-1277-x was the core miRNA of the late immune response in the gut of larvae infected with A. apis in the JAK-STAT signaling pathway and phagosome. The results showed that miRNA participated in the immune response of honeybees to A. apis infection by regulating the host’s energy metabolism, cellular immunity, and humoral immunity. The results of this study provide a basis for the regulation of miRNAs in A. c. cerana larvae in response to A. apis infection and provide new insights into host-pathogen interactions. Full article

Proteasome-mediated protein degradation is essential for maintaining cellular homeostasis, particularly during spermatogenesis, where extensive cellular transformations, such as spermatid differentiation, require precise protein turnover. A key player in this process is the ubiquitin–proteasome system (UPS). This study aimed to investigate proteasome enzymatic activity at different stages of the spermatogenic cycle within the seminiferous tubules of mice and explore the regulatory mechanisms that influence its proteolytic function. Specifically, we assessed the trypsin-like, chymotrypsin-like, and peptidyl-glutamyl-peptide-hydrolyzing (PGPH) activities of the proteasome. Additionally, we examined the expression of catalytic and structural subunits of the 20S core, the assembly of the 20S core with regulatory complexes, and the phosphorylation status of proteasome subunits in various segments of the seminiferous tubules. Our findings demonstrated distinct patterns of proteasomal enzymatic activity in the analyzed segments. While the expression levels of structural and catalytic subunits of the 20S core remained consistent, significant differences were detected in the assembly of the 20S core, the expression of regulatory complexes, and the phosphorylation of proteasome subunits mediated by protein kinase A. These results indicate that proteasomal activity is finely regulated through multiple mechanisms depending on the specific stage of the seminiferous epithelial cycle, highlighting the complexity of proteostasis during spermatogenesis. Full article

Enzyme-mediated protein degradation is a major concern in industrial fungal strain improvement, making low-proteolytic strains preferable for enhanced protein production. Here, we improved food-grade Aspergillus oryzae BCC7051 by manipulating the transcriptional regulation of protease-encoding genes. Genome mining of the transcription factor AoprtR and computational analysis confirmed its deduced amino acid sequence sharing evolutionary conservation across Aspergillus and Penicillium spp. The AoPrtR protein, which is classified into the Zn(II)2-Cys6-type transcription factor family, manipulates both intra- and extracellular proteolytic enzymes. Our transcriptional analysis indicated that the regulation of several protease-encoding genes was AoPrtR-dependent, with AoPrtR acting as a potent activator for extracellular acid-protease-encoding genes and a likely repressor for intracellular non-acid-protease-encoding genes. An indirect regulatory mechanism independent of PrtR may enhance proteolysis. Moreover, AoPrtR disruption increased extracellular esterase production by 2.55-fold, emphasizing its role in protein secretion. Our findings highlight the complexity of AoPrtR-mediated regulation by A. oryzae. Manipulation of regulatory processes through AoPrtR prevents secreted protein degradation and enhances the quantity of extracellular proteins, suggesting the low-proteolytic variant as a promising platform for the production of these proteins. This modified strain has biotechnological potential for further refinement and sustainable production of bio-based products in the food, feed, and nutraceutical industries. Full article

There has been noteworthy progress in molecular characterisation and therapeutics in soft tissue sarcomas. Novel agents have gained regulatory approval by the FDA. Examples are the tyrosine kinase inhibitors avapritinib and ripretinib in gastrointestinal stromal tumours (GIST), the immune check point inhibitor atezolizumab in alveolar soft part tissue sarcoma, the γ-secretase inhibitor nirogacestat in desmoid tumours, the NTRK inhibitors larotrectinib and entrectinib in tumours with NTRK fusions, the mTOR inhibitor nab-sirolimus in PEComa, and the EZH-2 inhibitor tazemetostat in epithelioid sarcoma. The FDA has also recently granted accelerated approval for autologous T-cell therapy with afami-cel in patients with HLA-A*02 and MAGE-A4-expressing synovial sarcoma. There are other promising treatments that are still investigational, such as MDM2 and CDK4/6 inhibitors in well-/dedifferentiated liposarcoma, immune checkpoint inhibitors in the head and neck angiosarcoma and a subset of patients with undifferentiated pleomorphic sarcoma, and PARP inhibitors in leiomyosarcoma. The challenges in drug development in soft tissue sarcoma are due to the rarity and the molecular heterogeneity of the disease and the fact that many subtypes are associated with complex karyotypes or non-targetable molecular alterations. We believe that progress maybe possible with a better understanding of the complex biology, the development of novel compounds for difficult targets such as proteolysis targeting chimeras (Protacs), the utilisation of modern clinical trial designs, and enhanced collaboration of academia with industry to develop treatments with a strong biologic rationale. Full article

Quercetin is a natural polyphenolic flavonoid widely found in plants, fruits, and vegetables, and has been reported to play pharmacological roles in numerous pathogenic conditions. The anti-inflammatory effects of quercetin in various inflammatory conditions and diseases have been well-documented. However, its regulatory role in noncanonical inflammasome activation has not yet been demonstrated. This study investigated the anti-inflammatory effects of quercetin in caspase-11 noncanonical inflammasome-activated inflammatory responses in macrophages and a mouse model of acute lethal sepsis. Quercetin protected J774A.1 macrophages from lipopolysaccharide (LPS)-induced cell death and caspase-11 noncanonical inflammasome-induced pyroptosis. It significantly decreased the production and mRNA expression of pro-inflammatory cytokines, such as interleukin (IL)-1β, IL-18, and IL-6, but not tumor necrosis factor (TNF)-α, and inflammatory molecules, such as nitric oxide (NO) and inducible NO synthase in caspase-11 noncanonical inflammasome-activated J774A.1 cells. Mechanistically, quercetin strongly suppressed the autoproteolysis and secretion of caspase-11 and the proteolysis of gasdermin D in caspase-11 noncanonical inflammasome-activated J774A.1 cells. However, quercetin did not inhibit the direct binding of caspase-11 to LPS. In vivo, the study revealed that quercetin increased the survival rate of mice with acute lethal sepsis and decreased serum levels of pro-inflammatory cytokines without causing significant toxicity. In conclusion, this study highlights quercetin-mediated anti-inflammatory action in inflammatory responses and acute lethal sepsis through a novel mechanism that targets the caspase-11 noncanonical inflammasome in macrophages, suggesting quercetin as a promising anti-inflammatory agent in natural medicine. Full article

The p53 protein has attracted huge research interest over several decades due to its role as one of the most important tumor suppressors in mammals, which orchestrates a synchronous response from normal cells in the body to various forms of stress. The diverse cellular activities of the p53 protein are regulated mainly via its post-translational modifications (PTMs). PTMs affect p53 on several levels: at the level of the assembly of tetrameric complexes on DNA to transactivate its target genes, at the level of the assembly of tetrameric complexes on DNA to transactivate its target genes; at the level of proteolysis in the absence of stress; and on the contrary, at the level of augmented protein stability in response to stress signals. Disruptions in these regulatory mechanisms can lead to deviations from normal cellular function, boosting tumor initiation and progression. Conversely, targeted interventions in these pathways could prove beneficial for the development of antitumor therapies. Advancing our understanding of p53 modifiers and the proteins involved in its regulation equips researchers with an expanded toolkit for studying cellular processes and for developing biologically active molecules that influence p53-mediated responses. Full article

Background: The thrombin-activatable fibrinolysis inhibitor (TAFI) is an important regulator in the balance between blood clot formation (coagulation) and dissolution (fibrinolysis), which is mainly activated by thrombin bonded with thrombomodulin (TM). Methods: In this study, the investigation focused on the unique target TAFI of fungi fibrinolytic compound 1 (FGFC1), a novel fibrinolytic compound sourced from the deep sea. In this sense, the regulation of TAFI by FGFC1, in comparison to established TAFI inhibitors such as DS-1040 and PCTI in hPPP, was investigated, which was validated through the molecular docking of FGFC1 to TAFI. The inhibitory effect of FGFC1 on TAFI-mediating coagulation (ex vivo and in vitro) and its fibrinolytic effect (ex vivo) were investigated in hPPP and hCMEC/D3 cells, respectively, followed by SEM. Results: FGFC1 solutions ranging from 0.023 to 0.736 mM effectively inhibited TAFI activation. Notably, the 0.023 mM concentration demonstrated significant suppression, comparable to DS-1040 and PCTI. These inhibitory effects of FGFC1 (0.023–0.368 mM) were further validated through the enhancement in TAFI (TAFIa) activation by fibrins in the coagulum prior to proteolysis, resulting in the cleavage of TAFIa from 33 kDa to 28 kDa. Furthermore, these regulatory effects of FGFC1 on TAFI were demonstrated to have minimal association with TM-mediated control, as confirmed through a molecular docking analysis. FGFC1 (0.023–0.092 mM) was suggested to have obstructive effects on TAFI-mediated coagulation in the hPPP, which was demonstrated by the inhibition of clot aggregation, protein crystallization, and platelet anchoring, as observed through SEM. Simultaneously, FGFC1 (0.023 to 0.368 mM) significantly enhanced TAFI-mediated fibrinolysis, which was also supported by increased levels of t-PA, u-PA, and plasmin. Conclusions: From the above findings, FGFC1 is identified as a novel dual-target bioactive compound participating in blood formation/dissolution that demonstrates anti-coagulation and fibrinolytic effects by regulating TAFI activation, inhibiting TAFIa–fibrin combination, and initiating proteolysis. It also provided convincing evidence that TAFI plays a critical role in thrombolysis as a molecular link between coagulation and fibrinolysis. Furthermore, the application of FGFC1 was indicated as a potential therapeutic strategy in thromboembolic and hemorrhagic diseases. Full article

In mammals, specificity protein 1 (SP1) was the first Cys2-His2 zinc finger transcription factor to be isolated within the specificity protein and Krüppel-like factor (Sp/KLF) gene family. SP1 regulates gene expression by binding to Guanine–Cytosine (GC)-rich sequences on promoter regions of target genes, affecting various cellular processes. Additionally, the activity of SP1 is markedly influenced by posttranslational modifications, such as phosphorylation, acetylation, glycosylation, and proteolysis. SP1 is implicated in the regulation of apoptosis, cell hypertrophy, inflammation, oxidative stress, lipid metabolism, plaque stabilization, endothelial dysfunction, fibrosis, calcification, and other pathological processes. These processes impact the onset and progression of numerous cardiovascular disorders, including coronary heart disease, ischemia-reperfusion injury, cardiomyopathy, arrhythmia, and vascular disease. SP1 emerges as a potential target for the prevention and therapeutic intervention of cardiac ailments. In this review, we delve into the biological functions, pathophysiological mechanisms, and potential clinical implications of SP1 in cardiac pathology to offer valuable insights into the regulatory functions of SP1 in heart diseases and unveil novel avenues for the prevention and treatment of cardiovascular conditions. Full article