Search Results (398)

Sarcopenia, the progressive loss of muscle mass and strength, is a common complication in patients with chronic kidney disease (CKD). This condition arises from a combination of factors including reduced physical activity, insufficient protein intake, hyperphosphatemia, chronic inflammation, and uremia itself; however, the underlying molecular mechanisms remain poorly understood. Proteolysis in skeletal muscle is primarily controlled by the ubiquitin–proteasome system, autophagy–lysosome system, and calpains (CAPNs) cysteine proteases, which degrade structural proteins and mediate cell signaling. This study aims to investigate the role of CAPNs in CKD-associated muscle deterioration. CKD was induced in mice through an adenine-rich diet for 2, 4 and 6 weeks. The involvement of CAPNs in CKD-related sarcopenia was assessed using mice that overexpressed the CAPNs endogenous inhibitor, calpastatin (CAST). Gastrocnemius muscle strength, structural integrity, and function were evaluated. Mice with CKD showed elevated CAPNs, particularly CAPN2, expression and activity in the gastrocnemius, in parallel with significant muscle deterioration, including strength loss, structural damage, and impaired muscle performance. Overexpression of CAST prevented muscle strength loss, improved muscle function and structure without affecting renal function, and reversed fibrosis, inflammation and adipogenesis expression markers. Targeting CAPN2 could be a promising therapeutic strategy to mitigate muscle damage and improve physical performance in CKD patients. Full article

The saliva of the medicinal leech Hirudo medicinalis contains a wide range of biologically active compounds, including multiple anticoagulants. Previously, we identified a novel cysteine-rich anticoagulant protein (CRA) from leech saliva and produced it recombinantly in Escherichia coli, demonstrating its potential as a basis for new anticoagulant drugs. In this study, we developed an optimized procedure for scalable production and purification of recombinant CRA. The purified protein was analyzed for common contaminants originating from E. coli, such as endotoxins, bacterial proteins, and DNA, and its anticoagulant properties were evaluated using standard clotting assays. Across three independent experiments, the yield of purified CRA ranged from 3.7 to 5.5 mg per liter of bacterial culture, with impurity levels per milligram of protein ranging from 7.1–31.2 ng of bacterial proteins, 1.2–15.1 ng of DNA, and 60–1445 EU of endotoxins. The purified CRA displayed electrophoretic and chromatographic homogeneity and retained strong anticoagulant activity. Additionally, a truncated form of CRA lacking the C-terminal region was produced and characterized. This variant lost membrane affinity and showed altered activity profiles, with higher thrombin time activity but reduced prothrombin time and activated partial thromboplastin time activities compared with the full-length protein. Full article

The controlled pro-inflammatory immune response is critical for fighting against external and endogenous threats, such as microbes/pathogens, allergens, xenobiotics, various antigens, and dying host cells and their mediators (DNA, RNA, and nuclear proteins) released into the circulation and cytosol (PAMPs, MAMPs, and DAMPs). Several pattern recognition receptors (PRRs) and their downstream adaptor molecules, expressed by innate and adaptive immune cells, are critical in generating the inflammatory immune response by recognizing PAMPs, MAMPs, and DAMPs. However, their dysregulation may predispose the host to develop inflammation-associated organ damage, neurodegeneration, autoimmunity, cancer, and even death due to the absence of the inflammation resolution phase. The cytosolic calcium (Ca²⁺) level regulates the survival, proliferation, and immunological functions of immune cells. Cysteine-rich proteases, specifically calpains, are Ca²⁺-dependent proteases that become activated during inflammatory conditions, playing a critical role in the inflammatory process and associated organ damage. Therefore, this article discusses the expression and function of calpain-1 and calpain-2 (ubiquitous calpains) in various innate (epithelial, endothelial, dendritic, mast, and NK cells, as well as macrophages) and adaptive (T and B cells) immune cells, affecting inflammation and immune regulation. As inflammatory diseases are on the rise due to several factors, such as environment, lifestyle, and an aging population, we must not just investigate but strive for a deeper understanding of the inflammation and immunoregulation under the calpain system (calpain-1 and calpain-2 and their endogenous negative regulator calpastatin) lens, which is ubiquitous and senses cytosolic Ca²⁺ changes to impact immune response. Full article

The production of green hydrogen by microalgae is a promising strategy to convert energy of sun light into a carbon-free fuel. Many problems must be solved before large-scale industrial applications. One solution is to find a microalgal species that is easy to grow, easy to manipulate, and that can produce hydrogen open-air, thus in the presence of oxygen, for periods of time as long as possible. In this work we investigate by means of predictive computational models, the [FeFe] hydrogenase enzyme of Nannochloropsis salina, a promising microcalga already used to produce high-value products in salt water. Catalysis of water reduction to hydrogen by [FeFe] hydrogenase occurs in a peculiar iron-sulfur cluster (H-cluster) contained into a conserved H-domain, well represented by the known structure of the single-domain enzyme in Chlamydomonas reinhardtii (457 residues). By combining advanced deep-learning and molecular simulation methods we propose for N. salina a two-domain enzyme architecture hosting five iron-sulfur clusters. The enzyme organization is allowed by the protein size of 708 residues and by its sequence rich in cysteine and histidine residues mostly binding Fe atoms. The structure of an extended F-domain, containing four auxiliary iron-sulfur clusters and interacting with both the reductant ferredoxin and the H-domain, is thus predicted for the first time for microalgal [FeFe] hydrogenase. The structural study is the first step towards further studies of the microalga as a microorganism producing pure hydrogen gas. Full article

The expression of the Secreted Protein, Acidic and Rich in Cysteine (SPARC) gene in human melanoma increases during progression and is associated with epithelial-to-mesenchymal transition (EMT), which is a major determinant of metastasis in melanoma patients. However, the underlying molecular mechanisms that control SPARC expression in this context remain elusive. Herein, we identified Paired-related homeobox 1 (PRRX1), an EMT transcription factor, as a transcriptional activator of SPARC by direct binding to the promoter, thereby increasing its activity. Moreover, we found a strong positive correlation between SPARC and PRRX1 expression levels in clinical samples and cell lines. Furthermore, the switch from the proliferative/melanocytic phenotype toward the invasive/mesenchymal-like phenotype favors the expression of TCF7L2, a β-catenin cofactor, which, together with Sp1, binds to the proximal SPARC promoter, thereby bolstering protein expression. We also show that SPARC is a target of the miR-29 family, whose members are expressed in clinical melanoma samples and cell lines. Indeed, we found that miR-29b1~a expression is inversely correlated with SPARC levels, and it is significantly reduced in samples with a mesenchymal-like phenotype. Taken together, SPARC expression in melanoma cells relies on transcriptional activation by PRRX1/TCF7L2-Sp1 and is modulated through miR-29b1~a, which provides fine-tuning regulation over the switch between phenotypic states. Full article

Cysteine-rich polycomb-like protein (CPP) transcription factors (TFs) play critical roles in the process of plant growth and development, as well as stress responses. To date, no reports about CPP TFs have been published for lettuce (Lactuca sativa). In this study, six CPP TFs (LsCPP1-LsCPP6) were identified in lettuce. Phylogenetic analysis showed that LsCPP TFs were classified into two clades (Clade I and Clade II). Six LsCPP genes were distributed across four chromosomes. Cis-elements, which are involved in environmental stress, hormone response, and development processes, were identified in the promoters of LsCPP genes. LsCPP genes were induced by different tissues and the stem enlargement processes of stem lettuce. Plant hormones (SA, ABA) and abiotic stress (salt, drought) induced the expression of LsCPP genes. LsCPP4 was significantly induced after drought stress for 12 h. Notably, the expression level of LsCPP4 increased more than 10 times (12 h) and 150 times (24 h) after salt stress. ABA and SA significantly induced the expression profile of LsCPP6. This study not only provides the basis for future functional research of LsCPP genes, particularly their roles in lettuce stress resistance, but also provides a foundation for molecular breeding to enhance the agricultural traits in lettuce. Full article

Liver fibrosis (LF) poses significant challenges in diagnosis and treatment. This study aimed to identify effective biomarkers for diagnosis and therapy, as well as to gain deeper insights into the immunological features associated with LF. LF-related datasets were retrieved from the Gene Expression Omnibus (GEO) database. Two datasets were merged to generate a metadata cohort for bioinformatics analysis and machine learning, while another dataset was reserved for external validation. Seventy-eight machine learning algorithms were employed to screen signature genes. The diagnostic performance of these genes was evaluated using receiver operating characteristic (ROC) curves, and their expression levels were validated via qRT-PCR experiments. The R language was utilized to delineate the immune landscape. Finally, correlation analysis was conducted to investigate the relationship between the signature genes and immune infiltration. Through the intersection of GEO datasets and Weighted Gene Co-expression Network Analysis (WGCNA), 42 genes were identified. Machine learning methods further narrowed down 13 signature genes (alpha-2-macroglobulin (A2M), ankyrin-3 (ANK3), complement component 7 (C7), cadherin 6 (CDH6), cysteine-rich motor neuron protein 1 (CRIM1), dihydropyrimidinase-like 3 (DPYSL3), F3, gamma-aminobutyric acid (GABA) receptor subunit epsilon (GABRE), membrane metalloendopeptidase (MME), solute carrier family 38 member 1 (SLC38A1), tropomyosin alpha-1 chain (TPM1), von Willebrand factor (VWF), and zinc finger protein 83 (ZNF83)), and qRT-PCR confirmed these genes’ expression patterns. Furthermore, these signature genes demonstrated strong correlations with multiple immune cell populations. In conclusion, the 13 genes (A2M, ANK3, C7, CDH6, CRIM1, DPYSL3, F3, GABRE, MME, SLC38A1, TPM1, VWF, and ZNF83) represent robust potential biomarkers for the diagnosis and treatment of LF. Among these genes, we first identified Gabre as related to LF and expressed in hepatocytes and cholangiocytes. The immune response mediated by these signature biomarkers plays a pivotal role in the pathogenesis and progression of LF through dynamic interactions between the biomarkers and immune-infiltrating cells. Full article

Background/Objectives: Stroke is a cerebrovascular disorder characterized by vessel occlusion or rupture, resulting in brain damage and subsequent physical impairment. Recent studies have implicated hevin–calcyon protein binding in the repair of brain injury. Secreted protein acidic and rich in cysteine–like 1 (SPARCL1) encodes hevin. This study investigated SPARCL1 gene polymorphisms in ischemic stroke to identify potential biomarkers for brain injury treatment. Methods: we examined the associations of SPARCL1 polymorphisms (rs1049544, rs1130643, rs7695558, rs1049539) with ischemic stroke. This case–control study involved 387 controls and 509 patients with ischemic stroke. Genotyping was performed via real-time polymerase chain reaction with the TaqMan™ SNP Genotyping Kit. Results: The rs1049544 polymorphism was significantly associated with ischemic stroke prevalence (GG vs. CC: adjusted odds ratio [AOR] = 0.642, p = 0.043; GG + GC vs. CC: AOR = 0.671, p = 0.045). Additionally, rs1049544 was significantly associated with large-artery disease prevalence (GG vs. CC: AOR = 0.489, p = 0.028; GG + GC vs. CC: AOR = 0.527, p = 0.033), and rs1130643 (TT vs. TC: AOR = 0.362, p = 0.039) was associated with cardioembolism prevalence in ischemic stroke subtype analysis. In haplotype analysis, G-G (rs1049544/rs7695558; odds ratio = 4.942, p = 0.001) and C-T (rs1049544/rs1049539; odds ratio = 0.776, p = 0.043) haplotypes were associated with ischemic stroke prevalence. Although some genotypes were not individually associated with ischemic stroke, the presence of the rs1049544 C allele appeared to enhance risk. Conclusions: These findings suggest that SPARCL1 polymorphisms are associated with ischemic stroke and may be considered potential biomarkers for risk assessment. Full article

Previous studies revealed that low expression of Selenoprotein S (SELS) could enhance osteogenic differentiation, but the underlying mechanisms remain unclear. In this study, we aimed to elucidate the role of SELS and its transcription-factor-based regulatory mechanism during osteogenic differentiation. In comparison with 12-week-old mice, which represent the stage of stable osteogenic differentiation, 3-week-old mice, representing the active ossification stage, showed significantly higher levels of SELS in the mandible. Transcriptomic analysis revealed that SELS is primarily associated with extracellular matrix organization and collagen biosynthesis during mandibular development. In bone marrow mesenchymal stem cells (BMSCs) with SELS knockdown, SP7 levels were elevated after 7 days of osteogenic induction in vitro. Consistently, immunohistochemical and immunofluorescence staining confirmed increased SP7 expression in the mandibles of 7-week-old Sels knockout mice. Dual-luciferase reporter assays and chromatin immunoprecipitation (ChIP) analysis demonstrated that SP7 directly binds to the heat shock protein 47 (HSP47) promoter and negatively regulates its transcription. Consequently, upregulation of SP7 following SELS knockdown led to downregulation of HSP47 and concurrent upregulation of the SP7 downstream targets, collagen type I alpha 1 chain (COL1A1) and Secreted protein acidic and rich in cysteine (SPARC). SELS expression is upregulated during active osteogenesis. Low expression of SELS regulates osteogenic differentiation in a bidirectional and fine-tuned manner through the SP7–HSP47/COL1A1/SPARC axis. Full article

The growing population and increasing concerns about food security and sustainability demand innovative solutions to minimize food waste and transform by-products into functional ingredients valuable to the food sector. Brewery by-products, including brewer’s spent grain (BSG) and brewer’s spent yeast (BSY), are underutilized resources despite their high protein contents and potential as sustainable food ingredients. This study aimed to transform BSG and BSY into protein hydrolysates (BSGH and BSYH, respectively) through enzymatic hydrolysis and thus add value to these brewery industry by-products to be used in the food industry. These protein hydrolysates were incorporated into non-alcoholic malt beverages at three different concentrations, and their effects on the physicochemical properties, including color, kinematic viscosity, turbidity, foaming capacity and foam stability, of the non-alcoholic malt beverages were evaluated. Both BSGH and BSYH exhibited higher water solubility (WS) and lower water binding capacity (WBC) values when compared to their native non-hydrolyzed forms, enhancing their suitability as ideal ingredients for protein supplementation of a wide range of food and beverage products. The production of peptides of varying sizes underscored the effectiveness of enzymatic hydrolysis which resulted in an increase in cysteine and methionine levels in BSYH but a decrease in BSGH. The addition of BSGH and BSYH increased the kinematic viscosity and turbidity but reduced the lightness values in color of the non-alcoholic malt beverages. When the properties of the protein hydrolysates were compared, BSYH was more effective than BSGH in forming foams and maintaining their stability for longer periods. These findings highlight the potential of brewery by-products, after enzymatic hydrolysis, as protein-rich ingredients that can support more sustainable food systems and contribute to the nutritional enhancement of various low-protein food and beverage products. Full article

Conidiobolus coronatus (Entomophthorales), a fungal pathogen with a broad insect host range, is a promising candidate for biocontrol applications. We sequenced a C. coronatus strain isolated from a Rhopalomyia sp. cadaver using PacBio long-read sequencing to elucidate the molecular basis of its wide host adaptability. The newly assembled 44.21 Mb genome exhibits high completeness (BUSCO score: 93.45%) and encodes 11,128 protein-coding genes, with 23.1% predicted to mediate pathogen–host interactions. Comparative genomics with the aphid-obligate pathogen C. obscurus revealed significant expansions in gene families associated with host adaptation mechanisms, including host recognition, transcriptional regulation, degradation of host components, detoxification, and immune evasion. Functional annotation highlighted enrichment in cellular component organization and energy metabolism. Pfam annotation identified one hundred twenty-five seven-transmembrane receptors (putative GPCRs), sixty-seven fungus-specific transcription factors, three hundred sixty-one peptidases (one hundred ninety-eight serine proteases and one hundred three metalloproteases), one hundred twenty-seven cytochrome P450 monooxygenases (P450s), thirty-five cysteine-rich secretory proteins, and fifty-five tyrosinases. Additionally, four hundred thirty carbohydrate-active enzymes (CAZymes) across six major modules were characterized. Untargeted metabolomics detected 22 highly expressed terpenoids, consistent with terpenoid biosynthesis gene clusters in the genome. Collectively, these expansions underpin the broad host range of C. coronatus by enabling cross-host signal decoding and gene expression reprogramming, breaching diverse host physicochemical barriers, and expanding its chemical ecological niche. This study provides genomic insights into broad host adaptability in entomopathogenic fungi, facilitating further understanding of pathogen–host interactions. Full article

This review explores the dual role of reactive oxygen species (ROS) and free radicals in the pathogenesis of endometriosis, aiming to deepen our understanding of these processes through a systematic literature review. To assess the induction and involvement of ROS in endometriosis, we conducted a comprehensive literature review using Cochrane Libraries, EMBASE, Google Scholar, PubMed, and SCOPUS databases. Of 30 qualifying papers ultimately reviewed, 28 reported a significant contribution of ROS to the pathogenesis of endometriosis, while two found no association. The presence of ROS in endometriosis is associated with infertility, irregular menstrual cycles, painful menstruation, and chronic pelvic discomfort. Among individual ROS types studied, hydrogen peroxide was most frequently investigated, followed by lipid peroxides and superoxide radicals. Notable polymorphisms associated with ROS in endometriosis include those for AT-rich interactive domain 1A (ARID1A) and quinone oxidoreductase 1 (NQO1) isoforms. Key enzymes for ROS scavenging and detoxification include superoxide dismutase, glutathione, and glutathione peroxidase. Effective inhibitors of ROS related to endometriosis are vitamins C and E, astaxanthin, fatty acid-binding protein 4, cerium oxide nanoparticles (nanoceria), osteopontin, sphingosine 1-phosphate, N-acetyl-L-cysteine, catalase, and a high-antioxidant diet. Elevated levels of ROS and free radicals are involved in the pathogenesis of endometriosis, suggesting that targeting these molecules could offer potential therapeutic strategies. Full article

In farmed animals, body color is not only an ecological trait but also an important trait that influences the commercial value of the animals. Melanin plays an important role in the formation of body color in animals, while the tyrosinase (TYR) gene family is a group of key enzymes that regulate melanogenesis. The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important reptiles in freshwater aquaculture. However, the potential role of the TYR gene family in the body color formation of P. sinensis remains unclear. This study aimed to investigate the expression and conservation of the TYR gene family in relation to body color variation in P. sinensis. Three core members of this gene family were identified from the P. sinensis genome. Following identification, the genomic features were analyzed. They shared similar physicochemical properties and conserved domains. Chromosome mapping showed that the three genes of P. sinensis were all located on the autosomes, while phylogenetic and collinearity analysis suggested that the protein functions of the three genes in the studied species were highly conserved. Amino acid sequence alignment indicated high conservation among the three TYR gene family proteins (TYR, TYRP1, and DCT) in multiple critical regions, particularly in their hydrophobic N-/C-terminal regions and cysteine/histidine-rich conserved domains. The qRT-PCR revealed that the TYR and DCT genes were highly expressed in the eyes of individuals with different body colors. The expression levels of TYR and TYRP1 genes in the skin were significantly higher in dark-colored individuals than in light-colored ones (p < 0.05). These results will lay the groundwork for functional studies and breeding programs targeting color traits in aquaculture. Full article

Crustins are a family of cysteine-rich antimicrobial peptides (AMPs), predominantly found in crustaceans, and play important roles in innate immunity. However, among the many reported crustins, few studies have explored their immunomodulatory functions. In this study, we investigated the immune function of a type I crustin (LvCrustinIa-2) in Litopenaeus vannamei, with particular emphasis on comparing the roles of its different domains. LvCrustinIa-2 possesses cationic patchy surface and amphipathic structure, and its expression was significantly induced in hemocytes after pathogen challenge. Both the recombinant LvCrustinIa-2 (rLvCrustinIa-2) and its whey acidic protein (WAP) domain (rLvCrustinIa-2-WAP) exhibited significant inhibitory activities against the tested Gram-positive bacteria. They also showed binding affinity not only for Gram-positive bacteria but also for Gram-negative bacteria. Furthermore, rLvCrustinIa-2 induced membrane leakage and structure damage in the target bacteria. Notably, chemotaxis assays revealed that rLvCrustinIa-2 and the synthetic cysteine-rich region (LvCrustinIa-2-CR) significantly enhanced the chemotactic activity of shrimp hemocytes in vitro. Knockdown of LvCrustinIa-2 triggered significant transcriptional activation of genes involved in calcium transport, inflammation, redox regulation, and NF-κB pathway. Taken together, these findings elucidate the distinct roles of the cysteine-rich region and WAP domain in type Ia crustin and provide the first evidence of a crustacean AMP with chemotactic and immunomodulatory activities. Full article

The Steinernema carpocapsae nematode is known to release several excretory/secretory products (ESPs) in its venom upon contact and during the parasitic infection process of insect hosts. A recurrent family of proteins found in this nematode’s venom is the CAP (cysteine-rich secretory protein/antigen 5/pathogenesis-related 1) protein, but the functional role of these proteins remains unknown. To elucidate the biological function, this study focused on characterising the secreted protein, first identified in the venom of the nematode’s parasitic stage, and the sequence retrieved from transcriptomic analysis. The structural comparisons of the Sc-CAP protein model, as determined by AlphaFold2, revealed related structures from other parasitic nematodes of vertebrates. Some of these closely related proteins are reported to have sterol-binding ability. The Sc-CAP recombinant protein was successfully produced in Escherichia coli in conjunction with a chaperone protein. The results showed that the Sc-CAP protein binds to cholesterol, and docking analyses of sterols on the protein revealed potential molecular interactions. Immunoassays performed in Galleria mellonella larvae revealed that this venom protein has an inhibitory effect against phenoloxidase and the antimicrobial response of insects. This suggests that the venom protein has an immunomodulatory function against insects, emphasising its importance during the parasite–host interaction. Full article