Visualization Analysis of Small Extracellular Vesicles in the Application of Bone-Related Diseases.

Small extracellular vesicles were shown to have similar functional roles to their parent cells without the defect of potential tumorigenicity, which made them a great candidate for regenerative medicine. The last twenty years have witnessed the rapid development of research on small extracellular vesicles. In this paper, we employed a scientometric synthesis method to conduct a retrospective analysis of small extracellular vesicles in the field of bone-related diseases. The overall background analysis consisted the visualization of the countries, institutions, journals, and authors involved in research. The current status of the research direction and future trends were presented through the analysis of references and keywords, which showed that engineering strategies, mesenchymal stem cell derived exosomes, and cartilage damage were the most concerning topics, and scaffold, osteoarthritis, platelet-rich plasma, and senescence were the future trends. We also discussed the current problems and challenges in practical applications, including the in-sight mechanisms, the building of relevant animal models, and the problems in clinical trials. By using CiteSpace, VOSviewer, and Bibliometrix, the presented data avoided subjective selectivity and tendency well, which made the conclusion more reliable and comprehensive. We hope that the findings can provide new perspectives for researchers to understand the evolution of this field over time and to search for novel research directions.

The first bioactive (angiotensin-converting enzyme-inhibitory) peptide isolated from pearl matrix protein.

In this research, we unveil the medical potential of pearls by identifying a novel bioactive peptide within them for the first time. The peptide, termed KKCHFWPFPW, emerges as a pioneering angiotensin I-converting enzyme (ACE) inhibitor, originating from the pearl matrix of Pinctada fucata. Employing quadrupole time-of-flight mass spectrometry, this peptide was meticulously selected and pinpointed. With a molecular weight of 1417.5 Da and a theoretical isoelectric point of 9.31, its inhibitory potency was demonstrated through a half-maximal inhibitory concentration (IC50) of 4.17 µM, established via high-performance liquid chromatography. The inhibition of ACE by this peptide was found to be competitive, as revealed by Lineweaver-Burk plot analysis, where an increase in peptide concentration correlated with an enhanced rate of ACE inhibition. To delve into the interaction between KKCHFWPFPW and ACE, molecular docking simulations were conducted using the Maestro 2022-1 Glide software, shedding light on the inhibitory mechanism. This investigation suggests that peptides derived from the P. martensii pearl matrix hold promise as a novel source for antihypertensive agents.

Identification of the shared molecular mechanisms between major depressive disorder and COVID-19 from postmortem brain transcriptome analysis.

OBJECTIVES: This study aims to investigate the molecular mechanisms underlying the interaction of major depressive disorder (MDD) and COVID-19, and on this basis, diagnostic biomarkers and potential therapeutic drugs are further explored. METHODS: Differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) were employed to identify common key genes involved in the pathogenesis of COVID-19 and MDD. Correlations with clinical features were explored. Detailed mechanisms were further investigated through protein interaction networks, GSEA, and immune cell infiltration analysis. Finally, Enrichr's Drug Signature Database and Coremine Medical were used to predict the potential drugs associated with key genes. RESULTS: The study identified 18 genes involved in both COVID-19 and MDD. Four key genes (MBP, CYP4B1, ERMN, and SLC26A7) were selected based on clinical relevance. A multi-gene prediction model showed good diagnostic efficiency for the two diseases: AUC of 0.852 for COVID-19 and 0.915 for MDD. GO and GSEA analyses identified specific biological functions and pathways associated with key genes in COVID-19 (axon guidance, metabolism, stress response) and MDD (neuron ensheathment, biosynthesis, glutamatergic neuron differentiation). The key genes also affected immune infiltration. Potential therapeutic drugs, including small molecules and traditional Chinese medicines, targeting these genes were identified. CONCLUSION: This study provides insights into the complex biological mechanisms underlying COVID-19 and MDD, develops an effective diagnostic model, and predicts potential therapeutic drugs, which may contribute to the prevention and treatment of these two prevalent diseases.

Study of the Anti-Inflammatory Mechanism of ß-Carotene Based on Network Pharmacology.

ß-carotene is known to have pharmacological effects such as anti-inflammatory, antioxidant, and anti-tumor properties. However, its main mechanism and related signaling pathways in the treatment of inflammation are still unclear. In this study, component target prediction was performed by using literature retrieval and the SwissTargetPrediction database. Disease targets were collected from various databases, including DisGeNET, OMIM, Drug Bank, and GeneCards. A protein-protein interaction (PPI) network was constructed, and enrichment analysis of gene ontology and biological pathways was carried out for important targets. The analysis showed that there were 191 unique targets of ß-carotene after removing repeat sites. A total of 2067 targets from the three databases were integrated, 58 duplicate targets were removed, and 2009 potential disease action targets were obtained. Biological function enrichment analysis revealed 284 biological process (BP) entries, 31 cellular component (CC) entries, 55 molecular function (MF) entries, and 84 cellular pathways. The biological processes were mostly associated with various pathways and their regulation, whereas the cell components were mainly membrane components. The main molecular functions included RNA polymerase II transcription factor activity, DNA binding specific to the ligand activation sequence, DNA binding, steroid binding sequence-specific DNA binding, enzyme binding, and steroid hormone receptors. The pathways involved in the process included the TNF signaling pathway, sphingomyelin signaling pathway, and some disease pathways. Lastly, the anti-inflammatory signaling pathway of ß-carotene was systematically analyzed using network pharmacology, while the molecular mechanism of ß-carotene was further explored by molecular docking. In this study, the anti-inflammatory mechanism of ß-carotene was preliminarily explored and predicted by bioinformatics methods, and further experiments will be designed to verify and confirm the predicted results, in order to finally reveal the anti-inflammatory mechanism of ß-carotene.

The regulatory effect of NF-κB signaling pathway on biomineralization and shell regeneration in pearl oyster, Pinctada fucata.

Pinctada fucata is an important pearl production shellfish in aquaculture. The formation of shells and pearls is a hot research topic in biomineralization, and matrix proteins secreted by the mantle tissues play the key role in this process. However, upstream regulatory mechanisms of transcription factors on the matrix protein genes remain unclear. Previous studies have shown that NF-κB signaling pathway regulated biomineralization process through expression regulation of specific matrix proteins, including Nacrein, Prismalin-14 and MSI60. In this study, we systematically investigated the regulatory effect of the NF-κB signaling pathway key factor Pf-Rel and inhibitory protein poI-κB on the biomineralization and shell regeneration process. We applied RNA interference and antibody injection assays to study in vivo function of transcription factor Pf-Rel and characterized shell morphology changes using scanning electron microscopy and Raman spectroscopy. We found that transcription factor Pf-Rel plays a positive regulatory role in the growth regulation of the prismatic and nacreous layers, while the function of inhibitory protein poI-κB is to prevent excessive growth and accumulation of both layers. RNA-seq was conducted based on RNA interference animal model to identify potential regulatory genes by transcription factor Pf-Rel. Shell damage repair experiments were performed to simulate shell regeneration process, and observations of newly formed shells revealed that NF-κB signaling pathway had different functions at different times. This study provides us with a more macroscopic perspective based on transcription factors to investigate biomineralization and shell regeneration.

Safe and Durable Treatment of Dentin Hypersensitivity via Nourishing and Remineralizing Dentin Based on ß-Chitooligosaccharide Graft Derivative.

Dentin hypersensitivity (DH) is a common symptom of various dental diseases that usually produces abnormal pain with external stimuli. Various desensitizers are developed to treat DH by occluding dentine tubules (DTs) or blocking intersynaptic connections of dental sensory nerve cells. However, the main limitations of currently available techniques are the chronic toxic effects of chemically active ingredients and their insufficiently durable efficacy. Herein, a novel DH therapy with remarkable biosafety and durable therapeutic value based on ß-chitooligosaccharide graft derivative (CAD) is presented. Particularly, CAD indicates the most energetic results, restoring the amino polysaccharide protective membrane in DTs, significantly promoting calcium and phosphorus ion deposition and bone anabolism, and regulating the levels of immunoglobulin in saliva and cellular inflammatory factors in plasma. Exposed DTs are occluded by remineralized hydroxyapatite with a depth of over 70 µm, as shown in in vitro tests. The bone mineral density of Sprague-Dawley rats' molar dentin increases by 10.96%, and the trabecular thickness of bone improves to about 0.03 µm in 2 weeks in the CAD group compared to the blank group. Overall, the ingenious concept that modified marine biomaterial can be a safe and durable therapy for DH is demonstrated by nourishing and remineralizing dentin.

Study on bioactive compounds of microalgae as antioxidants in a bibliometric analysis and visualization perspective.

Natural antioxidants are more attractive than synthetic chemical oxidants because of their non-toxic and non-harmful properties. Microalgal bioactive components such as carotenoids, polysaccharides, and phenolic compounds are gaining popularity as very effective and long-lasting natural antioxidants. Few articles currently exist that analyze microalgae from a bibliometric and visualization point of view. This study used a bibliometric method based on the Web of Science Core Collection database to analyze antioxidant research on bioactive compounds in microalgae from 1996 to 2022. According to cluster analysis, the most studied areas are the effectiveness, the antioxidant mechanism, and use of bioactive substances in microalgae, such as carotene, astaxanthin, and tocopherols, in the fields of food, cosmetics, and medicine. Using keyword co-occurrence and keyword mutation analysis, future trends are predicted to improve extraction rates and stability by altering the environment of microalgae cultures or mixing extracts with chemicals such as nanoparticles for commercial and industrial applications. These findings can help researchers identify trends and resources to build impactful investigations and expand scientific frontiers.

Direct control of shell regeneration by the mantle tissue in the pearl oyster Pinctada fucata.

Molluscs rapidly repair the damaged shells to prevent further injury, which is vital for their survival after physical or biological aggression. However, it remains unclear how this process is precisely controlled. In this study, we applied scanning electronic microscope and histochemical analysis to examine the detailed shell regeneration process in the pearl oyster Pinctada fucata. It was found that the shell damage caused the mantle tissue to retract, which resulted in relocation of the partitioned mantle zones with respect to their correspondingly secreting shell layers. As a result, the relocated mantle tissue dramatically altered the shell morphology by initiating de novo precipitation of prismatic layers on the former nacreous layers, leading to the formation of sandwich-like "prism-nacre-prism-nacre" structure. Real-time PCR revealed the up-regulation of the shell matrix protein genes, which was confirmed by the thermal gravimetric analysis of the newly formed shell. The increased matrix secretion might have led to the change of CaCO3 precipitation dynamics which altered the mineral morphology and promoted shell formation. Taken together, our study revealed the close relationship between the physiological activities of the mantle tissue and the morphological change of the regenerated shells.

The Matrix Protein Cysrichin, a Galaxin-like Protein from Hyriopsis cumingii, Induces Vaterite Formation In Vitro.

In this study, we cloned a novel matrix protein, cysrichin, with 16.03% homology and a similar protein structure to the coral biomineralized protein galaxin. Tissue expression analysis showed that cysrichin was mainly expressed in mantle and gill tissues. In situ hybridization indicated that cysrichin mRNA was detected in the entire epithelium region of mantle tissue. RNAi analysis and shell notching experiment confirmed that cysrichin participates in the prismatic layer and nacreous layer formation of the shell. An in vitro crystallization experiment showed that the cysrichin protein induced lotus-shaped and round-shaped crystals, which were identified as vaterite crystals. These results may provide new clues for understanding the formation of vaterite in freshwater shellfish.

A novel matrix protein PNU5 facilitates the transformation from amorphous calcium carbonate to calcite and aragonite.

For both nacre formation and biomineralization in mollusks, understanding the molecular mechanism is imperative. Biomineralization, especially shell formation, is dedicatedly regulated by multiple matrix proteins. However, ACC conversion to stable crystals still lacks positive factors. In this research, we found a novel matrix protein named PNU5 in Pinctada fucata that plays a regulatory role in both prismatic layer and nacreous layer formation. Functional studies in vivo and in vitro have shown that it might be involved in shell formation in a positive manner. RT-qPCR analysis showed that pnu5 was highly expressed in mantle pallial and participated in shell repairing and regeneration. RNAi-mediated repression of pnu5 could affect the normal structure of prismatic layer and nacreous layer. The recombinant protein rPNU5 significantly enhanced the precipitation rate of CaCO3 both in the calcite and aragonite crystallization systems, as well as altering the morphology of the crystals. Based on ACC transition experiments, the recombinant protein rPNU5 facilitated amorphous calcium carbonate (ACC) transformation into stable calcite or aragonite. This study could provide us with a better understanding of how positive regulatory mechanisms contribute to biomineralization.

In situ observations of tungsten speciation and partitioning behavior during fluid exsolution from granitic melt.

Most economically important tungsten (W) deposits are of magmatic-hydrothermal origin. The species and partitioning of W during fluid exsolution, considered to be the controlling factors for the formation of ore deposits, are thus of great significance to investigate. However, this issue has not been well addressed mainly due to the significant difference in reported partition coefficients (e.g., from strongly incompatible to strongly compatible) between fluid and melt (DWfluid/melt). Here, we used an in situ Raman spectroscopic approach to describe the W speciation, and to quantitatively determine the Dfluid/melt of individual and total W species in granite melts and coexisting Na2WO4 solutions at elevated temperatures (T; 700-800 °C) and pressures (P; 0.35-1.08 GPa). Results show that WO42- and HWO4- are predominant W species, and the fractions of these two species are similar in melt and coexisting fluid. The partitioning behaviors of WO42- and HWO4- are comparable, exhibiting strong enrichment in the fluid. The total DWfluid/melt ranges from 8.6 to 37.1. Specifically, DWfluid/melt decreases with rising T-P, indicating that shallow exsolution favors enrichment of W in evolved fluids. Furthermore, Rayleigh fractionation modeling based on the obtained DWfluid/melt data was used to describe the fluid exsolution processes. Our results strongly support that fluid exsolution can serve as an important mechanism to generate W-rich ore-forming fluids. This study also indicates that in situ approach can be used to further investigate the geochemical behavior of ore-forming elements during the magmatic-hydrothermal transition, especially for rare metals associated with granite and pegmatite.

A novel bifunctional protein PNU7 in CaCO3 polymorph formation: Vaterite stabilization and surface energy minimization.

CaCO3, which occurs in three crystalline anhydrous polymorphs named calcite, aragonite, and vaterite, is always found in mineralized skeletons or growing shells of many marine organisms. However, understanding how these organisms achieve this control has been a significant challenge in biomineralization. In this work, we proposed a novel vaterite stabilizer acidic matrix protein PNU7 that existed in both prism and nacre of Pinctada fucata, and identified its functional domain DDDDDDHDDVEETED. Our experiments reveal that PNU7 triggers a stable large vaterite formation with Mg2+ deficiency even under low Ca2+. Increasing PNU7 in the calcium carbonate crystallization system with Mg2+ leads to a significant shrinking in crystal size and rising in nucleation quantity. Moreover, it converts an atomically rough dome-like shape to a smooth sphere on unsiliconized glass. These effects rescind after removing the asp-rich region at the C-terminus. We also find that decreasing pnu7 mRNA in vivo leads to nacreous inner surface growth substantially lessened. Thus, PNU7 may not only supply vaterite in shell formation but also involve the nacreous regulation via surface energy minimization.

Research on Anomaly Identification and Screening and Metallogenic Prediction Based on Semisupervised Neural Network.

This paper firstly introduces the background of the research on neural network and anomaly identification screening and mineralization prediction under semisupervised learning, then introduces supervised learning, semisupervised learning, unsupervised learning, and reinforcement learning, analyzes and compares their advantages and disadvantages, and concludes that unsupervised learning is the best way to process the data. In the research method, this paper classifies the obtained geochemical data by using semisupervised learning and then trains the obtained samples using the convolutional neural network model to obtain the mineralization prediction model and check its correctness, which finally provides the direction for the subsequent mineralization prediction research.

DCSr-NL: A Novel Method to Semiquantitatively Probe the Growth Rate of Nacre.

Matrix proteins play critical roles in regulating the prismatic and nacreous layer formation in the shell. However, due to the dearth of in vivo experiments, their specific roles during shell formation are still unclear. In this study, a new method to detect the content of Sr in the nacreous layer (DCSr-NL), which can semiquantitatively measure the nacreous growth rate, has been proposed. In vitro experiments show that during in vitro crystallization, the Sr element can replace Ca partially, resulting in isomorphism. In vivo experiments show that the best labeling conditions are when the Sr/Ca in seawater is 0.3, at 24 °C, and at 4 days of culture. Although a surface morphological difference in the inner layer of nacre is seldom detected by scanning electron microscopy (SEM), knockdown of the classical gene nacrein or unknown gene NU9, combined with DCSr-NL, shows that both significantly decrease the nacreous layer formation rate. The knockdown of the classical gene Pif177 or unknown genes NU3 or MRPN affects the surface morphology and decreases the nacreous layer formation rate. In general, thanks to DCSr-NL, we can efficiently analyze the growth rate of the nacre with or without morphological changes by SEM, and it is of considerable significance for exploring the target gene's function in forming the nacre in vivo.

Shell Matrix Protein N38 of Pinctada fucata, Inducing Vaterite Formation, Extends the DING Protein to the Mollusca World.

In the animal kingdom, DING proteins were only found in Chordata and Aschelminthes. At present study, a potential DING protein, matrix protein N38, was isolated and purified from the shell of Pinctada fucata. Tandem mass spectrometry analysis revealed that 14 peptide segments matched between N38 and human phosphate-binding protein (HPBP). HPBP belongs to the DING protein family and has a "DINGGG-" sequence, which is considered a "signature" of HPBP. In this study, the mass spectrometry analysis results showed that N38 had a "DIDGGG-" sequence; this structure is a mutation from the "DINGGG-" structure, which is a distinctive feature of the DING protein family. The role of N38 during calcium carbonate formation was explored through the in vitro crystallization experiment. The results of scanning electron microscopy and Raman spectrum analysis indicated that N38 induced vaterite formation. These findings revealed that N38 might regulate and participate in the precise control of the crystal growth of the shell, providing new clues for biomineralization mechanisms in P. fucata and DING protein family studies. In addition, this study helped extend the research of DING protein to the Mollusca world.

Mantle tissue in the pearl oyster Pinctada fucata secretes immune components via vesicle transportation.

Molluscan bivalves secrete shell matrices into the extrapallial space (EPS) to guide the precipitation of rigid shells. Meanwhile, immune components are present in the EPS and shell matrices, which are pivotal in resistant to invaded pathogens, thus ensuring the shell formation process. However, the origin of these components remains unclear. In this study, we revealed numerous vesicles were secreted from the outer mantle epithelial cells by using light and electron microscopes. The secreted vesicles were isolated by gradient centrifugation and confirmed by transmission electron microscopy. Proteomics analysis showed that the secreted vesicles were composed of cytoplasmic and immune components, most of which do not have signal peptides, indicating that they were secreted by a non-classical pathway. Moreover, real-time PCR revealed that some immune components were highly expressed in the mantle tissue, compared to the hemocytes. FTIR analysis verified the presence of lipids in the shell matrices, indicating that the vesicles have integrated into the shell layers. Taken together, our results suggested that mantle epithelial cells secreted some important immune components into the EPS via secreted vesicle transportation, thus cooperating with the hemocytes to play a vital role in immunity during shell formation.

Microplastics impact shell and pearl biomineralization of the pearl oyster Pinctada fucata.

Microplastics are extremely widespread aquatic pollutants that severely detriment marine life. In this study, the influence of microplastics on biomineralization was investigated. For the first time, multiple forms and types of microplastics were detected and isolated from the shells and pearls of Pinctada fucata. According to the present study, the abundance of microplastics in shells and pearls was estimated at 1.95 ± 1.43 items/g and 0.53 ± 0.37 items/g respectively. Interestingly, microplastics were less abundant in high-quality round pearls. Microplastics may hinder the growth of calcite and aragonite crystals, which are crucial components required for shell formation. During the process of biomineralization microplastics became embedded in shells, suggesting the existence of a novel pathway by which microplastics accumulate in bivalves. After a 96-h exposure to microplastics, the expression level of typical biomineralization-related genes increased, including amorphous calcium carbonate binding protein (ACCBP) gene which experienced a significant increase. ACCBP promotes the formation of amorphous calcium carbonate (ACC), which is the pivotal precursor of shell formation-related biominerals. ACCBP is highly expressed during the developmental stage of juvenile oysters and the shell-damage repair process. The increased expression of ACCBP suggests biomineralization is enhanced as a result of microplastics exposure. These results provide important evidence that microplastics exposure may impact the appearance of biominerals and the expression of biomineralization-related genes, posing a new potential threat to aquatic organisms.

Heterogeneous distribution of shell matrix proteins in the pearl oyster prismatic layer.

Shell formation in molluscan bivalves is regulated by organic matrices composed of biological macromolecules, but how these macromolecules assemble in vitro remains elusive. Prismatic layer in the pearl oyster Pinctada fucata consists of polygonal prisms enveloped by thick organic matrices. In this study, we found that the organic matrices were heterogeneously distributed, with highly acidic fractions (EDTA-soluble and EDTA-insoluble) embedded inside the prism columns, while basic EDTA-insoluble faction as inter-column framework enveloping the prisms. The intra-column matrix was enriched in aspartic acid whereas the inter-column matrix was enriched in glycine, tyrosine and phenylalanine. Moreover, the intra-column matrix contained sulfo group further contributing to its acidic property. Proteomics data showed that the intra-column proteins mainly consisted of acidic proteins, while some typical matrix proteins were absent. The absent matrix proteins such as shematrin family and KRMP family were highly basic and contained aromatic amino acids, suggesting that electric charge and hydrophobic effect might play a role in the matrix heterogeneity. Interestingly, chitin metabolism related proteins were abundant in the inter-column matrix, which may be involved in reconstructing the prism organic matrix. Overall, our study suggests that each single prism grew in an enclosed organic envelope and the organic matrix undergoes rearrangement, thus leading to the peculiar growth of the prismatic layer.

Transition from horizontal expansion to vertical growth in the oyster prismatic layer.

Biomimetic materials inspired by biominerals have substantial applications in various fields. The prismatic layer of bivalve molluscs has extraordinary flexibility compared to inorganic CaCO3. Previous studies showed that in the early stage, minerals expanded horizontally and formed prism domains as a Voronoi division, while the evolution of the mature prisms were thermodynamically driven, which was similar to grain growth. However, it was unclear how the two processes were correlated during shell formation. In this study, we used scanning electronic microscopy and laser confocal scanning microscopy to look into the microstructure of the columnar prismatic layer in the pearl oyster Pinctada fucata. The Dirichlet centers of the growing domains in mature prisms were calculated, and the corresponding Voronoi division was reconstructed. It was found that the domain pattern did not fit the Voronoi division, indicating the driving forces of the mature prisms evolution and the initiation stage were different. During the transition from horizontal expansion to vertical growth, the minerals broke through the inner periostracum and squeezed out the organic materials to the inter-prism space. Re-arrangement of the organic framework pattern was driven by elastic relaxation at the vertices, indicating the transition process was thermodynamically driven. Our study provided insights into shell growth in bivalves and pave the way to synthesize three-dimensional material biomimetically.

Identification of novel adhesive proteins in pearl oyster by proteomic and bioinformatic analysis.

Byssuses, which are proteinaceous fibers secreted by mollusks, are remarkable underwater adhesives. Although mussel adhesives are well known, much less is known about the byssal proteins of pearl oysters especially in the adhesive regions. In this study, adhesive proteins from the pearl oyster Pinctada fucata were studied in depth by transcriptomics and proteomics approaches. In total, 16 novel proteins were identified including a von Willebrand factor type A domain-containing protein, a thrombospondin-1-like protein, tyrosinase, mucin-like proteins, protease inhibitors, and Pinctada unannotated foot protein 3 (PUF3) to PUF6. Interestingly, PUF3-6 are enriched with glycine, serine, and PXG (X = F/Y/W/K/L) motifs and are highly expressed in the foot. The identification of byssal proteins of the pearl oyster is a key step for understanding byssus formation and may inspire the synthesis of novel adhesives for underwater use and the development of anti-biofouling strategies.