Publications by authors named "RongQing Zhang"

Article Synopsis
  • Histone modifications play a crucial role in regulating gene expression, but the complexity of their combinations makes them difficult to study through traditional biological methods.
  • To address this, a tool called CatLearning has been created, which uses a specialized type of deep learning network to analyze histone marks and predict gene expression.
  • CatLearning can accurately predict gene expression based on a single histone mark and simulates changes in histone modifications, aiding in the understanding of epigenetic changes related to various diseases.
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The frequent occurrence of viral infections poses a serious threat to human life. Identifying effective antiviral components is urgent. In China, pearls have been important traditional medicinal ingredients since ancient times, exhibiting various therapeutic properties, including detoxification properties.

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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.

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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 . Employing quadrupole time-of-flight mass spectrometry, this peptide was meticulously selected and pinpointed.

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β-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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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CaCO, 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.

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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.

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Matrix proteins play critical roles in regulating the prismatic and nacreous layer formation in the shell. However, due to the dearth of 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.

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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).

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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.

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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.

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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.

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Biomimetic materials inspired by biominerals have substantial applications in various fields. The prismatic layer of bivalve molluscs has extraordinary flexibility compared to inorganic CaCO. 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.

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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 were studied in depth by transcriptomics and proteomics approaches.

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Biomineralization is a widespread biological process, involved in the formation of shells, teeth, and bones. Shell matrix proteins have been widely studied for their importance during shell formation. In 2015, our group identified 72 unique shell matrix proteins in Pinctada fucata, among which PU14 is a matrix protein detected in the soluble fraction that solely exists in the prismatic layer.

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The hard tissues of animals, such as skeletons and teeth, are constructed by a biologically controlled process called biomineralization. In invertebrate animals, biominerals are considered important for their evolutionary success. These biominerals are hieratical biocomposites with excellent mechanical properties, and their formation has intrigued researchers for decades.

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Biomineralization, especially shell formation, is a sophisticated process regulated by various matrix proteins. Pinctada fucata chitinase-like protein 1 (Pf-Clp1), which belongs to the GH18 family, was discovered by our group using in-depth proteomic analysis. However, its function is still unclear.

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