INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
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2019
·Vol. 21
·期 1
·54
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IF 4.183
Lei Zhang,Chunyan Jiao,Yunpeng Cao,Xi Cheng,Jian Wang,Qing Jin,Yongping Cai
Studies have shown that the type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) genes produce secondary metabolites and flavor volatiles in plants, and TDC (tryptophan decarboxylase), a member of thePLP_deCfamily, plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs). In this study, we identified eightPLP_deCgenes inDendrobium officinale(D. officinale) and six inPhalaenopsis equestris(P. equestris), and their structures, physicochemical properties, response elements, evolutionary relationships, and expression patterns were preliminarily predicted and analyzed. The results showed thatPLP_deCgenes play important roles inD. officinaleand respond to different exogenous hormone treatments; additionally, the results support the selection of appropriate candidates for further functional characterization ofPLP_deCgenes inD. officinale.Keywords:Dendrobium officinale;PLP_deC;bioinformatics;expression pattern analysis;evolution
研究领域:
植物学
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遗传学
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分子生物学
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PubMed
高影响因子
JOURNAL OF BIOMATERIALS APPLICATIONS
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2020
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IF 2.22
Feng Xiao,Jiayu Liu,Yongbo Zheng,Zhen Quan,Wei Sun,Yao Fan,Chunli Luo,Hailiang Li,Xiaohou Wu
Prostate cancer is an epithelial malignant tumor of the prostate, and it is one of the malignant tumors with a high incidence of urogenital system in men. The local treatment of prostate cancer is mainly radical resection and radical radiotherapy, but they are not applicable to advanced prostate cancer. Systemic therapy mainly includes targeted therapy and immunotherapy which could cause many complications, and will affect the prognosis and quality of life of patients. It is urgent to find new treatments for prostate cancer. Bioinformatics offers hope for us to find reliable therapeutic targets. Bioinformatics can use the tumor informations in database and analyze them to screen out the best differentially expressed genes. Using the selected differentially expressed genes as targets, a gene interference plasmid was designed, and the constructed plasmid was used for targeted gene therapy. There are some problems about gene therapy that need to be solved, such as how to transfer genes to target cells is also an important challenge. Due to their large molecular weight and hydrophilic nature, they cannot enter cells through passive diffusion mechanisms. Here we synthesized a DNA carrier used surface modified iron based nanoparticles, and used it to load plasmid including ShRNA which can inhibit the expression of oncogene SLC4A4 selected by bioinformatics’ method. After that we use this iron based nanoparticles/plasmid DNA nanocomposite to treat prostate cancer cells in vitro and in vivo. The target gene SLC4A4 we had selected using bioinformatics had a strong effect on the proliferation of prostate cells; Our nanocomposite could inhibit the expression of SLC4A4 effectively, it had strong inhibitory effects on prostate cancer cells both in vivo and in vitro, and can be used as a potential method for prostate cancer treatment.
研究领域:
肿瘤学
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分子生物学
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纳米医学
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DOI
PubMed
高影响因子
MOLECULES
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2023
·Vol. 28
·期 5
·2082
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IF 4.6
Shuocun Wang,Liming Fan,Hanyu Pan,Yingying Li,Xin Zhao,Yan Qiu,Yiming Lu
The abuse of antibiotics and lack of new antibacterial drugs has led to the emergence of superbugs that raise fears of untreatable infections. The Cathelicidin family of antimicrobial peptide (AMP) with varying antibacterial activities and safety is considered to be a promising alternative to conventional antibiotics. In this study, we investigated a novel Cathelicidin peptide named Hydrostatin-AMP2 from the sea snakeHydrophis cyanocinctus. The peptide was identified based on gene functional annotation of theH. cyanocinctusgenome and bioinformatic prediction. Hydrostatin-AMP2 showed excellent antimicrobial activity against both Gram-positive and Gram-negative bacteria, including standard and clinical Ampicillin-resistant strains. The results of the bacterial killing kinetic assay demonstrated that Hydrostatin-AMP2 had faster antimicrobial action than Ampicillin. Meanwhile, Hydrostatin-AMP2 exhibited significant anti-biofilm activity including inhibition and eradication. It also showed a low propensity to induce resistance as well as low cytotoxicity and hemolytic activity. Notably, Hydrostatin-AMP2 apparently decreased the production of pro-inflammatory cytokines in the LPS-induced RAW264.7 cell model. To sum up, these findings indicate that Hydrostatin-AMP2 is a potential peptide candidate for the development of new-generation antimicrobial drugs fighting against antibiotic-resistant bacterial infections.Keywords:bacterial resistance;Cathelicidin;antimicrobial peptide;sea snake;infection;bioinformatic prediction
研究领域:
微生物学
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药理学
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免疫学
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生物信息学
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PubMed
高影响因子
Biology-Basel
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2025
·Vol. 14
·期 4
·411
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IF 3.5
Qun Zhang,Xiuyue Xu,Ling Yang
Simple SummaryIn this study, theWOXgene family of Korean pine was analyzed, and 21 family members were identified using bioinformatics methods. The results showed that the total number of amino acids in all proteins is between 164 and 488 aa, with molecular weights between 18,456.30 and 53,893.18 Da and isoelectric point values between 5.56 and 9.80. According to the predicted results, the average hydrophilicity coefficient of thePkWOXproteins is between −0.993 and −0.565. The phylogenetic tree divides thePkWOXgenes into three sub-branches. A total of 21PkWOXgenes are unevenly distributed on 7 of 12 chromosomes. ThePkWOXpromoters contain cis-acting elements such as stress response, light response, hormone response, and meristem regulation. GO entry forPkWOXis a biological process and molecular function.PkWOX16was expressed in all tissues.PkWOX2,3had higher expression in the embryonic callus, non-embryonic callus, somatic embryo, and zygotic embryo.PkWOX2,3,and16were located in the nucleus and in the cell membrane. ThePkWOX2and3proteins exhibited transcriptional self-activation activity, whilePkWOX16did not. In this study, the members of the WOX transcription factor family were identified and systematically analyzed in Korean pine, laying a foundation for the research on their functions.(1) Background:WOX(WUSCHEL-related homologous box) is a plant-specific transcription factor involved in plant development and stress response. It has been reported to be involved in processes such as growth and development, stem cell division and differentiation, and organ development; (2) Methods: In this study, bioinformatics was used to identify and analyze theWOXgene family of Korean pine. The gene characteristics were identified and analyzed through yeast transcriptional activation assays as well as subcellular localization experiments; (3) Results: A total of 21 members of theWOXgene family of Korean pine were identified in this study. The phylogenetic tree divides thePkWOXgenes into three sub-branches. 21PkWOXgenes are unevenly distributed on 7 of the 12 chromosomes.PkWOX16was expressed in all tissues.PkWOX2,3had higher expression in the embryonic callus, non-embryonic callus, somatic embryo, and zygotic embryo.PkWOX2,3and16were located in the nucleus and in the cell membrane. ThePkWOX2and3proteins exhibited transcriptional self-activation activity, whilePkWOX16did not; (4) Conclusions: In this study, the members of the WOX transcription factor family in Korean pine were identified and systematically analyzed, laying a foundation for their subsequent functional research.
研究领域:
植物学
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遗传学
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分子生物学
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PubMed
高影响因子
BIOCHEMICAL GENETICS
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2025
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IF 1.6
Tang Zhiqi,Nong Jiacong,Qiu Xue,Huang Junwen,Feng Xueyi,Tu Guangpeng,Li Lang
Acute myocardial infarction (AMI) continues to pose a substantial risk to human lives worldwide. Endoplasmic reticulum stress (ERS) is increasingly recognized as one of the potential mechanisms of myocardial injury following AMI. The primary goal of this study is to investigate the correlation between ERS and AMI through machine learning-based bioinformatics analysis, explore key genes, and conduct in vivo and in vitro experimental validation. We performed differential analysis and Weighted Gene Co-expression Network Analysis (WGCNA) on gene expression data from the GEO database (GSE62646). The intersection with ERS-related genes (ERSRGs) was taken to obtain AMI-ERS-related genes (MIEGs), and machine learning algorithms were further used to identify key genes (Hubs) from the MIEGs. The validation set GSE59867 was used to assess the expression levels and predictive capabilities of the Hubs for AMI. An AMI rat model was established to detect the mRNA and protein expression levels of the Hubs. The protein inhibitor of the key gene FURIN was used to treat H9C2 cells under oxygen–glucose deprivation (OGD) to explore the effects of FURIN on ERS and apoptosis. Bioinformatics analysis identified 27 MIEGs, and machine learning further determined 5 Hubs highly associated with AMI and ERS: RELA, FURIN, ERGIC3, TPP1, and BGLAP. The expression of these Hubs was significantly elevated in AMI patients within both the training and validation sets, and the area under the curve (AUC) indicated good diagnostic value. Our experiments confirmed that the mRNA levels of Furin and RelA were significantly elevated in AMI rats. Furin protein was increased in AMI rats and OGD H9C2. Furin inhibitor could alleviate OGD-induced ERS and apoptosis in H9C2. Our study demonstrates that Hubs play a pivotal role in myocardial infarction. Notably, Furin and its mediated ERS and apoptosis are significant in the pathogenesis of AMI, potentially serving as target for AMI diagnosis and treatment.
研究领域:
医学
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生物信息学
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DOI
PubMed
高影响因子
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
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2025
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IF 1.3
Jiawei Liang,Chaoqiang Zeng,Wendi Li,Peng Zhou
Glioma represents the prevalent neoplasm type, distinguished by invasive growth and a significant rate of recurrence. This research investigates the prognostic significance and possible molecular mechanisms of miR-551a in gliomas, thereby offering a novel biomarker for gliomas treatment. This study selected 77 glioma patients and 52 craniocerebral injury patients from 2017 to 2023. The expression of miR-551a was assessed by qPCR. The ROC, Cox regression, and KM curve analyses were conducted to evaluate the diagnostic utility and prognostic value of miR-551a. The effects of inhibiting miR-551a on glioma cell functions were evaluated through CCK-8 and transwell assays. miR-551a target genes was conducted by GO and KEGG enrichment analyses, as well as PPI analysis, to elucidate potential gene regulatory relationship. miR-551a exhibited a significant up-regulation in the cerebrospinal fluid of glioma patients (P < 0.001). miR-551a possessed a robust predictive capacity for gliomas (AUC = 0.792, P < 0.001) and serves as a risk factor for unfavorable prognoses (HR = 3.858, P < 0.01), with patients exhibiting low levels of miR-551a showing favorable prognosis (P = 0.004). The inhibition of miR-551a diminished the proliferative (P < 0.05), migratory (P < 0.01), and invasive (P < 0.001) capabilities of glioma cells. miR-551a functioned as an oncogene, with CALM3 identified as critical regulatory targets (P < 0.001). miR-551a is a biological indicator for glioma prediction. It participates in the disease progression of glioma by regulating the functions of glioma cells via CALM3.
研究领域:
生物信息学
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分子生物学
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肿瘤学
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神经病学
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遗传学
✓ 已验证
DOI
PubMed
高影响因子
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
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2024
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IF 1.6
Jianghong Wang,Xiaoyuan Wang,Yanru Song,Zilin Huang,Han Wu,Liang Chang,Bingjie Huo,Guanwei Fan
Background: The Precancerous Lesion of Gastric Cancer (PLGC) is an early stage in the development of gastric cancer. The clinical application of HPXLD has been found to be effective in treating PLGC, but the mechanism of how HPXLD acts on PLGC is still unclear. Objective: The objectives of this study were to reveal the molecular mechanism of how HPXLD can be used to treat PLGC and investigate this mechanism through bioinformatics and experimental validation. Methods: PLGC-associated target genes were identified through bioinformatics analysis. A rat model of PLGC was induced using N-methyl-N'-nitro-N-nitrosoquanidine (MNNG) in combination with ranitidine, hot saline, ethanol, and intermittent fasting, with interventions by HPXLD. The pathological alterations in gastric mucosa were assessed through Hematoxylin-eosin staining (HE). Immunohistochemistry (IHC) and Western blot analyses were employed to evaluate the changes in expression levels of inflammation-related proteins. Results: After conducting bioinformatics analysis, it was found that there were 23 HPXLDPLGC crossover genes, which were significantly enriched in the IL-17 signaling pathway, TNF signaling pathway, and NF-kappa B signaling pathway. The results of HE showed that HPXLD was effective in improving gastric mucosal histopathological changes. Additionally, the IHC results demonstrated that HPXLD was able to downregulate the expression of IL-6, COX-2, MCP- 1, and MMP-9. Furthermore, Western blot analysis revealed that HPXLD was able to downregulate the expressions of IL-6, IL-17RA, ACT1, NF-κB, and TNF-α. Conclusion: HPXLD has been shown to improve PLGC by reducing the expression of inflammation- related proteins. This suggests that HPXLD may potentially be a treatment option for PLGC.
研究领域:
肿瘤学
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中医药学
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分子生物学
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DOI
PubMed
高影响因子
TOXICOLOGY AND APPLIED PHARMACOLOGY
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2022
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IF 4.46
Xiao Wang,Yi Wu,Junlei Liu,Xuetao Xu,Zhaojun Sheng,Wenfeng Liu,Min Chen,Yanyan Ma,Denggao Zhao,Dongli Li,Xi Zheng
Purpose Our previous studies have confirmed that aspirin combined with Lipitor inhibited the development of prostate cancer (PCa), but the mechanisms need to be comprehensively expounded. The study aims to screen out the hub genes of combination therapy and to explore their association with the pathogenesis and prognosis of PCa. Methods Gene expressions were quantified by RNA sequencing (RNA-seq). Altered biological function, pathways of differentially expressed genes (DEGs), protein-protein interaction network, the filtering of hub genes, gene co-expression and the pathogenesis and prognosis were revealed by bioinformatics analysis. The correlation between hub gene expression and patient survival was validated by Kaplan-Meier. The effects of silent DNA replication and sister chromatid cohesion 1 (siDSCC1) combined with Lipitor and aspirin on DSCC1 expression, viability, invasion and migration of PCa cells were detected by qRT-PCR, Wound healing and transwell assays. Results 157 overlapped DEGs involved in FoxO, PI3K-Akt and p53 signaling pathways were identified. Ten hub genes (NEIL3, CDC7, DSCC1, CDC25C, PRIM1, MCM10, FBXO5 , DTL, SERPINE1 , EXO1) were verified to be correlated with the pathology and prognosis of PCa. DSCC1 silencing not only inhibited the viability, migration and invasion of PCa cells, but also strengthened the suppressing effects of Lipitor and aspirin alone or in combination on PCa cells. Conclusion The enrichment pathways and targets of Lipitor combined with aspirin in PCa are discovered, and DSCC1 silencing can potentiate the effect of Lipitor combined with aspirin in the treatment of PCa.
研究领域:
肿瘤学
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药理学
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生物信息学
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DOI
PubMed
高影响因子
Journal of Inflammation Research
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2024
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IF 4.2
Jianmin Gong,Bo Shi,Ping Yang,Adeel Khan,Tao Xiong,Zhiyang Li
Background Hypertrophic cardiomyopathy (HCM) is a dominantly inherited disease associated with sudden immune cell associations that remain unclear. The aim of this study was to comprehensively screen candidate markers associated with HCM and immune cells and explore potential pathogenic pathways.Methods First, download the GSE32453 dataset to identify differentially expressed genes (DEGs) and perform Gene Ontology and pathway enrichment analysis using DAVID and GSEA. Next, construct protein-protein interaction (PPI) networks using String and Cytoscape to identify hub genes. Afterward, use CIBERSORT to determine the proportion of immune cells attributed to key genes in HCM and conduct ROC analysis based on the external dataset GSE36961 to evaluate their diagnostic value. Finally, validate the expression of key genes in the hypertrophic cardiomyocyte model through qRT-PCR using data from the HPA database.Results Comprehensive analysis revealed that there were 254 upregulated genes and 181 downregulated genes in HCM. The enrichment study underscored pathways of inflammatory signaling, including MAPK and PI3K-Akt pathways. Pathways abundant in genes associated with HCM encompassed myocardial contraction and NADH dehydrogenase activity. Additionally, the analysis of immune infiltration revealed a notable increase in macrophages, NK cells, and monocytes in the HCM group, showing statistically significant variances in CD4 memory resting T cell infiltration when compared to the healthy control group. Within the validation dataset GSE36961, the Area Under the Curve (AUC) scores for eight crucial genes (FOS, CD86, CD68, BDNF, PIK3R1, PLEK, RAC2, CCL2) each exceeded 0.8. The HPA database revealed the positioning traits and paths of these eight crucial genes in smooth muscle cells, myocardial cells, and fibroblasts. The outcomes of the qRT-PCR were aligned with the sequencing findings.Conclusion Bioinformatics analysis unveiled pivotal genes, pathways, and immune involvement, illuminating the molecular underpinnings of HCM. These findings suggest promising therapeutic targets for clinical applications.
研究领域:
医学
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遗传学
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生物信息学
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DOI
PubMed
高影响因子
Biosensors-Basel
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2023
·Vol. 13
·期 1
·115
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IF 5.4
Jun Xia,Jiabei Luo,Boya Chang,Chuanyue Sun,Kerui Li,Qinghong Zhang,Yaogang Li,Hongzhi Wang,Chengyi Hou
Bioinformation plays an imperative role in day-to-day life. Wearable bioelectronics are important for sensing bioinformation in real-time and conductive hydrogel fibers are a key component in next generation wearable bioelectronics. However, current conductive hydrogel fibers have remarkable disadvantages such as insufficient conductivity, stability, and bioinformation sensing ability. Here, we report the synthesis of a zwitterionic organohydrogel (ZOH) fiber by the combination of the mold method and solvent replacement strategy. The ZOH fiber shows transparency (92.1%), stretchability (905.8%), long-term stability, anti-freezing ability (−35–60 °C), and low light transmission loss (0.17 dB/cm). Then, we integrate the ZOH fiber into fabric for use as a bioinformation sensor, the results prove its capability as a bioinformation monitor, monitoring information such as motion and bioelectric signals. In addition, the potential of the ZOH fiber in optogenetic applications is also confirmed.
研究领域:
材料科学
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生物医学工程
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电子工程
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DOI
PubMed
高影响因子
Journal of Inflammation Research
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2025
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IF 4.1
Chao Song,Weijun Song,Yong Liu,Daqian Zhou,Weiye Cai,Yongliang Mei,Fei Liu,Feng Jiang,Feng Chen,Zongchao Liu
Background Osteoarthritis (OA) is a widespread chronic inflammatory disease in orthopedics, and its molecular mechanisms are still poorly understood.Objective The purpose of this work was to detect the immunological infiltration of OA and the manner of cell death utilizing bioinformatics and single-cell analysis in order to provide guidelines for clinical therapy and medicine.Methods Ferroptosis -associated genes were sourced from the ferroptosis Database, single-cell and bioinformatic expression profiles were chosen from the Gene Expression Comprehensive Database, and OA gene information was taken from GeneCards. To ascertain the categorization status of OA cells, single-cell analysis was conducted. Protein-protein interaction networks were established by SRING analysis, and functional enrichment was examined in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. The important proteins of immune-ferroptosis death in OA were elucidated through co-analysis. Last but not least, network pharmacology and molecular docking support the mechanism by which resveratrol controls Ferroptosis in OA.Results The development of OA was found to be tightly related to chondrocytes and immune cells, particularly T and macrophage cells, according to single-cell analysis profile. In patients with OA, immune infiltration also revealed a notable infiltration of T cells, B cells, NK cells, monocytes, and macrophages. The hub genes were shown to be enriched in immunological responses, chemokine-mediated signaling pathways, and inflammatory responses, according to enrichment analysis. The main signaling pathways included autophagy, ferroptosis, the HIF-1 signaling pathway, the PI3K-Akt signaling pathway, and the FoxO signaling pathway. Ferroptosis is a significant cell death mechanism that contributes to the advancement of osteoarthritis. Ferroptosis in chondrocytes is lessened by resveratrol regulation of GPX4, TFRC, and SLC7A11.Conclusion Various immune cell infiltrates, especially T cells and macrophages, play an important role in the progression of OA, and resveratrol ameliorates OA by modulating chondrocyte ferroptosis.
研究领域:
医学
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生物学
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产品关联
DOI
PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
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2018
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IF 4.61
Hai-Ming Zhao,Rui-Wen Hu,Huan Du,Xiao-Ping Xin,Yan-Wen Li,Hui Li,Quan-Ying Cai,Ce-Hui Mo,Jie-Sheng Liu,Dong-Mei Zhou,Ming-Hung Wong,Zhen-Li He
Microbial degradation is considered the most promising method for removing phthalate acid esters (PAEs) from polluted environments; however, a comprehensive genomic understanding of the entire PAE catabolic process is still lacking. In this study, the repertoire of PAE catabolism genes in the metabolically versatile bacterium Rhodococcus sp. 2G was examined using genomic, metabolic, and bioinformatic analyses. A total of 4930 coding genes were identified from the 5.6 Mb genome of the 2G strain, including 337 esterase/hydrolase genes and 48 transferase and decarboxylase genes that were involved in hydrolysing PAEs into phthalate acid (PA) and decarboxylating PA into benzoic acid (BA). One gene cluster ( xyl ) responsible for transforming BA into catechol and two catechol-catabolism gene clusters controlling the ortho ( cat ) and meta ( xyl & mhp ) cleavage pathways were also identified. The proposed PAE catabolism pathway and some key degradation genes were validated by intermediate-utilising tests and real-time quantitative polymerase chain reaction. Our results provide novel insight into the mechanisms of PAE biodegradation at the molecular level and useful information on gene resources for future studies.
研究领域:
微生物学
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环境科学
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基因组学
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DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）