Characteristics of Atmospheric Fine Particulate Matter(PM2.5)Induced Differentially Expressed Proteins Determined by Proteomics and Bioinformatics Analyses

Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from Shenzhen and Taiyuan for 24 h.To detect overall protein expression,the Q Exactive mass spectrometer was used.Gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and Perseus software were used to screen DEPs.Results Overall,67 DEPs were screened in the Shenzhen sample-treated group,of which 46 were upregulated and 21 were downregulated.In total,252 DEPs were screened in the Taiyuan sampletreated group,of which 134 were upregulated and 118 were downregulated.KEGG analysis demonstrated that DEPs were mainly enriched in ubiquitin-mediated proteolysis and HIF-1 signal pathways in Shenzhen PM2.5 samples-treated group.The GO analysis demonstrated that Shenzhen sample-induced DEPs were mainly involved in the biological process for absorption of various metal ions and cell components.The Taiyuan PM2.5-induced DEPs were mainly involved in biological processes of protein aggregation regulation and molecular function of oxidase activity.Additionally,three important DEPs,including ANXA2,DIABLO,and AIMP1,were screened.Conclusion Our findings provide a valuable basis for further evaluation of PM2.5-associated carcinogenesis.

Computational and bioinformatics tools for understanding disease mechanisms

Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.

Molecular Cloning and Bioinformatics Analysis of sucC Gene of Vibrio alginolyticus Strain HY9901

[Objectives]To clone the sucC gene of Vibrio alginolyticus strain HY9901 and conduct the bioinformatics analysis.[Methods]Based on the sucC gene of V.alginolyticus strain HY9901,specific primers were designed to amplify the full length sequence by PCR and make further analysis.[Results]The theoretical molecular weight of SucC protein was about 41528.45 Da,and the full length was 1167 bp,encoding 388 amino acids.It has no signal peptide and transmembrane region,and has a variety of functional sites.It is predicted that it is mainly located in the cytoplasm,and the ubiquitin and lactate modification sites overlap,and it has high gene homology with Vibrio parahaemolyticus.Theα-helix,random coil and extended strand are the main secondary structures.The similarity between the constructed three-level structure model and the template is high.[Conclusions]This study reveals the structural characteristics and functional potential of SucC protein,and provides a theoretical basis for the study of drug resistance mechanism and prevention strategies.

Identification of Prognosis-Related Genes and Key Target Genes for Pancreatic Cancer: A Bioinformatics Analysis

Objective: The mortality and morbidity rates associated with pancreatic cancer (PaCa) are extremely high. Various studies have demonstrated that pancreatic cancer will be the fourth cancer-related death by 2030, raising more concern for scholars to find effective methods to prevent and treat in order to improve the pancreatic cancer outcome. Using bioinformatic analysis, this study aims to pinpoint key genes that could impact PaCa patients’ prognosis and could be used as therapeutic targets. Methods: The TCGA and GEO datasets were integratively analyzed to identify prognosis-related differentially expressed genes. Next, the STRING database was used to develop PPI networks, and the MCODE and CytoNCA Cytoscape in Cytoscape were used to screen for critical genes. Through CytoNCA, three kinds of topology analysis were considered (degree, betweenness, and eigenvector). Essential genes were confirmed as potential target treatment through Go function and pathways enrichment analysis, a developed predictive risk model based on multivariate analysis, and the establishment of nomograms using the clinical information. Results: Overall, the GSE183795 and TCGA datasets associated 1311 and 2244 genes with pancreatic cancer prognosis, respectively. We identified 132 genes that were present in both datasets. The PPI network analysis using, the centrality analysis approach with the CytoNCA plug-in, showed that CDK2, PLK1, CCNB1, and TOP2A ranked in the top 5% across all three metrics. The independent analysis of a risk model revealed that the four key genes had a Hazard Ratio (HR) > 1. The monogram showed the predictive risk model and individual patient survival predictions were accurate. The results indicate that the effect of the selected vital genes was significant and that they could be used as biomarkers to predict a patient’s outcome and as possible target therapy in patients with pancreatic cancer. GO function and pathway analysis demonstrated that crucial genes might affect the P53 signaling pathway and FoxO signaling pathway, through which Meiotic nuclear division and cell cycle may have a significant function in essential genes affecting the outcome of patients who have pancreatic cancer. Conclusions: This study suggests that CDK2, CCNB1, PLK1 and TOP2A are four key genes that have a significant influence on PaCa migration and proliferation. CDK2, CCNB1, PLK1, and TOP2A can be used as potential PaCa prognostic biomarkers and therapeutic targets. However, experimental validation is necessary to confirm these predictions. Our study comes into contributions to the development of personalized target therapy for pancreatic cancer patients.

Molecular Cloning and Bioinformatics Analysis of TypeⅢSecretion System Effector Protein Va1686 Gene of Vibrio alginolyticus

In this study, Va 1686 gene was cloned from Vibrio alginolyticus . The total length of the gene is 1 164 bp, and it could encode 387 amino acids. The physicochemical properties, protein structure, genetic evolutionary relationship and antigenic characteristics of the effect protein Va1686 of V. alginolyticus HY9901 type Ⅲ secretion system were studied and analyzed by bioinformatics methods and tools. The results showed that Va1686 is a stable hydrophilic and acidic protein without a transmembrane region and a signal peptide, and secondary structure to α-helix. The evolutionary analysis showed that V. alginolyticus HY9901 and V. harveyi were clustered together, which indicated that the genetic relationship between the two species was the closest. Va1686 contains a Fic superfamily conserved domain associated with cell division. Bioinformatics analysis showed that the B-cell preponderant epitopes of Va1686 might be localized in the regions of 48-49, 82-85, 125-126, 150-153, 185-186, 236-237 and so on. The 3D structure model of Va1686 subunit was simulated by SWISS-MODEL software and it was found that the vopS of V. parahaemolyticus was similar and the similarity was 89.46%. In this study, the feasibility of Va1686 as a common antigen of Vibrio was verified from the perspective of bioinformatics, which laid the foundation for the next step in vaccine development.

Identification of four differentially expressed genes associated with acute and chronic spinal cord injury based on bioinformatics data

Complex pathological changes occur during the development of spinal cord injury(SCI),and determining the underlying molecular events that occur during SCI is necessary for the development of promising molecular targets and therapeutic strategies.This study was designed to explore differentially expressed genes(DEGs)associated with the acute and chronic stages of SCI using bioinformatics analysis.Gene expression profiles(GSE45006,GSE93249,and GSE45550)were downloaded from the Gene Expression Omnibus database.SCI-associated DEGs from rat samples were identified,and Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed.In addition,a protein-protein interaction network was constructed.Approximately 66 DEGs were identified in GSE45550 between 3–14 days after SCI,whereas 2418 DEGs were identified in GSE450061–56 days after SCI.Moreover,1263,195,and 75 overlapping DEGs were identified between these two expression profiles,3,7/8,and 14 days after SCI,respectively.Additionally,16 overlapping DEGs were obtained in GSE450061–14 days after SCI,including Pank1,Hn1,Tmem150c,Rgd1309676,Lpl,Mdh1,Nnt,Loc100912219,Large1,Baiap2,Slc24a2,Fundc2,Mrps14,Slc16a7,Obfc1,and Alpk3.Importantly,3882 overlapping DEGs were identified in GSE932491–6 months after SCI,including 3316 protein-coding genes and 567 long non-coding RNA genes.A comparative analysis between GSE93249 and GSE45006 resulted in the enrichment of 1135 overlapping DEGs.The significant functions of these 1135 genes were correlated with the response to the immune effector process,the innate immune response,and cytokine production.Moreover,the biological processes and KEGG pathways of the overlapping DEGs were significantly enriched in immune system-related pathways,osteoclast differentiation,the nuclear factor-κB signaling pathway,and the chemokine signaling pathway.Finally,an analysis of the overlapping DEGs associated with both acute and chronic SCI,assessed using the expression profiles GSE93249 and GSE45006,identified four overlapping DEGs:Slc16a7,Alpk3,Lpl and Nnt.These findings may be useful for revealing the biological processes associated with SCI and the development of targeted intervention strategies.

Prokaryotic expression,identification and bioinformatics analysis of fbpB-esxA fusing gene from Mycobacterium tuberculosis

Objective:To obtain fbpB-esxA fusing gene of Mycobacterium tuberculosis（MTU）,express the encoded fusing protein in Escherichia coli（E.coli）,identify protein acquired,and predict the structure and function of the protein utilizing methods of bioinformatics.Methods:fbpB and esxA gene were amplified from genome of MTB H37Rv by PCR.The fbpB-esxA fusing gene Iigated by（Gly4Ser）3 linker was gained by means of Gene Splicing by Overlapping Extension PCU（SOEPCR）, and fusing gene was cloned into expression vector pET-30a.The recombinant plasmid was sequenced and expressed in E.coli BL21（DE3）.The protein was identified by Western blot using anti-HIS antibody.Secondary structure and antigenic epitopes of the protein were predicting using tools of bioinformatics.Results:The UNA sequences fbpB-esxA were identical with that published by GenBank.The Ag85B-ESAT-6 fusion protein about 50 kDa comprised 485 amino acids was efficiently produced from expression system in E.coli B1.21（DE3） under the induction of IPTG.Bioinformatics analysis showed the protein contained one transmembrane region and fourteen potential antigenic epitopes.Conclusions:The Ag85B-ESAT-6 fusion protein is successfully expressed with N-terminal HIS-tag.Gel filtration demonstrated that it exists as insoluble inclusion bodies mainly.The existence of linker doesn’t affect immunogenicity of Ag85B and ESAT-6.It will allow lor characterization in vitro and establish a foundation of further function research such as vaccine or diagnostic reagent.

Identification of microRNAs and messenger RNAs involved in human umbilical cord mesenchymal stem cell treatment of ischemic cerebral infarction using integrated bioinformatics analysis

In recent years,a large number of differentially expressed genes have been identified in human umbilical cord mesenchymal stem cell(hUMSC)transplants for the treatment of ischemic cerebral infarction.These genes are involved in various biochemical processes,but the role of microRNAs(miRNAs)in this process is still unclear.From the Gene Expression Omnibus(GEO)database,we downloaded two microarray datasets for GSE78731(messenger RNA(mRNA)profile)and GSE97532(miRNA profile).The differentially expressed genes screened were compared between the hUMSC group and the middle cerebral artery occlusion group.Gene ontology enrichment and pathway enrichment analyses were subsequently conducted using the online Database for Annotation,Visualization,and Integrated Discovery.Identified genes were applied to perform weighted gene co-suppression analyses,to establish a weighted co-expression network model.Furthermore,the protein-protein interaction network for differentially expressed genes from turquoise modules was built using Cytoscape(version 3.40)and the most highly correlated subnetwork was extracted from the protein-protein interaction network using the MCODE plugin.The predicted target genes for differentially expressed miRNAs were also identified using the online database starBase v3.0.A total of 3698 differentially expressed genes were identified.Gene ontology analysis demonstrated that differentially expressed genes that are related to hUMSC treatment of ischemic cerebral infarction are involved in endocytosis and inflammatory responses.We identified 12 differentially expressed miRNAs in middle cerebral artery occlusion rats after hUMSC treatment,and these differentially expressed miRNAs were mainly involved in signaling in inflammatory pathways,such as in the regulation of neutrophil migration.In conclusion,we have identified a number of differentially expressed genes and differentially expressed mRNAs,miRNA-mRNAs,and signaling pathways involved in the hUMSC treatment of ischemic cerebral infarction.Bioinformatics and interaction analyses can provide novel clues for further research into hUMSC treatment of ischemic cerebral infarction.

Molecular Cloning and Bioinformatics Analysis of TypeⅢSecretion System Effector Protein HY 322 Gene of Vibrio alginolyticus

In this study,Hy322 gene was cloned from Vibrio alginolyticus.The total length of its gene was 969 bp,and it could encode 322 amino acids.The physicochemical properties,protein structure,genetic evolutionary relationship and antigenic characteristics of the effector protein Hy322 of V.alginolyticus HY9901 type Ⅲ secretion system were studied and analyzed by bioinformatics methods and tools.The results showed that Hy322 is an unstable hydrophilic and acidic protein without a transmembrane region and a signal peptide,and secondary structure to α-helix.The evolutionary analysis showed that V.alginolyticus HY9901 and V.harveyi were clustered together,which indicated that the genetic relationship between the two species was closest.HY322 contains a FliN super family conserved domain associated with Flagellar motor switch.Bioinformatics analysis showed that the B-cell preponderant epitopes of Hy322 might be localized in the regions of 32-33,100-102,138-140,215-216,235-238 and 246-249.The 3D structure model of Hy322 subunit was simulated by SWISS-MODEL software and itwas found that the yscQ of Yersinia were similar and the similarity was 42.25%.In this study,the feasibility of Hy322 as a common antigen of Vibrio was verified from the perspective of bioinformatics,which laid the foundation for the next step in vaccine development.

Prot-Class: A bioinformatics tool for protein classification based on amino acid signatures

Knowledge about characteristics shared across known members of a protein family enables their identification within the complete set of proteins in an organism. Shared features are usually expressed through motifs, which can incorporate specific patterns and even amino acid (AA) biases. Based on a set of classification patterns and biases it can be determined which additional proteins may belong to a specific family and share its functionality. A bioinformatics tool (Prot-Class) was implemented to examine protein sequences and characterize them based upon user-defined AA composition percentages and user defined AA patterns. In addition the tool allows for the identification of repeated AA patterns, biased AA compositions within windows of user-defined length, and the characteristics of putative signal peptides and glycosylphosphatidylinositol (GPI) lipid anchors. ProtClass is general purpose and can be applied to analyze protein sequences from any organism. The Prot-Class source code is available through the GNU General Public License v3 and can be accessed via the Google Code Repository: http://code.google.com/p/prot-class/.

Protective effect and mechanism insight of purified Antarctic krill phospholipids against mice ulcerative colitis combined with bioinformatics

Antarctic krill oil is functional oil and has a complex phospholipids composition that poses difficulties in elucidating its effect mechanism on ulcerative colitis(UC).The mechanism of UC action was studied by bioinformatics,and the therapeutic effect of Antarctic krill phospholipids(APL)on dextran sulfate sodium(DSS)-induced colitis mice was verified.GO functional enrichment analysis uncovered an enrichment of these genes in the regulation of cell-cell adhesion,membrane region,signaling receptor activator activity,and cytokine activity.Meanwhile,the KEGG results revealed the genes were enriched in the TNF signaling pathway,pathogenic Escherichia coli infection,inflammatory bowel disease and tight junction.Animal experiments showed that APL treatment alleviated the UC symptoms and reduced inflammatory damage.Meanwhile,the expressions of the tight junction(TJ)proteins,ZO-1 and occludin,were restored,and the levels of IL-6 and TNF-αwere reduced.Moreover,Firmicutes/Bacteroidetes ratio in the intestinal microbiota was regulated,and the contents of short-chain fatty acids metabolites were raised.These findings would provide an insight for the beneficial effects of APL and dietary therapy strategies for UC.

Association between heat shock factor protein 4 methylation and colorectal cancer risk and potential molecular mechanisms:A bioinformatics study

BACKGROUND We previously demonstrated that heat shock factor protein 4(HSF4)facilitates colorectal cancer(CRC)progression.DNA methylation,a major modifier of gene expression and stability,is involved in CRC development and outcome.AIM To investigate the correlation between HSF4 methylation and CRC risk,and to uncover the underlying molecular mechanisms.METHODS Differences in β values of HSF4 methylation loci in multiple malignancies and their correlation with HSF4 mRNA expression were analyzed based on Shiny Methylation Analysis Resource Tool.HSF4 methylation-related genes were identified by LinkedOmics in CRC,and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed.Protein-protein interaction network of HSF4 methylation-related genes was constructed by String database and MCODE algorithm.RESULTS A total of 19 CpG methylation loci were identified in HSF4,and their β values were significantly increased in CRC tissues and exhibited a positive correlation with HSF4 mRNA expression.Unfortunately,the prognostic and diagnostic performance of these CpG loci in CRC patients was mediocre.In CRC,there were 1694 HSF4 methylation-related genes;1468 of which displayed positive and 226 negative associations,and they were involved in regulating phenotypes such as immune,inflammatory,and metabolic reprogramming.EGFR,RELA,STAT3,FCGR3A,POLR2K,and AXIN1 are hub genes among the HSF4 methylation-related genes.CONCLUSION HSF4 is highly methylated in CRC,but there is no significant correlation between it and the prognosis and diagnosis of CRC.HSF4 methylation may serve as one of the ways in which HSF4 mediates the CRC process.

Structure analysis and function prediction of human P2X7R based on bioinformatics

Objective:To analyze the structural features of human P2X7R protein,meanwhile homology,protein-protein interaction,and cell epitope were predicted to provide theoretical basis for the diagnosis and treatment of related diseases.Methods:Human P2X7R protein was analyzed and predicted by ProtParam、TMHMM、ProtScale and SignalP 5.0 Server et al.Results:Human P2X7R protein is composed of 595 amino acids,the molecular formula is C 3077 H 4749 N 835 O 871 S 40,with the theoretical isoelectric point PI of 8.62,the instability coefficient is 46.07,the total average hydrophilicity is-0.317,and the protein is an hydrophilic protein instead of secreted protein,no any signal peptide,but transmembrane region is contained,which belong to transmembrane protein.There are 157αhelices and 288 random coils in the secondary structure of human P2X7R protein,accounting for 26.39%and 48.40%of all amino acids,The coverage rate of the three-level structure prediction results is 100%,and the sequence consistency is 80.34%,and the ramachandran plot show that the predicted structure is relatively stability.The interaction of proteins show that there are a variety of proteins interacting with human P2X7R,and P2X7R was closely related to inflammation;this protein had many B and T cell epitopes,which could provide ideas for vaccine development.Conclusion:The results indicate that the analysis of human P2X7R protein that is based on bioinformatics method has certain reliability.P2X7R is involved in the development of inflammatory diseases,and the antigenic epitope of B,Th and CTL cells screened out by prediction will provide the treatment scheme for diseases.

Expression and clinical significance of PRKCD in liver hepatocellular carcinoma analyzed based on bioinformatics

Objective:To analyze the expression of protein kinase C delta(PKCδ,PRKCD)in Liver hepatocellular carcinoma and its clinical significance based on bioinformatics,in order to provide a new direction for the study of therapeutic targets for Liver hepatocellular carcinoma.Methods:The PRKCD gene expression data and patient clinical information data in Liver hepatocellular carcinoma tissues and adjacent tissues were downloaded from The TCGA(The Cancer Genome Atlas)and UCSC Xena databases.The mRNA expression of PRKCD in Liver hepatocellular carcinoma was analyzed,and the protein expression of PRKCD in Liver hepatocellular carcinoma was analyzed by Human Protein Atlas(HPA)databases.Furthermore,its relationship with clinicopathological features and prognosis in patients with Liver hepatocellular carcinoma was analyzed.GSEA enrichment analysis were carried out for PRKCD in Liver hepatocellular carcinoma.Finally,the causes of changes in PRKCD expression were analyzed from the perspective of genetic and epigenetics based on collated liver hepatocellular carcinoma data.Results:Both the mRNA and protein expression level of PRKCD gene in Liver hepatocellular carcinoma tissues was significantly higher than that in adjacent tissues.Its expression level was correlated with TNM stage,Histologic grade,Alpha fetoprotein(AFP)and Living status in clinicopathological features,and its expression level has certain clinical diagnostic accuracy.Kaplan-Meier analysis showed that the prognosis of patients with low PRKCD expression was significantly better than that with high PRKCD expression.Univariate and multivariate Cox regression analysis showed that PRKCD was an independent prognostic factor in patients with Liver hepatocellular carcinoma,and it was also found that the risk ratio of TNM stage III and stage IV survival curve(HR)was significantly greater than that of stage I and stage II.GSEA analysis showed that it was enriched in cell cycles and DNA replication,and was positively correlated with PRKCD.Enrichment analysis found that PRKCD is mainly involved in the chemokine signaling pathway,NOD-like receptor signaling pathway,PPAR signaling pathway,adipocytokine signaling pathway and T-cell receptor signaling pathway.Finally,through genetic and epigenetic analysis,it is found that the increase in the number of copies of genes will increase the expression level of PRKCD,and the methylation level is negatively correlated with the expression level of PRKCD.Conclusion:PRKCD gene is upregulated in Liver hepatocellular carcinoma tissues,and its overexpression level is closely related to patient poor prognosis.

A bioinformatics-based study of the mechanism of JQ-1 on BET protein and atherosclerosis induced by vascular smooth muscle cell proliferation

Background:Based on previous theoretical studies,JQ-1 as a common inhibitor of bromodomain and extraterminal(BET)proteins was used to treat a variety of diseases.Therefore,we aimed to explore the mechanism of action of JQ-1 on BET proteins based on bioinformatics and build the novel hypothesis of JQ-1 in treating atherosclerosis(AS)caused by proliferation of vascular smooth muscle cells(VSMCs).Methods:We selected the chip GSE138323 which was searched with the key words“Vascular smooth muscle cell proliferation”in Gene Expression Omnibus(GEO)database,and differential gene analysis was performed between the GRO and JQ-1 groups.Then the top twenty significantly up-regulated genes and the top twenty significantly down-regulated genes were selected for Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis.Thirdly,structured the PPI network of forty differential genes,and the core genes were screened by using the MCC algorithm which in“Cytohubba”plugin in the Cytoscapev3.9.1 software.After that,single gene Gene Set Enrichment Analysis(GSEA)enrichment analysis was performed on the selected core genes in R language.Finally molecular docking validation was performed.Results:Five core genes was selected:H3C2,H3C4,H3C7,H3C10 and AREG.The GO enrichment analysis results showed that there were twenty-five entries in biological process,eight entries in cellular components(CC),and twenty-five entries in molecular function.The KEGG enrichment analysis results showed that there were seven pathways,mainly including systemic lupus erythematosus and external neutrophil trap formation.The GSEA results showed that the five genes were mainly through the regulation of cytochrome P450 metabolism,PPAR signaling pathway and other pathways.The molecular docking results showed that JQ-1 had binding activity with these five genes.Conclusions:JQ-1 may regulate the expression of the genes that H3C2,H3C4,H3C7,H3C10 and AREG,to mainly regulate the genes in cytochrome P450 metabolism,PPAR singling pathway and other pathways,to make some influence in the proliferation of VSMCs,and improved atherosclerotic symptoms due to vascular smooth muscle proliferation,thus treating cardiovascular disease.

Construction and Validation of an RNA-Binding Protein-Related Bladder Cancer Prognostic Model Based on Bioinformatics

Objective: This study aimed to construct a bladder cancer prognostic model using bioinformatics to predict the survival of bladder cancer patients. Methods: RNA sequences and corresponding clinical data were downloaded from The Cancer Genome Atlas (TCGA) database, and the differentially expressed RNA-binding proteins (RBPs) were screened for analysis using the limma software package. Then, GO enrichment analysis and KEGG pathway analysis were performed on these differentially expressed RNA-binding proteins, and a PPI network was constructed. Finally, a risk model was constructed based on the screened central RBP, and a Kaplan-Meier survival curve was drawn to evaluate the prognostic value of central RBP and predict the prognosis of bladder Cancer(BLCA) patients with this model. Finally, the human protein atlas (HPA) online database (http://www.proteinatlas.org/) was used to further detect the differential expression of central hub RBP at the protein level between tumor tissue and normal tissue. Results: The bladder cancer prognostic model constructed with these six central RBPs had good sensitivity and specificity in predicting the prognosis of bladder cancer patients. Conclusion: This study explored the genes and regulatory networks of bladder cancer prognosis-related RNA-binding protein and bladder cancer, and constructed a bladder cancer prognosis model, which provides a theoretical basis for the development of new bladder cancer prognosis biomarkers in the future.

Dissection the endocytic routes of viral capsid proteins-coated upconversion nanoparticles by single-particle tracking

Real-time exploring the cellular endocytic pathway of viral capsid proteins(VCPs)functionalized nanocargos at the single-particle level can provide deep insight into the kinetic information involved in virus infection.In this work,porcine circovirus type 2(PCV2)VCPs with different functions are modified onto the surface of upconversion nanoparticles(VCPs-UCNPs)to investigate the cellular internalization process in real-time.Clathrin-mediated endocytosis is found to be the essential uptake mechanism for these VCPs-UCNPs.Besides,it is verified that P_(1)-UCNPs(PCV2 VCPs with nuclear localization signal,namely P1)can be easily assembled close to the perinuclear area,which is different from that of P_(2)-UCNPs(PCV2 VCPs without nuclear localization signal,namely P_(2)).Interestingly,multistep entry processes are observed.Particularly,confined diffusion is observed during the transmembrane process.The intracellular transport of VCPs-UCNPs is dependent on microtubules toward the cell interior.During this process,P_(1)-UCNPs display increased velocities with active transport,while diffusion much faster around the perinuclear area.But for P_(2)-UCNPs,there are only two phases involved in their endocytosis process.This study presents distinct dynamic mechanisms for the nanocargos with different functions,which would make a useful contribution to the development of robust drug delivery systems.

Homology Modelling and Structural Comparisons of Capsid-Associated Proteins from Circoviruses Reveal Important Virus-Specific Surface Antigens

Circoviridae represent a growing family of small animal viruses. Some of these viruses have veterinary and medical importance, although, a vast amount of these newly discovered viruses have unknown effects on their hosts. The capsid-associated protein (Cap) of circoviruses is of interest because of its role in viral structure, immune evasion, host cell entry, and nuclear shuttling of viral components. The structure of the porcine circovirus 2 (PCV2) Cap has been solved and offered insight to these functions. Based on the crystallographic PCV2 Cap structure, models from circoviruses isolated from avian, fish, and mammalian hosts have been constructed and analyzed to better understand the roles of these proteins in the virus family. A high degree of conservation is observed in the models, however, the surface antigens differ among viruses. This is likely a reflection of the small genome harbored by circoviruses, and therefore the requirement of their few proteins to carry out specific vital functions, while maintaining enough variation to successfully infect their hosts. Here we describe the putative structures of a range of Cap proteins from circoviruses based on the crystallographic determination of porcine Cap, identifying key regions for function and inhibition of crystal formation.

Bioinformatic Analysis of Non-VP1 Capsid Protein of Coxsackievirus A6

This study bioinformatically analyzed the non-VP1 capsid proteins（VP2-VP4） of Coxasckievirus A6（CVA6）, with an attempt to predict their basic physicochemical properties, structural/functional features and linear B cell eiptopes. The online tools Sub Loc, Target P and the others from Ex PASy Bioinformatics Resource Portal, and SWISS-MODEL（an online protein structure modeling server）, were utilized to analyze the amino acid（AA） sequences of VP2-VP4 proteins of CVA6. Our results showed that the VP proteins of CVA6 were all of hydrophilic nature, contained phosphorylation and glycosylation sites and harbored no signal peptide sequences and acetylation sites. Except VP3, the other proteins did not have transmembrane helix structure and nuclear localization signal sequences. Random coils were the major conformation of the secondary structure of the capsid proteins. Analysis of the linear B cell epitopes by employing Bepipred showed that the average antigenic indices（AI） of individual VP proteins were all greater than 0 and the average AI of VP4 was substantially higher than that of VP2 and VP3. The VP proteins all contained a number of potential B cell epitopes and some eiptopes were located at the internal side of the viral capsid or were buried. We successfully predicted the fundamental physicochemical properties, structural/functional features and the linear B cell eiptopes and found that different VP proteins share some common features and each has its unique attributes. These findings will help us understand the pathogenicity of CVA6 and develop related vaccines and immunodiagnostic reagents.

血管生成素样蛋白4通过调节成纤维细胞和内皮细胞功能影响糖尿病足进程

背景:研究表明,血管因素对糖尿病足的发生具有重要影响。目的:探讨血管生成素样蛋白4在糖尿病足形成中的重要作用。方法:①对糖尿病足患者的基因表达谱数据进行生物信息学分析,找到关键基因。收集糖尿病足患者以及无糖尿病健康人的皮肤标本进行苏木精-伊红染色、免疫组化染色以及qRT-PCR实验,检测血管生成素样蛋白4表达情况。②培养人永生化皮肤成纤维细胞系和原代人脐静脉内皮细胞,将2种细胞分别分为对照组和外源性补充血管生成素样蛋白4组,通过划痕实验以及CCK-8实验分别检测成纤维细胞的迁移能力和增殖能力,通过Ki67实验检测内皮细胞的增殖能力。结果与结论:①生信分析发现,血管生成素样蛋白4基因的下调可能是导致糖尿病足形成的关键基因。②苏木精-伊红染色结果显示,与正常皮肤相比,血管生成素样蛋白在糖尿病足皮肤内弱表达,且其mRNA水平相对表达量降低(P<0.01)。③划痕实验结果显示,与对照组相比,血管生成素样蛋白4组成纤维细胞迁移能力明显增强;CCK-8细胞增殖实验显示,血管生成素样蛋白4组成纤维细胞的吸光度值在24,48 h均高于对照组(P<0.01,P<0.001);提示血管生成素样蛋白4可增强高糖处理的成纤维细胞迁移及增殖能力。④Ki67实验结果显示,与对照组相比,血管生成素样蛋白4组内皮细胞Ki67阳性细胞数目明显多于对照组;CCK-8细胞增殖实验显示,血管生成素样蛋白4组内皮细胞的吸光度值在24,48 h均高于对照组(P<0.05,P<0.001)。(5)以上结果均提示血管生成素样蛋白4可增强高糖处理内皮细胞的增殖能力。