Duchenne muscular dystrophy (DMD) protein- protein interaction mapping

ObjectiveDuchenne muscular dystrophy as one of the mortal diseases is prominent to study in terms of molecular investigation. In this study, the protein interaction map of this muscle-wasting condition is generated to gain a better knowledge of interactome profile of DMD.Materials & Methods Applying Cytoscape and String Database, the protein-protein interaction network was constructed and the gene ontology of the constructed network was analyzed for biological process, molecular function, and cell component annotations.ResultsThe results indicate that among 100 proteins that are related to DMD, Dystrophin, Utrophin, Caveolin 3, and Myogenic differentiation 1 play key roles in DMD network. In addition, the gene ontology analysis showed that regulation processes, kinase activity and sarcoplasmic reticulum are the highlighted biological processes, molecular function, and cell component enrichments respectively for the proteins related to DMD.  ConclusionIn conclusion, the central proteins and the enriched ontologies can be suggested as possible prominent agents in DMD; however, the validation studies may be required

Interaction network prediction and analysis of Anorexia Nervosa

ObjectivesAnorexia Nervosa (AN) as a mental condition is a common eating disorder among young women. This study aims to shed lights on molecular behavior of this serious disorder in terms of protein interacting profile to provide further insight about its complexity.Materials & MethodsThe AN related genes were extracted from STRING database and included in interactome via Cytoscape software. The central nodes of the network were enriched via gene ontology (GO) by ClueGO+CluePedia and the action relationship between the nodes were determined by CluePedia.ResultsSix genes including LEP, INS, POMC, GCG, SST, and ALB were introduced as hub-bottlenecks that among them LEP, INS, and POMC were the super hub-bottlenecks based on further analysis. Action map analysis showed prominent role of hubs relative to bottlenecks in the network. Regulation of behavior, regulation of carbohydrate biosynthetic process, and regulation of appetite are the top associated processes for the identified hub genes.ConclusionThe topological analysis proposed the five hub-bottlenecks as the most central genes in the network, these genes and their contributing biological terms may suggest additional importance in AN pathogenesis and thereby possible candidates for therapeutic usage.  However, further studies is required to justify these findings.

Evaluation of skin response after erbium:yttrium–aluminum–garnet laser irradiation: a network analysis approach

Introduction: Application of laser in medicine and cosmetic purposes has raised grossly in recent years. There are contradictory finding about its side effects. In this research critical differentially expressed proteins after irradiation erbium:yttrium–aluminum–garnet (Er:YAG) laser on skin are investigated.Methods: Proteome data including 31 proteins were obtained from a proteomics investigation of laser irradiation, Er:YAG on female mouse skin that are published by Pan et al. The query proteins and 100 related ones were included in the protein-protein interaction (PPI) network. The central nodes were determined and all of nodes were included in action maps. Expression, activation, inhibition, binding, and reaction were considered in action plan.Results: Numbers of 16 proteins were recognized by STRING database and were included in the network. Except PHRF1, the other 15 query proteins were included in the main connected component of the constructed network. Ten central nodes of the network and ten numbers of top query proteins based on degree value were identified as central proteins of the network. All nodes of the network analyzed via action maps and the important acted nodes were determined as RPSA, GAPDH, TPT1, DCTN2, HSPB1, and PDIA3.Conclusion: Two balanced processes including cancer promotion and cancer prevention were after irradiation were identified

Protein-protein interaction network analysis for a biomarker panel related to human esophageal adenocarcinoma

Background: Esophageal adenocarcinoma (EAC) is one of the mostlethal cancers in the world with a very poor prognosis. Identification of molecular diagnostic methods is an important goal. Since protein-protein interaction (PPI) network analysis is a suitable method for molecular assessment, in the present research a PPI network related to EAC was targeted. Material and Method: Cytoscape software and its applications including STRING DB, Cluster ONE and ClueGO were applied to analyze the PPI network. Result: Among 182 EAC-related proteins which were identified, 129 were included in a main connected component. Proteins based on centrality analysis of characteristics such as degree, betweenness, closeness and stress were screened and key nodes were introduced. Two clusters were determined of which only one was significant statistically. Gene ontology revealed 50 terms in three groups associated with EAC. Conclusion: The findings indicate nine crucial proteins could form a candidate biomarker panel for EAC. Furthermore, an important cluster with 27 proteins related to the disease was identified. Gene ontology analysis of this cluster showed main related terms to closely correspond with those for colorectal cancer

Protein-protein interaction network analysis for a biomarker panel related to human esophageal adenocarcinoma

Background: Esophageal adenocarcinoma (EAC) is one of the mostlethal cancers in the world with a very poor prognosis. Identification of molecular diagnostic methods is an important goal. Since protein-protein interaction (PPI) network analysis is a suitable method for molecular assessment, in the present research a PPI network related to EAC was targeted. Material and Method: Cytoscape software and its applications including STRING DB, Cluster ONE and ClueGO were applied to analyze the PPI network. Result: Among 182 EAC-related proteins which were identified, 129 were included in a main connected component. Proteins based on centrality analysis of characteristics such as degree, betweenness, closeness and stress were screened and key nodes were introduced. Two clusters were determined of which only one was significant statistically. Gene ontology revealed 50 terms in three groups associated with EAC. Conclusion: The findings indicate nine crucial proteins could form a candidate biomarker panel for EAC. Furthermore, an important cluster with 27 proteins related to the disease was identified. Gene ontology analysis of this cluster showed main related terms to closely correspond with those for colorectal cancer

Assessment of Dysregulation of HERC6 and Essential Biological Processes in Response to Laser Therapy of Human Arm Skin

Introduction: The widespread application of lasers in medicine, especially in the treatment of diseases implies more investigations to understand the precious molecular mechanism of the laser effect on the human body. In the present study, the prominent role of HERC6 in response to CO2 Laser therapy of human skin is investigated.Methods: The numbers of 16 gene expression profiles before and after the treatment with the CO2 laser are downloaded from Gene Expression Omnibus (GEO), and differentially-expressed genes (DEGs) are analyzed to find the significant DEGs. Gene ontology analysis revealed that HERC6 and a set of its neighbors played a significant role in response to laser application.Results: The expression changes of 52 significant DEGs were compared via heat map analysis and 27 significant DEGs were introduced as the critical genes which are involved in response to laser irradiation. “Thymidylate kinase activity” among 9 clusters of biological terms was highlighted as an important biological process related to the identified DEGs. HERC2 was proposed as a critical DEG which was related to several essential cellular processes in response to laser application.Conclusion: The findings from the present study indicate that HERC6 and the numbers of its first neighbors are involved in the essential cellular response to laser therapy of human skin

Designing and manufacturing of the extremely low frequency electromagnetic field generator and detector

Electromagnetic fields (EMFs) are inevitable consequences of modern civilizations and the era of technology. Many investigations have been carried out in order to determine the effects of EMFs on biological organisms specially on human being. In one hand, most of the generators used in these kinds of experiment are not able to expose a large number of animals simultaneously and on the other hand, many environmental electromagnetic fields could be hazardous for exposing people while a portable, low cost and reliable electromagnetic detector is not commercially available. In this study, we introduced an ELF/EMFs generator capable of exposing a large experimental space and a detector of environmental ELF/EMFs which can define their spatial parameters and relevant biological effects

Protein interaction mapping related to Becker Muscular Dystrophy

ObjectiveBecker Muscular Dystrophy (BMD) is a neuromuscular disorder which is incurable. In this research protein interaction network of most associated proteins with Becker muscular dystrophy to provide a better clarification of disorder underlying mechanism is investigated.Materials & Methods The related genes to BMD were retrieved via string data base and conducted by Cytoscape and the related algorithms. The network centrality analysis was performed based on degree, betweennes, closeness and stress parameters. Gene ontology and clustering were performed via ClueGO analysis.ResultsThe results indicate that DMD as the super-hub as well as other central proteins including UTRN, TTN, DNM2 and RYR1 are important in BMD in terms of interaction features. The impairment of muscular contraction may be vital in BMD disease pathogenesis as it is the highlighted biological process term obtained by ClueGO analysis.ConclusionIt is possible that DMD targeting may be the main concern for dystrophy clinical approaches. However the other suggested proteins should be evaluated.  In conclusion, targeting these key proteins are required for treatment goals following extensive validation studies

The study of fibroblast proteome changes in the presence of Ethanol

    Ethanol known as ethyl alcohol is being widely used around the world. Many serious diseases are related with its consumption.  Alcohol posses many divers effects on human body including risk of cirrhosis and/or hepatocellular carcinoma. Therefore, analysis of this component is prominent. Fibroblast cells were cultured in various dosages of ethanol. The effective dosage was then investigated by proteomic methods.  Separated proteins of fibroblast cells by Two-Dimensional Gel (2DG) Electrophoresis method based on pI and MW were analyzed based on spots alteration by Same Spot Software. Furthered analysis was carried out with vigorous statistical analysis based on significant folding changes and one-way ANOVA. About 372 protein spots were identified and among them 65 of them were having significant expression profile, which is evaluated as p <0.05. Therefore, ethanol can induce a great impact on protein profile of fibroblast. It is concluded that altering morphologic features and viability, as well as protein expression changes, confirm toxic properties of ethanol in human body.