scholarly journals Evaluation of Skin Response After Erbium:Yttrium– Aluminum–Garnet Laser Irradiation: A Network Analysis Approach

2019 ◽  
Vol 10 (3) ◽  
pp. 194-199 ◽  
Author(s):  
Majid Rezaei-Tavirani ◽  
Mostafa Rezaei Tavirani ◽  
Mona Zamanian Azodi ◽  
Hamideh Moravvej Farshi ◽  
Mohammadreza Razzaghi
Keyword(s):  
Laser Irradiation ◽  
Er:Yag Laser ◽  
Action Plan ◽  
Mouse Skin ◽  
Differentially Expressed Proteins ◽  
Connected Component ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Skin Response ◽  
Contradictory Finding

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.

scholarly journals Assessment of the SRC Inhibition Role in the Efficacy of Breast Cancer Radiotherapy

2019 ◽  
Vol 10 (5) ◽  
pp. S18-S22
Author(s):  
Shabnam Shahrokh ◽  
Vahid Mansouri ◽  
Mohammadreza Razzaghi
Keyword(s):  
Breast Cancer ◽  
Network Analysis ◽  
Breast Cancer Cells ◽  
Cancer Cell Line ◽  
Network Analyzer ◽  
Differentially Expressed Proteins ◽  
Ppi Network ◽  
Γ Radiation ◽  
Protein Protein Interaction ◽  
Breast Cancer Radiotherapy

Introduction: Radiotherapy (RT) is an effective therapeutic method for preventing the recurrence of breast cancer after surgery. The development and improvement of RT are of interest to scientists. Possible improvement of RT via study of dysregulated proteins of breast cancer cell line MDA-MB-231 which is exposed to 10 Gray (Gy) radiation is aim of this study. Methods: Using protein-protein interaction (PPI) network analysis by means of running Cytoscape software via the STRING database, the up-regulated proteins of MDA-MB-231 breast cancer cells irradiated by a single and fractioned 10 Gy 137Cs γ-radiation were analyzed. The network was analyzed by using the Network analyzer to characterize the central genes. The action map was mapped for the queried genes and the added neighbors via CluePedia-STRING ACTIONS-v10.5- 20.11.2017. Results: The 14 differentially expressed proteins (DEPs) plus 10 neighbors interacted to construct a network. Among the 14 queried DEPs, FN1, CSPG4, LRP1, GSN, RTN4, and CTSD were highlighted as a complex set in the analysis. The analysis revealed that SRC as an added neighbor was activated by the critical DEPs. The activation of other oncogenes like AKT1 was also determined. Conclusion: The results indicate that the inhibition of SRC activity or the inhibition of its activators is a useful function of breast cancer RT

scholarly journals Identification of Key Candidate Proteins and Pathways Associated with Temozolomide Resistance in Glioblastoma Based on Subcellular Proteomics and Bioinformatical Analysis

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Guo-zhong Yi ◽  
Wei Xiang ◽  
Wen-yan Feng ◽  
Zi-yang Chen ◽  
Yao-min Li ◽  
...  
Keyword(s):  
Focal Adhesion ◽  
Kegg Pathway ◽  
Bioinformatic Analysis ◽  
Differentially Expressed Proteins ◽  
Ppi Network ◽  
Network Construction ◽  
Protein Protein Interaction ◽  
Kegg Pathway Analysis ◽  
Tcga Dataset ◽  
U87 Cells

TMZ resistance remains one of the main reasons why treatment of glioblastoma (GBM) fails. In order to investigate the underlying proteins and pathways associated with TMZ resistance, we conducted a cytoplasmic proteome research of U87 cells treated with TMZ for 1 week, followed by differentially expressed proteins (DEPs) screening, KEGG pathway analysis, protein–protein interaction (PPI) network construction, and validation of key candidate proteins in TCGA dataset. A total of 161 DEPs including 65 upregulated proteins and 96 downregulated proteins were identified. Upregulated DEPs were mainly related to regulation in actin cytoskeleton, focal adhesion, and phagosome and PI3K-AKT signaling pathways which were consistent with our previous studies. Further, the most significant module consisted of 28 downregulated proteins that were filtered from the PPI network, and 9 proteins (DHX9, HNRNPR, RPL3, HNRNPA3, SF1, DDX5, EIF5B, BTF3, and RPL8) among them were identified as the key candidate proteins, which were significantly associated with prognosis of GBM patients and mainly involved in ribosome and spliceosome pathway. Taking the above into consideration, we firstly identified candidate proteins and pathways associated with TMZ resistance in GBM using proteomics and bioinformatic analysis, and these proteins could be potential biomarkers for prevention or prediction of TMZ resistance in the future.

scholarly journals Neuroprotective Properties of Photobiomodulation in Retinal Regeneration in Rats: Perspectives From Interaction Levels

2020 ◽  
Vol 11 (3) ◽  
pp. 280-286
Author(s):  
Vahid Mansouri ◽  
Mohammadreza Razzaghi ◽  
Mohammad Rostami-Nejad ◽  
Majid Rezaei-Tavirani ◽  
Mohammad Hossein Heidari ◽  
...  
Keyword(s):  
Light Therapy ◽  
Gene Expression Omnibus ◽  
Cellular Mechanism ◽  
Light Damage ◽  
Connected Component ◽  
Ppi Network ◽  
Rat Retina ◽  
Protein Protein Interaction ◽  
Biochemical Pathways ◽  
Level Laser

Introduction: Photobiomodulation (PBM) is known as low-level laser (or light) therapy and is applied in different fields of medicine. However, it is required that its molecular and cellular mechanism be investigated. This study aims to assess the neuroprotective properties of PBM in the rat retina. Methods: GSE22818 was downloaded from Gene Expression Omnibus (GEO) and the regulation of the significant differentially expressed genes (DEGs) which are produced by light damage in the rat retina by the pretreatment of PBM application was assessed via network analysis and gene ontology enrichment. Results: The 78 produced DEGs by light-damage in the rat retina were protected via PBM pretreatment action. Among these determined DEGs, 53 individuals were included in the main connected component of the constructed protein-protein interaction (PPI) network. Ccl2, Icam1, Cxcl10, Timp1, and Fos were determined as hub nodes. Eight clusters including 26 regulated biochemical pathways by PBM pretreatment were identified. The critical DEGs based on the action maps were introduced. Conclusion: The finding indicates that PBM treatment protects rat retina against light damage via the prevention of Fos, Ccl2, Icam1, Cxcl10, and Myc dysregulation.

Protein-Protein Interaction (PPI) Network: Recent Advances in Drug Discovery

2017 ◽  
Vol 18 (1) ◽  
pp. 5-10 ◽  
Author(s):  
Alexiou Athanasios ◽  
Vairaktarakis Charalampos ◽  
Tsiamis Vasileios ◽  
Ghulam Ashraf
Keyword(s):  
Drug Discovery ◽  
Protein Interaction ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Recent Advances

scholarly journals Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein–protein interaction network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Suthanthiram Backiyarani ◽  
Rajendran Sasikala ◽  
Simeon Sharmiladevi ◽  
Subbaraya Uma
Keyword(s):  
Candidate Genes ◽  
Protein Interaction ◽  
Target Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Auxin Signaling ◽  
Pathway Enrichment Analysis ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
The Difference

AbstractBanana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein–protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)–WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

scholarly journals Differential Expression of mRNAs in Peripheral Blood Related to Prodrome and Progression of Alzheimer’s Disease

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Weishuang Xue ◽  
Jinwei Li ◽  
Kailei Fu ◽  
Weiyu Teng
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Gene Expression Omnibus ◽  
Venn Diagram ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks

Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease that affects the quality of life of elderly individuals, while the pathogenesis of AD is still unclear. Based on the bioinformatics analysis of differentially expressed genes (DEGs) in peripheral blood samples, we investigated genes related to mild cognitive impairment (MCI), AD, and late-stage AD that might be used for predicting the conversions. Methods. We obtained the DEGs in MCI, AD, and advanced AD patients from the Gene Expression Omnibus (GEO) database. A Venn diagram was used to identify the intersecting genes. Gene Ontology (GO) and Kyoto Gene and Genomic Encyclopedia (KEGG) were used to analyze the functions and pathways of the intersecting genes. Protein-protein interaction (PPI) networks were constructed to visualize the network of the proteins coded by the related genes. Hub genes were selected based on the PPI network. Results. Bioinformatics analysis indicated that there were 61 DEGs in both the MCI and AD groups and 27 the same DEGs among the three groups. Using GO and KEGG analyses, we found that these genes were related to the function of mitochondria and ribosome. Hub genes were determined by bioinformatics software based on the PPI network. Conclusions. Mitochondrial and ribosomal dysfunction in peripheral blood may be early signs in AD patients and related to the disease progression. The identified hub genes may provide the possibility for predicting AD progression or be the possible targets for treatments.

Effects of the Er:YAG Laser Irradiation on Titanium Implant Materials and Contaminated Implant Abutment Surfaces

2003 ◽  
Vol 21 (1) ◽  
pp. 7-17 ◽  
Author(s):  
Tomoko Matsuyama ◽  
Akira Aoki ◽  
Shigeru Oda ◽  
Takayuki Yoneyama ◽  
Isao Ishikawa
Keyword(s):  
Laser Irradiation ◽  
Er:Yag Laser ◽  
Titanium Implant ◽  
Implant Materials ◽  
Implant Abutment

Surface temperature during cavity preparation on human tooth by Er:YAG laser irradiation

CIRP Annals ◽  
2011 ◽  
Vol 60 (1) ◽  
pp. 555-558 ◽  
Author(s):  
T. Furumoto ◽  
T. Ueda ◽  
A. Kasai ◽  
A. Hosokawa
Keyword(s):  
Surface Temperature ◽  
Laser Irradiation ◽  
Er:Yag Laser ◽  
Human Tooth ◽  
Cavity Preparation

scholarly journals Er:YAG laser-induced damage to a dental composite in simulated clinical scenarios for inadvertent irradiation: an in vitro study

2021 ◽  
Author(s):  
Katharina Kuhn ◽  
Carmen U. Schmid ◽  
Ralph G. Luthardt ◽  
Heike Rudolph ◽  
Rolf Diebolder
Keyword(s):  
Laser Irradiation ◽  
Laser Fluence ◽  
Ablation Threshold ◽  
Er:Yag Laser ◽  
In Vitro Study ◽  
Vitro Study ◽  
Crater Diameter ◽  
Clinical Scenarios ◽  
Laser Induced Damage

AbstractInadvertent Er:YAG laser irradiation occurs in dentistry and may harm restorative materials in teeth. The aim of this in vitro study was to quantify Er:YAG laser-induced damage to a nanohybrid composite in simulated clinical scenarios for inadvertent direct and indirect (reflection) laser irradiation. The simulation was performed by varying the output energy (OE;direct˃indirect) reaching the specimen and the operating distance (OD;direct˂indirect). Composite specimens were irradiated by an Er:YAG laser. The ablation threshold was determined and clinically relevant parameters were applied (n = 6 for each OE/OD combination) for direct (OE: 570 mJ/OD: 10 mm, OE: 190 mJ/OD: 10 mm) and indirect irradiation (OE: 466 mJ/OD: 15 mm, OE: 57 mJ/OD: 15 mm, OE: 155 mJ/OD: 15 mm, OE: 19 mJ/OD: 15 mm). The extent of damage in the form of craters was evaluated using a laser scanning microscope (LSM) and a conventional light microscope (LM). The ablation threshold was determined to be 2.6 J/cm2. The crater diameter showed the highest value (LM: 1075 ± 18 µm/LSM: 1082 ± 17 µm) for indirect irradiation (reflectant:dental mirror) (OE: 466 mJ/OD: 15 mm). The crater depth showed the highest and comparable value for direct (OE: 570 mJ/OD: 10 mm; LSM: 89 ± 2 µm) and indirect irradiation (OE: 466 mJ/OD: 15 mm; LSM: 90 ± 4 µm). For each OD, the crater diameter, depth, and volume increased with higher laser fluence. However, the OD—and thus the laser spot diameter—also had an enlarging effect. Thus, indirect irradiation (reflectant:dental mirror) with only 47% of the laser fluence of direct irradiation led to a larger diameter and a comparable depth. The three-dimensional extent of the crater was large enough to cause roughening, which may lead to plaque accumulation and encourage caries, gingivitis, and periodontitis under clinical conditions. Clinicians should be aware that reflected irradiation can still create such craters.

Sign in / Sign up

Export Citation Format

Share Document