scholarly journals Compound-Protein Interaction Analysis in Condition Following Cardiac Arrest

2018 ◽  
Vol 7 ◽  
pp. e1380
Author(s):  
Mona Zamanian Azodi ◽  
Mostafa Rezaei-Tavirani ◽  
Majid Rezaei-Tavirani
Keyword(s):  
Gene Expression ◽  
Cardiac Arrest ◽  
Human Body ◽  
Interaction Analysis ◽  
Gene Expression Omnibus ◽  
Survey Result ◽  
Literature Survey ◽  
The Body ◽  
Biochemical Compounds ◽  
Chloride Sulfate

Background: Cardiac arrest (CA) and differentially expressed genes (DEGs) relative to post-CA have attracted the attention of scientist to prevent damages, which threaten patients. In the present study, metabolites relevant to DEGs of post-CA condition investigated via protein-compound interaction to understand the pathological mechanisms in the human body. Materials and Methods: STITCH plug-in integrated into Cytoscape V.3.6.1 was used to detect the most significant interacting compounds relative to DEGs of pig’s brain after 5 minutes’ CA. The genes were obtained from the Gene Expression Omnibus database. The identified elements were considered for further evaluation and validation by literature survey. Result: Findings indicate that biochemical compounds including magnesium, calcium, glucose, glycerol, hydrogen, chloride, sulfate, and estradiol interact with DEGs in the two up- and down-regulated networks. Conclusion: The compounds interacting with DEGs are suitable subjects to analysis for re-regulation of the body after CA.[GMJ.2018;7:e1380]     

scholarly journals Examining the Effector Mechanisms of the Feishu Acupoint (BL13) in the Treatment of Pneumonia Based on Systematic Acupuncture and Moxibustion Research

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Yan Xu ◽  
Jiali Cai ◽  
Weibin Li ◽  
Jingkun Miao ◽  
Yan Mei ◽  
...  
Keyword(s):  
Immune System ◽  
Chinese Medicine ◽  
Interaction Analysis ◽  
Gene Expression Omnibus ◽  
Mechanisms Of Action ◽  
The Body ◽  
Cytokine Signaling ◽  
Physical Stimulation ◽  
Ncbi Gene Expression Omnibus ◽  
Acupuncture And Moxibustion

Background. Pneumonia is a serious global health problem. In traditional Chinese medicine, acupuncture or moxibustion is used to directly stimulate select acupoints on the surface of the human body and produce physical stimulation to further stimulate regulatory functions in the body, strengthening bodily resistance, eliminating disease, and adjusting the viscera. However, this Chinese medicine knowledge does not include the specific mechanisms of action or targets of acupoints. Therefore, an in-depth research is needed. Methods. An acupoint-element database was constructed, and the target elements of the Feishu point were screened. The UniProt-Swiss-Prot sublibrary was used to obtain correct gene name information. The National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database and GEO2R were used to analyze differentially expressed genes in pneumonia. The STRING database was used to analyze interactions, construct a network of the Feishu point efficacy system in pneumonia, and elucidate the mechanisms of action. Results. The Feishu point comprises 34 elements in total. The protein interaction analysis has 38 nodes and 115 edges. The Feishu point efficacy system-pneumonia system network shows that cytokine signaling in the immune system, signaling by interleukins (ILs), IL-4 and IL-13 signaling, and the immune system may be related to immunity and inflammation. The Feishu point efficacy system regulating pneumonia showed that FCER2, IL4R, FASLG, TGFB1, IL6R, STAT6, IL1B, CASP3, IL5RA, IL2RB, MYD88, SQSTM1, IL12RB1, IFNGR1, ADAM17, and CDH1 are the main targets. Conclusion. From the perspective of systematic acupuncture and moxibustion, the Feishu point regulates cytokine signaling in the immune system, signaling by ILs, IL-4 and IL-13 signaling, and the immune system by targeting FCER2, IL4R, FASLG, TGFB1, IL6R, STAT6, IL1B, CASP3, IL5RA, IL2RB, MYD88, SQSTM1, IL12RB1, IFNGR1, ADAM17, and CDH1, thereby regulating pneumonia.

scholarly journals Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database

2019 ◽  
Author(s):  
Joshua D Fortriede ◽  
Troy J Pells ◽  
Stanley Chu ◽  
Praneet Chaturvedi ◽  
DongZhuo Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Model Organism ◽  
Gene Expression Omnibus ◽  
The Body ◽  
Data Mapping ◽  
Model Organism Database ◽  
Ncbi Gene Expression Omnibus ◽  
Network Analyses ◽  
Deep Integration ◽  
Next Generation Sequencing Ngs

Abstract Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated ‘gene expression as a phenotype’ and gene regulatory network analyses.

Screening and Interaction Analysis of Key Genes in miR-542-3p Over- Expressed Osteosarcoma Cells by Bioinformatics

2020 ◽  
Vol 23 (5) ◽  
pp. 411-418
Author(s):  
Zhongqiu Li ◽  
Peng Zhang ◽  
Feifei Feng ◽  
Qiao Zhang
Keyword(s):  
Gene Expression ◽  
Interaction Analysis ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
P53 Signaling ◽  
Cancer Genome Atlas ◽  
Key Genes ◽  
Gene Expression Profile Data

Background: Osteosarcoma is one of the most serious primary malignant bone tumors that threaten the lives of children and adolescents. However, the mechanism underlying and how to prevent or treat the disease have not been well understood. Aims & Objective: This aim of the present study was to identify the key genes and explore novel insights into the molecular mechanism of miR-542-3p over-expressed Osteosarcoma. Materials & Methods: Gene expression profile data GDS5367 was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened using GEO2R, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the DAVID database. And protein-protein interaction (PPI) network was constructed by the STRING database. In addition, the most highly connected module was screened by plugin MCODE and hub genes by plugin CytoHubba. Furthermore, UALCAN and The Cancer Genome Atlas were performed for survival analysis. Result: In total, 1421 DEGs were identified, including 598 genes were up-regulated and 823 genes were down-regulated. GO analysis showed that DEGs were classified into three groups and DEGs mainly enriched in Steroid biosynthesis, Ubiquitin mediated proteolysis and p53 signaling pathway. Six hub genes (UBA52, RNF114, UBE2H, TRIP12, HNRNPC, and PTBP1) may be key genes with the progression of osteosarcoma. Conclusion: The results could better understand the mechanism of osteosarcoma, which may facilitate a novel insight into treatment targets.

Correction of Posture Deviations in the Sagittal Plane Using the Pilates Method

2019 ◽  
pp. 3-13
Author(s):  
Alexandru Cîtea ◽  
George-Sebastian Iacob
Keyword(s):  
Low Back Pain ◽  
Back Pain ◽  
Postural Control ◽  
Human Body ◽  
Sagittal Plane ◽  
The Body ◽  
Lower Limbs ◽  
Low Back ◽  
Pilates Method ◽  
The Relationship

Posture is commonly perceived as the relationship between the segments of the human body upright. Certain parts of the body such as the cephalic extremity, neck, torso, upper and lower limbs are involved in the final posture of the body. Musculoskeletal instabilities and reduced postural control lead to the installation of nonstructural posture deviations in all 3 anatomical planes. When we talk about the sagittal plane, it was concluded that there are 4 main types of posture deviation: hyperlordotic posture, kyphotic posture, rectitude and "sway-back" posture.Pilates method has become in the last decade a much more popular formof exercise used in rehabilitation. The Pilates method is frequently prescribed to people with low back pain due to their orientation on the stabilizing muscles of the pelvis. Pilates exercise is thus theorized to help reactivate the muscles and, by doingso, increases lumbar support, reduces pain, and improves body alignment.

Representation of a Human Body: A Comparison Study between Balinese and Javanese Traditional House

Humaniora ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 83-90
Author(s):  
Anak Agung Ayu Wulandari ◽  
Ade Ariyani Sari Fajarwati
Keyword(s):  
Comparative Study ◽  
Human Body ◽  
Qualitative Method ◽  
Descriptive Analysis ◽  
The Body ◽  
Comparison Study ◽  
Architectural Drawing ◽  
Study Approach ◽  
The Comparative Study ◽  
Head Area

The research would look further at the representation of the human body in both Balinese and Javanese traditional houses and compared the function and meaning of each part. To achieve the research aim, which was to evaluate and compare the representation of the human body in Javanese and Balinese traditional houses, a qualitative method through literature and descriptive analysis study was conducted. A comparative study approach would be used with an in-depth comparative study. It would revealed not only the similarities but also the differences between both subjects. The research shows that both traditional houses represent the human body in their way. From the architectural drawing top to bottom, both houses show the same structure that is identical to the human body; head at the top, followed by the body, and feet at the bottom. However, the comparative study shows that each area represents a different meaning. The circulation of the house is also different, while the Balinese house is started with feet and continued to body and head area. Simultaneously, the Javanese house is started with the head, then continued to body, and feet area.

Decoding Psoriasis: Integrated Bioinformatics Approach to Understand Hub Genes and Involved Pathways

2020 ◽  
Vol 26 (29) ◽  
pp. 3619-3630
Author(s):  
Saumya Choudhary ◽  
Dibyabhaba Pradhan ◽  
Noor S. Khan ◽  
Harpreet Singh ◽  
George Thomas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Gene ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Keratinocyte Differentiation ◽  
Hub Genes ◽  
Lesional Skin ◽  
Ncbi Gene Expression Omnibus

Background: Psoriasis is a chronic immune mediated skin disorder with global prevalence of 0.2- 11.4%. Despite rare mortality, the severity of the disease could be understood by the accompanying comorbidities, that has even led to psychological problems among several patients. The cause and the disease mechanism still remain elusive. Objective: To identify potential therapeutic targets and affecting pathways for better insight of the disease pathogenesis. Method: The gene expression profile GSE13355 and GSE14905 were retrieved from NCBI, Gene Expression Omnibus database. The GEO profiles were integrated and the DEGs of lesional and non-lesional psoriasis skin were identified using the affy package in R software. The Kyoto Encyclopaedia of Genes and Genomes pathways of the DEGs were analyzed using clusterProfiler. Cytoscape, V3.7.1 was utilized to construct protein interaction network and analyze the interactome map of candidate proteins encoded in DEGs. Functionally relevant clusters were detected through Cytohubba and MCODE. Results: A total of 1013 genes were differentially expressed in lesional skin of which 557 were upregulated and 456 were downregulated. Seven dysregulated genes were extracted in non-lesional skin. The disease gene network of these DEGs revealed 75 newly identified differentially expressed gene that might have a role in development and progression of the disease. GO analysis revealed keratinocyte differentiation and positive regulation of cytokine production to be the most enriched biological process and molecular function. Cytokines -cytokine receptor was the most enriched pathways. Among 1013 identified DEGs in lesional group, 36 DEGs were found to have altered genetic signature including IL1B and STAT3 which are also reported as hub genes. CCNB1, CCNA2, CDK1, IL1B, CXCL8, MKI 67, ESR1, UBE2C, STAT1 and STAT3 were top 10 hub gene. Conclusion: The hub genes, genomic altered DEGs and other newly identified differentially dysregulated genes would improve our understanding of psoriasis pathogenesis, moreover, the hub genes could be explored as potential therapeutic targets for psoriasis.

Anti-Diabetic and Angio-Protective Effect of Guluronic Acid (G2013) as a New Nonsteroidal Anti-Inflammatory Drug in the Experimental Model of Diabetes

2020 ◽  
Vol 20 (3) ◽  
pp. 446-452
Author(s):  
Seyed S. Mortazavi-Jahromi ◽  
Shahab Alizadeh ◽  
Mohammad H. Javanbakht ◽  
Abbas Mirshafiey
Keyword(s):  
Gene Expression ◽  
Blood Glucose ◽  
Food Intake ◽  
Experimental Model ◽  
Serum Insulin ◽  
Fasting Blood Glucose ◽  
Diabetic Control ◽  
The Body ◽  
Sprague Dawley ◽  
Guluronic Acid

Background: This study aimed to investigate the effects of guluronic acid (G2013) on blood sugar, insulin, and gene expression profile of oxLDL receptors (SR-A, CD36, LOX-1, and CD68) in the experimental model of diabetes. Methods: 18 Sprague Dawley rats were randomly assigned to three groups of healthy control, diabetic control, and G2013 group. Diabetes was induced through intraperitoneal (IP) injection of 60 mg/kg streptozotocin. The subjects were IP treated with 25 mg/kg of G2013 per day for 28 days. The body weight, food intake, fasting blood glucose and insulin were measured. In addition, the expression of mentioned genes was investigated through quantitative real-time PCR. Results: The data showed that the final weight increased significantly in the G2013-treated subjects compared to the diabetic control (p < 0.05). The results indicated that final food intake significantly reduced in the G2013-treated subjects compared to the diabetic control (p < 0.05). The study findings also suggested that the final fasting blood glucose significantly reduced in the G2013-treated group, whereas the final fasting serum insulin level significantly increased in this group compared to the diabetic control (p < 0.05). Moreover, the gene expression levels of SR-A, CD36, LOX-1, and CD68 in the G2013 group significantly reduced compared to the diabetic control (p < 0.05). Conclusion: This study showed that G2013, could reduce blood glucose and increase insulin levels and reduce the gene expression level of oxLDL receptors. In addition, it may probably play an important role in reducing the severity of diabetes-induced inflammatory symptoms.

scholarly journals CircFAM13B promotes the proliferation of hepatocellular carcinoma by sponging miR-212, upregulating E2F5 expression and activating the P53 pathway

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Xie ◽  
Xiaofeng Hang ◽  
Wensheng Xu ◽  
Jing Gu ◽  
Yuanjing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
In Vivo Studies ◽  
Circular Rnas ◽  
Novel Target ◽  
Underlying Mechanisms

Abstract Background Most of the biological functions of circular RNAs (circRNAs) and the potential underlying mechanisms in hepatocellular carcinoma (HCC) have not yet been discovered. Methods In this study, using circRNA expression data from HCC tumor tissues and adjacent tissues from the Gene Expression Omnibus database, we identified out differentially expressed circRNAs and verified them by qRT-PCT. Functional experiments were performed to evaluate the effects of circFAM13B in HCC in vitro and in vivo. Results We found that circFAM13B was the most significantly differentially expressed circRNA in HCC tissue. Subsequently, in vitro and in vivo studies also demonstrated that circFAM13B promoted the proliferation of HCC. Further studies revealed that circFAM13B, a sponge of miR-212, is involved in the regulation of E2F5 gene expression by competitively binding to miR-212, inhibits the activation of the P53 signalling pathway, and promotes the proliferation of HCC cells. Conclusions Our findings revealed the mechanism underlying the regulatory role played by circFAM13B, miR-212 and E2F5 in HCC. This study provides a new theoretical basis and novel target for the clinical prevention and treatment of HCC.

scholarly journals Novel Epigenetic Eight-Gene Signature Predictive of Poor Prognosis and MSI-Like Phenotype in Human Metastatic Colorectal Carcinomas

Cancers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 158
Author(s):  
Valentina Condelli ◽  
Giovanni Calice ◽  
Alessandra Cassano ◽  
Michele Basso ◽  
Maria Grazia Rodriquenz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Poor Prognosis ◽  
Cpg Island ◽  
Colon Adenocarcinoma ◽  
Gene Signature ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Cpg Island Methylator Phenotype ◽  
Prognostic Information ◽  
Global Methylation

Epigenetics is involved in tumor progression and drug resistance in human colorectal carcinoma (CRC). This study addressed the hypothesis that the DNA methylation profiling may predict the clinical behavior of metastatic CRCs (mCRCs). The global methylation profile of two human mCRC subgroups with significantly different outcome was analyzed and compared with gene expression and methylation data from The Cancer Genome Atlas COlon ADenocarcinoma (TCGA COAD) and the NCBI GENE expression Omnibus repository (GEO) GSE48684 mCRCs datasets to identify a prognostic signature of functionally methylated genes. A novel epigenetic signature of eight hypermethylated genes was characterized that was able to identify mCRCs with poor prognosis, which had a CpG-island methylator phenotype (CIMP)-high and microsatellite instability (MSI)-like phenotype. Interestingly, methylation events were enriched in genes located on the q-arm of chromosomes 13 and 20, two chromosomal regions with gain/loss alterations associated with adenoma-to-carcinoma progression. Finally, the expression of the eight-genes signature and MSI-enriching genes was confirmed in oxaliplatin- and irinotecan-resistant CRC cell lines. These data reveal that the hypermethylation of specific genes may provide prognostic information that is able to identify a subgroup of mCRCs with poor prognosis.

Embodying the culture of achievement: Culture between illness and perfection is a ‘thin line’ – obtaining the ideal female body as an act of achievement

2021 ◽  
pp. 1354067X2110040
Author(s):  
Josefine Dilling ◽  
Anders Petersen
Keyword(s):  
Experimental Study ◽  
Human Body ◽  
Female Body ◽  
The Body ◽  
Thin Line ◽  
Complex Processes ◽  
The Individual ◽  
Different Levels ◽  
The Ideal ◽  
Body Ideals

In this article, we argue that certain behaviour connected to the attempt to attain contemporary female body ideals in Denmark can be understood as an act of achievement and, thus, as an embodiment of the culture of achievement, as it is characterised in Præstationssamfundet, written by the Danish sociologist Anders Petersen (2016) Hans Reitzels Forlag . Arguing from cultural psychological and sociological standpoints, this article examines how the human body functions as a mediational tool in different ways from which the individual communicates both moral and aesthetic sociocultural ideals and values. Complex processes of embodiment, we argue, can be described with different levels of internalisation, externalisation and materialisation, where the body functions as a central mediator. Analysing the findings from a qualitative experimental study on contemporary body ideals carried out by the Danish psychologists Josefine Dilling and Maja Trillingsgaard, this article seeks to anchor such theoretical claims in central empirical findings. The main conclusions from the study are used to structure the article and build arguments on how expectations and ideals expressed in an achievement society become embodied.

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