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

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

Assessment of Cytokine-Mediated Signaling Pathway Dysregulation in Arm Skin After CO2 Laser Therapy

Introduction: Laser therapy is known as an efficient approach in dermatology surgery. CO2 laser therapy is a gold standard treatment in skin surgery. This study aimed to evaluate the interferons change after CO2 laser surgeryMethods: Significant differentially-expressed genes (DEGs) of arm skin after 7 days of treatment by the CO2 laser relative to the controls are downloaded from Gene Expression Omnibus (GEO) and are included in the protein-protein interaction network via a STRING database (an application of Cytoscape software). The central DEGs were identified and enriched via gene ontology by using Clue GO software.  Results: A network including 78 DEGs and 100 neighbors was constructed and STAT1, MX1, ISG15, OAS1, IFIT1, IRF8, OASL, OAS2, and RSAD2 as hubs and STAT1, PTPRC, MX1, IRF8, ISG15, IL6, RORC, SAMSN1, and IFIT1 as bottlenecks were introduced. The cytokine-mediated signaling pathway, interferon gamma signaling, hepatitis C, interferon alpha/beta signaling, and the type I interferon signaling pathway were identified as five clusters of biological terms which are related to the central nodes.Conclusion: It can be concluded that the cytokine-mediated signaling pathway is the major pathway that is dysregulated after laser application in the treated skin.

Identification of VIM and IMP genes and metallo-betalactamase enzymes in Escherichia coli isolates by molecular and phenotypic methods in shahrekord educational hospitals

Background and aims:: Among urine pathogens, Escherichia coli (E. coli) causes 80% of urinary tract infections (UTIs). Due to the destructive nature of penicillins, cephalosporins and carbapenems (except for monobactam such as aztreonam) and carbapenemase enzymes have created many problems for treating infectious diseases. Therefore, this study aimed to investigate the phenotypic and molecular characterization of metallo-beta-lactamase (MBL) genes produced by E. coli isolates in an educational hospital during 2016- 2017. Methods: This cross-sectional study investigated 80 UTI samples affected by E. coli. In addition, antibiotic susceptibility was evaluated by disk diffusion and E-test methods for two antibiotics of meropenem and imipenem. Phenotypic tests containing modified Hodge test, ethylenediaminetetraacetic acid (EDTA) disk synergy test, and AmpC Disk were performed to identify MBL enzyme-producing strains. Finally, the frequency of Verona integron-encoded metallo-β-lactamase (VIM) and imipenemase (IMP) genes was determined by polymerase chain reaction (PCR). Results: Among 80 E. coli samples, 21 (26.25%) isolates were resistant to meropenem and imipenem as detected by the disk-diffusion method and E-test. Further, phenotypic tests including modified Hodge test, EDS test, and AmpC disk test showed the positivity of 15 (18.75%), 15 (18.75%), and 8 (10%) isolates, respectively (P < 0.001). Eventually, polymerase chain reaction (PCR) test results for the VIM gene showed 19 (23.75%) positive isolates of E. coli, but the IMP gene was observed in none of the isolates (P<0.001). Conclusion: In general, the emergence of E. coli producing MBL enzymes is a serious threat among clinical infections. The findings of this study indicated the presence of E. coli producing MBL. These enzymes can degrade carbapenems antibiotics, the last class current treatment of multiple drug-resistance infections. Keywords: Escherichia coli, Drug resistance, VIM, IM

Characterization of radio active aerosols in Tehran research reactor containment

The objectives of this research were to determine the levels of radioactivity in the Tehran research reactor containment and to investigate the mass-size distribution, composition, and concentration of radio nuclides during operation of the reactor. A cascade impactor sampler was used to determine the size-activity distributions of radioactive aerosols in each of the sampling stations. Levels of α and β activities were determined based on a counting method using a liquid scintillation counter and smear tests. The total average mass fractions of fine particles (particle diameter dp &lt;1 µm) in all of the sampling stations were approximately 26.75 , with the mean and standard deviation of 52.15 ± 19.75 µg/m3. The total average mass fractions of coarse particles were approximately 73.2, with the mean and standard deviation of 71.34 ± 24.57 µg/m3. In addition to natural radionuclides, artificial radionuclides, such as 24Na,91Sr,131I,133I,103Ru,82Br, and 140La, may be released into the reactor containment structure. Maximum activity was associated with accumulation-mode particles with diameters less than 400 nm. The results obtained from liquid scintillation counting suggested that the mean specific activity of alpha particles in fine and coarse-modes were 89.7 and 10.26 , respectively. The mean specific activity of beta particles in fine and coarse-modes were 81.15 and 18.51 , respectively. A large fraction ofthe radionuclides' mass concentration in the Tehran research reactor containment was associated with coarse-mode particles, in addition, a large fraction of the activity in the aerosol particles was associated with accumulation-mode particles. © 2015, Vinca Inst Nuclear Sci. All rights reserved

Analysis of Laser Therapy Effects on Squamous Cell Carcinoma Patients: A System Biology Study

Introduction: Mechanism of Laser therapy and also its safety are two important features of application of different types of laser in medicine. Aim of this study is investigating the critical affected genes after treatment of squamous cell carcinoma patients.Methods: Gene expression profiles of 4 squamous cell carcinoma patients that are treated via chemoradiotherapy plus laser relative to the 3 similar patients without laser exposure from Gene Expression Omnibus (GEO) are downloaded and are screen to find critical genes via network analysis. STRING database, Cytoscape software, and Clue GO plug in of Cytoscape software are used.  Results: The genes; HSX70 and NCC27 as neighbors and HSPA1B, CLIC1, RAB13, PPIF, and LCE3D were determined as hub genes. Over-expression of LCE3D was interpreted as side effect of laser therapy. Apoptosis and cell cycle were the dominant biological processes that regulated by the HSP molecules in laser treated patients.Conclusion: Laser was effected the main biological processes and simultaneously issued side effects.

The Frequency of PAI, aer and traT Genes in Escherichia coli Commensal and Urinary Pathogenic E. coli Isolates in Shahrekord and the Relationship Between the Two Groups by Multiplex PCR

Background: Nosocomial infections are acquired during hospital treatment or in a hospital environment. One such infecting agent is uropathogenic Escherichia coli and many virulence genes enable it to become pathogenic, thereby causing damage to the host. Objectives: This study aimed to identify aer, traT, and PAI genes in E. coli isolates collected from fecal and urinary tract infection (UTI) specimens and determine the relationship between them in both populations studied in a center in Iran by multiplex polymerase chain reaction (PCR) assay. Methods: Seventy-five isolates of E. coli from the urine of inpatients and 75 isolates from commensal fecal without UTI and diarrhea were collected. The E. coli bacteria were detected and isolated, using biochemical techniques and supplementary tests in the Microbiology Laboratory of Shahrekord University of Medical Sciences. Antibiotic susceptibility pattern for 14 antibiotics was done utilizing the disc diffusion method. The existence of aer, traT, and PAI virulence genes among all isolates was investigated by multiplex PCR. Results: Among the urinary pathogenic E. coli isolates, the highest antibiotic resistance was observed in cefazolin, ampicillin, and cotrimoxazole antibiotics. The prevalence rates of aer, traT, and PAI genes in the fecal isolates were 92%, 90.6%, and 46.6%, respectively. Further, their prevalence rates in urine isolates were 96%, 97.3%, and 41.3%, in that order. Conclusions: The presence of the high frequency of pathogenic islands (PAIs), especially in fecal samples, is important because these genes are easily transmitted and convert a commensal bacterium into a pathogen. Because only the genome of pathogenic bacteria has been unwrapped, little attention has been paid to PAIs in commensal bacteri

Muscle Recovery Is Highlighted by IR Laser Therapy

Introduction:In sports medicine, laser application has been well-established for the recovery of muscles. The mechanisms by which benefits of this kind of therapy can be studied is molecular research approach. Protein-protein interaction network analysis as one of the important complementary studies of proteomics can accelerate this goal by the identification of novel contributing markers.Methods:By the use of Cytoscape V3.7.1 and its applications, a network of differential expressed proteins (DEPs) from IR laser treatment samples were constructed and analyzed. Six hub-bottlenecks were determined, 4 of which were from differentially expressed proteins.Results:ClueGO discovered 4 biological processes related to these hub-bottlenecks that their function could alter due to IR laser therapy.Conclusion:In fact, by the expression changes of hub-bottlenecks including the up-regulation of HSP90s, one of the prominent biological processes in muscle recovery could be activated. This process is called nitric oxide synthase (NOS) activation that could be proposed as one of the underlying mechanisms of IR laser treatments in muscle recovery.

CFD simulation of nanofluid forced convection inside a three-dimensional annulus by two-phase mixture approach: Heat transfer and entropy generation analyses

The final publication is available at Elsevier via https://dx.doi.org/10.1016/j.ijmecsci.2018.08.002 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/The behavior of water–Al2O3 nanofluid inside the three-dimensional horizontal concentric annulus is investigated by the two-phase mixture procedure regarding the first and second laws of thermodynamics. The annulus walls are subjected to constant temperature boundary condition. Heat transfer and entropy generation rates, nanoparticle distribution, skin friction coefficient, and temperature distribution are evaluated at different concentrations and Reynolds numbers. The results show that nanoparticle concentration at the bottom of annulus and the upper side of inner cylinder is greater than other regions. In addition, the heat transfer and thermal entropy generation rates increase with increment of concentration and Reynolds number. Moreover, the lowest and highest thermal entropy generation rates happen in the annulus central part and near the walls, respectively. Bejan number is very close to 1 at all cases under study, which shows the dominance of thermal entropy generation

The occurrence of antibiotic resistance, ESBLs, MBL and NDM-1 in Uropathogenic Escherichia coli in Central part of Iran

Broad-spectrum β-lactamase enzymes capable of destroying the antibiotics of β-lactam, cephalosporin, and Metallo-β-lactamase enzymes can also deactivate all β-lactams and carbapenems. This study aimed to determine ESBLs and MBLs enzymes and the frequency of NDM-1 gene­. In this study, 200 Escherichia coli isolates of women with urinary tract infection were collected (100 inpatients and 100 outpatients). Minimum inhibitory concentration (MIC) for ceftazidime and meropenem was determined by E-test. A phenotypic confirmation test was used to detect ESBL enzymes. MBLs production was performed with modified Hodge test (MHT) and EDTA disk synergy (EDS) test. PCR was used for detecting the presence of NDM-1 gene. From 200 isolates, 93 isolates produce ESBL enzymes. Overall, 97 isolates were resistant to ceftazidime, and 38 isolates resistant to meropenem. The results of the MHT and EDS positive tests were 41 and 16 isolates, respectively. NDM-1 was not found in any of the patients. The prevalence of E. coli isolates producing both ESBLs and MBLs enzymes, is a serious threat to clinical infections. Accordingly, for the control and treatment of these strains, rapid and accurate identification can be greatly helpful