scholarly journals The Expression Patterns of BECN1, LAMP2, and PINK1 Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study

2020 ◽  
Vol 9 (12) ◽  
pp. 4020
Author(s):  
Martyna Bednarczyk ◽  
Edyta Fatyga ◽  
Sylwia Dzięgielewska-Gęsiak ◽  
Dariusz Waniczek ◽  
Beniamin Grabarek ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
In Silico ◽  
Expression Patterns ◽  
Cpg Islands ◽  
In Silico Analysis ◽  
Epigenetic Changes ◽  
Grid Infrastructure ◽  
In Silico Study ◽  
Silico Analysis

Background: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in BECN1, LAMP2, and PINK1 regulation and to determine the possible role of the epigenetic changes in examined colorectal cancer using an in silico approach. Methods: A total of 44 pairs of surgically removed tumors at clinical stages I‒IV and healthy samples (marginal tissues) from patients’ guts were analyzed. Analysis of the obtained results was conducted using the PL-Grid Infrastructure and Statistica 12.0 program. The miRNAs and CpG islands were estimated using the microrna.org database and MethPrimer program. Results: The autophagy-related genes were shown to be able to be regulated by miRNAs (BECN1—49 mRNA, LAMP2—62 mRNA, PINK1—6 mRNA). It was observed that promotion regions containing at least one CpG region were present in the sequence of each gene. Conclusions: The in silico analysis performed allowed us to determine the possible role of epigenetic mechanisms of regulation gene expression, which may be an interesting therapeutic target in the treatment of colorectal cancer.

The role of cell surface proteins gene expression in diagnosis, prognosis, and drug resistance of colorectal cancer: In silico analysis and validation

2021 ◽  
Vol 123 ◽  
pp. 104688
Author(s):  
Nasrin Nazempour ◽  
Mohammad Hossein Taleqani ◽  
Navid Taheri ◽  
Amir Hossein Haji Ali Asgary Najafabadi ◽  
Alireza Shokrollahi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Drug Resistance ◽  
Cell Surface ◽  
In Silico ◽  
In Silico Analysis ◽  
Surface Proteins ◽  
Cell Surface Proteins ◽  
Silico Analysis

scholarly journals Intracellular Na+ Modulates Pacemaking Activity in Murine Sinoatrial Node Myocytes: An In Silico Analysis

2021 ◽  
Vol 22 (11) ◽  
pp. 5645
Author(s):  
Stefano Morotti ◽  
Haibo Ni ◽  
Colin H. Peters ◽  
Christian Rickert ◽  
Ameneh Asgari-Targhi ◽  
...  
Keyword(s):  
Heart Failure ◽  
Membrane Potential ◽  
In Silico ◽  
Sinoatrial Node ◽  
In Silico Analysis ◽  
Ankyrin B ◽  
Deficient Mice ◽  
Silico Analysis ◽  
Bursting Activity

Background: The mechanisms underlying dysfunction in the sinoatrial node (SAN), the heart’s primary pacemaker, are incompletely understood. Electrical and Ca2+-handling remodeling have been implicated in SAN dysfunction associated with heart failure, aging, and diabetes. Cardiomyocyte [Na+]i is also elevated in these diseases, where it contributes to arrhythmogenesis. Here, we sought to investigate the largely unexplored role of Na+ homeostasis in SAN pacemaking and test whether [Na+]i dysregulation may contribute to SAN dysfunction. Methods: We developed a dataset-specific computational model of the murine SAN myocyte and simulated alterations in the major processes of Na+ entry (Na+/Ca2+ exchanger, NCX) and removal (Na+/K+ ATPase, NKA). Results: We found that changes in intracellular Na+ homeostatic processes dynamically regulate SAN electrophysiology. Mild reductions in NKA and NCX function increase myocyte firing rate, whereas a stronger reduction causes bursting activity and loss of automaticity. These pathologic phenotypes mimic those observed experimentally in NCX- and ankyrin-B-deficient mice due to altered feedback between the Ca2+ and membrane potential clocks underlying SAN firing. Conclusions: Our study generates new testable predictions and insight linking Na+ homeostasis to Ca2+ handling and membrane potential dynamics in SAN myocytes that may advance our understanding of SAN (dys)function.

In silico analysis of selenoprotein N (Gallus gallus): absence of EF-hand motif and the role of CUGS-helix domain in antioxidant protection

Metallomics ◽  
2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Shi-Yong Zhu ◽  
Li-Li Liu ◽  
Yue-Qiang Huang ◽  
Xiao-Wei Li ◽  
Milton Talukder ◽  
...  
Keyword(s):  
In Silico ◽  
Common Ancestor ◽  
In Silico Analysis ◽  
Antioxidant Protection ◽  
Jnk Pathway ◽  
Downstream Target ◽  
Ef Hand ◽  
Silico Analysis

Abstract Selenoprotein N (SEPN1) is critical to the normal muscular physiology. Mutation of SEPN1 can raise congenital muscular disorder in human. It is also central to maturation and structure of skeletal muscle in chicken. However, human SEPN1 contained an EF-hand motif, which was not found in chicken. And the biochemical and molecular characterization of chicken SEPN1 remains unclear. Hence, protein domains, transcription factors, and interactions of Ca2+ in SEPN1 were analyzed in silico to provide the divergence and homology between chicken and human in this work. The results showed that vertebrates’ SEPN1 evolved from a common ancestor. Human and chicken's SEPN1 shared a conserved CUGS-helix domain with function in antioxidant protection. SEPN1 might be a downstream target of JNK pathway, and it could respond to multiple stresses. Human's SEPN1 might not combine with Ca2+ with a single EF-hand motif in calcium homeostasis, and chicken SEPN1 did not have the EF-hand motif in the prediction, indicating the EF-hand motif malfunctioned in chicken SEPN1.

scholarly journals IN SILICO STUDY OF THE ANTIMICROBIAL PROFILE OF β-CITRONELLOL: POTENTIAL AS AN ANTIFUNGAL

2019 ◽  
Vol 16 (32) ◽  
pp. 894-898
Author(s):  
D. F. SILVA ◽  
H. D. NETO ◽  
M. D. L. FERREIRA ◽  
A. A. O. FILHO ◽  
E. O. LIMA
Keyword(s):  
In Silico ◽  
Fungal Infections ◽  
In Silico Analysis ◽  
Fungal Species ◽  
In Silico Study ◽  
Pass Online ◽  
Therapeutic Alternatives ◽  
Bioactivity Profile ◽  
Silico Analysis

β-citronellol (3,7-dimethyl-6-octen-1-ol) has been exhibiting a number of pharmacological effects that creates interest about its antimicrobial potential, since several substances of the monoterpene class have already demonstrated to possess activity in this profile. In addition, the emergence of fungal species resistant to current pharmacotherapy poses a serious challenge to health systems, making it necessary to search for new effective therapeutic alternatives to deal with this problem. In this study, the antimicrobial profile of β-citronellol was analyzed. The Prediction of Activity Spectra for Substances (PASS) online software was used to study the antimicrobial activity of the β-citronellol molecule by the use of in silico analysis. In contrast, an in vitro antifungal study of this monoterpene was carried out. For this purpose, the Minimum Inhibitory Concentration (MIC) was determined by the microdilution technique in 96-well plates in Saboraud Dextrose Broth/RPMI against sensitive strains of Candida albicans, and this assay was performed in duplicate. In the in silico analysis of the antimicrobial profile, it was revealed that the monoterpene β-citronellol had a diverse antimicrobial bioactivity profile. For the antifungal activity, it presented a percentage value with Pa: 58.4% (predominant) and its MIC of 128 μg/mL, which was equivalent for all strains tested. The in silico study of the β-citronellol molecule allowed us to consider that the monoterpenoid is very likely to be bioactive against agents that cause fungal infections.

Serum Micrornas can Detect Colorectal Cancer; two Validation Study after In-Silico Analysis

2017 ◽  
Vol 152 (5) ◽  
pp. S1018
Author(s):  
Hiroyuki Takamaru ◽  
Yutaka Saito ◽  
Taku Sakamoto ◽  
Seiichiro Abe ◽  
Masayoshi Yamada ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Validation Study ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis ◽  
Serum Micrornas

scholarly journals Influence of cantilever position and implant connection in a zirconia custom implant-supported fixed partial prosthesis: in silico analysis

2018 ◽  
Vol 47 (4) ◽  
pp. 223-229
Author(s):  
Juliana Maria Coutinho BASTOS ◽  
Dimorvan BORDIN ◽  
Andréa Araújo de VASCONCELLOS ◽  
Milton Edson MIRANDA
Keyword(s):  
In Silico ◽  
Maximum Stress ◽  
In Silico Analysis ◽  
Compression Stress ◽  
Vertical Load ◽  
Occlusal Force ◽  
Tension Distribution ◽  
Custom Implant ◽  
In Silico Study ◽  
Silico Analysis

Abstract Introduction A better tension distribution on implants and abutments in implant-supported fixed partial prosthesis is essential in the rehabilitation of posterior mandible area. Objective: To evaluate the influence of cantilever position and implant connection in a zircônia custom implant-supported fixed partial prosthesis using the 3-D finite element method. Material and method: Four models were made based on tomographic slices of the posterior mandible with a zirconia custom three-fixed screw-retained partial prosthesis. The investigated factors of the in silico study were: cantilever position (mesial or distal) and implant connection (external hexagon or morse taper). 100 N vertical load to premolar and 300 N to molar were used to simulate the occlusal force in each model to evaluate the distribution of stresses in implants, abutments, screws and cortical and cancellous bone. Result: The external hexagon (EH) connection showed higher cortical compression stress when compared to the morse taper (MT). For both connections, the molar cantilever position had the highest cortical compression. The maximum stress peak concentration was located at the cervical bone in contact with the threads of the first implant. The prosthetic and abutment screws associated with the molar cantilevers showed the highest stress concentration, especially with the EH connection. Conclusion: Morse taper implant connetions associated with a mesial cantilever showed a more favorable treatment option for posterior mandible rehabilitation.

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