scholarly journals XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T Gene Polymorphisms Associated with Male Infertility Risk: Evidences from Case-Control and In Silico Studies

2017 ◽  
Vol 2017 ◽  
pp. 1-16 ◽  
Author(s):  
Danial Jahantigh ◽  
Abasalt Hosseinzadeh Colagar
Keyword(s):  
Male Infertility ◽  
In Silico ◽  
Gene Polymorphisms ◽  
Tandem Repeats ◽  
In Silico Analysis ◽  
Severe Oligozoospermia ◽  
Nuclear Factors ◽  
Increased Risk ◽  
In Silico Studies ◽  
Increased Susceptibility

We evaluate the association between genetic polymorphisms of XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T with male infertility susceptibility. A total of 392 men including 178 infertile males (102 idiopathic azoospermia and 76 severe oligozoospermia) and 214 healthy controls were recruited. XRCC6 -61C>G and XRCC7 6721G>T genotyping was performed by PCR-RFLP whereas XRCC5 VNTR was performed by PCR. The 2R allele and 2R allele carriers of XRCC5 VNTR polymorphism significantly decreased risk of male infertility. The mutant GG genotypes and carriers of the CG and GG genotypes of XRCC6 -61C>G showed increased risk for the male infertility. Furthermore, the G allele of the XRCC6 -61C>G was correlated with increased susceptibility to male infertility. Likewise, the T allele of the XRCC7 6721G>T polymorphism was associated with increased susceptibility to male infertility in azoospermia. In silico analysis predicted that the presence of tandem repeats in XRCC5 gene prompter can be sequence to bind to more nuclear factors. Also, rs2267437 (C>G) variant was located in a well-conserved region in XRCC6 promoter and this variation might lead to differential allelic expression. The XRCC7 6721G>T gene polymorphism occurred in an acceptor-splicing site, but this polymorphism has no severe modification on XRCC7 mRNA splicing. Our results indicate the association of XRCC5 VNTR, XRCC6 -61C>G, and XRCC7 6721G>T gene polymorphisms with male infertility in Iranian men.

Association of VEGFA gene polymorphisms with susceptibility to non-Hodgkin's lymphoma: Evidences from population-based and in silico studies

Gene Reports ◽  
2020 ◽  
Vol 20 ◽  
pp. 100696 ◽  
Author(s):  
Mohammad Ali Mashhadi ◽  
Narges Arbabi ◽  
Saman Sargazi ◽  
Fatemeh Kazemi-Lomedasht ◽  
Danial Jahantigh ◽  
...  
Keyword(s):  
In Silico ◽  
Gene Polymorphisms ◽  
Hodgkin’S Lymphoma ◽  
Population Based ◽  
Hodgkin's Lymphoma ◽  
Non Hodgkin’S Lymphoma ◽  
Non Hodgkin's Lymphoma ◽  
In Silico Studies ◽  
Vegfa Gene

In silico, Physico-chemical characterization and analysis of Sandalwood proteins

2018 ◽  
Vol 3 (02) ◽  
pp. 150-157
Author(s):  
Asad Amir ◽  
Neelesh Kapoor ◽  
Hirdesh Kumar ◽  
Mohd. Tariq ◽  
Mohd. Asif Siddiqui
Keyword(s):  
Secondary Structure ◽  
In Silico ◽  
Chemical Characterization ◽  
In Silico Analysis ◽  
Chemical Parameters ◽  
Physico Chemical ◽  
In Silico Studies ◽  
The Family ◽  
Silico Analysis

Sandalwood is a commercially and culturally important plant species belonging to the family Santalaceae and the genus Santalum. In Indian sandalwood is renowned for its oil, which is highly rated for its sweet, fragrant, persistent aroma and the fixative property which is highly demanded by the perfume industry. For better production and varieties, requires to understanding the functions of proteins, their analysis and characterization of proteins sequences and their structures, their localizations in cell and their interaction with other functional partner. Due to limited number of in silico studies on sandalwood, in the present study we have performed in silico analysis by characterization of sandalwood proteins. Total 23 proteins were obtained and characterization using UniProtKB, identifying their physico-chemical parameters using ProtParam tool and prediction of their secondary structure elements using GOR of all 23 proteins.

scholarly journals Tumor necrosis factor (TNF)-α- 308 G/A gene polymorphism (rs1800629) in Egyptian patients with alopecia areata and vitiligo, a laboratory and in silico analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240221
Author(s):  
Talal Abd El-Raheem ◽  
Rania H. Mahmoud ◽  
Enas M. Hefzy ◽  
Mohamed Masoud ◽  
Reham Ismail ◽  
...  
Keyword(s):  
Risk Factors ◽  
Alopecia Areata ◽  
In Silico ◽  
In Silico Analysis ◽  
Nucleotide Polymorphisms ◽  
Sp1 Transcription Factor ◽  
Increased Risk ◽  
Tnf Α ◽  
Egyptian Patients ◽  
Subsequent Effect

Purpose & methods Several single-nucleotide polymorphisms (SNPs) in the promoter region of the TNF-α gene can cause variations in the gene regulatory sites and act as risk factors for some autoimmune disorders as alopecia areata (AA) and vitiligo. This study aimed to detect the serum TNF-α (sTNF) level (by ELISA) and the rs1800629 (by real-time PCR) among AA and vitiligo Egyptian patients and to determine their relation with disease duration and severity. In silico analysis of this SNP to study the molecular regulation of the mutant genotypes was also done. Results In AA patients, no risk was associated with the mutant genotypes vs. the normal genotype, or with A allele vs. G allele. The risk of vitiligo was significantly higher with the G/A and A/A genotypes compared with HCs (p = 0.011). Similarly, a significantly increased risk was noted in patients with A allele vs. G allele (p<0.0001). In AA and vitiligo patients, a significant increase in sTNF-α levels was noted in the mutant G/A genotypes vs. the normal G/G genotype (p<0.0001) and in the A allele vs the G allele (p<0.0001). According to the in silico analysis, this SNP could mainly affect the SP1 transcription factor binding site with subsequent effect on TNF-α expression. Conclusion According to results of the laboratory and the in silico study, the mutant TNF-α (308) genotypes were risk factors that conferred susceptibility to vitiligo among Egyptian patients but had no effect on the susceptibility to AA.

scholarly journals Association between HLA gene polymorphisms and mortality of COVID‐19: An in silico analysis

2020 ◽  
Vol 8 (4) ◽  
pp. 684-694
Author(s):  
Yusuke Tomita ◽  
Tokunori Ikeda ◽  
Ryo Sato ◽  
Takuro Sakagami
Keyword(s):  
In Silico ◽  
Gene Polymorphisms ◽  
In Silico Analysis ◽  
Silico Analysis

Bioactive isolates of Morus species as antibacterial agents and their insilico profiling

2020 ◽  
Vol 17 ◽  
Author(s):  
Aditya Rao ◽  
Venugopal T.M ◽  
Jayanna N.D ◽  
Paramesha Mahadevappa ◽  
Ramesh C.K
Keyword(s):  
In Silico ◽  
Antibacterial Effect ◽  
In Silico Analysis ◽  
Antimicrobial Effect ◽  
Bactericidal Effect ◽  
Traditional System ◽  
In Silico Studies ◽  
The Rich ◽  
Synthase Inhibitor ◽  
Phosphate Synthase

Background: The genus Morus is one of the rich sources of phytomedicine and considered as a beneficial natural source for the drugs with potential antimicrobial effect under the traditional system of medicine. Introduction: In the present study, three bioactive compounds were isolated from the leaves of two species of genus Morus and their antibacterial effect against selective pathogens were assessed. Methods: The inhibitory effects of the three molecules isolated were assessed for their minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) against selected pathogens. The in-silico studies provided the toxicity profile and the binding interactions with glucosamine-6-phosphate synthase for all the isolates. Results and Discussion: Results and Discussion: Among the three compounds tested, cathafuran-B showed prominent bacteriostatic and bactericidal effect which is supported by the results of in-silico analysis suggesting cathafuran-B could be a potential glucosamine-6- phosphate synthase inhibitor. Conclusion: The biomolecule isolated from less explored Morus laevigata exhibiting higher antibacterial effect among the compounds tested warranted opening a new prospect in phytomedicinal research in exploring its pharmacological properties and lowering the utilization load present on highly explored Morus alba.

scholarly journals C-C chemokine receptor type 5 links COVID-19, Rheumatoid arthritis, and Hydroxychloroquine: In silico analysis 

2020 ◽  
Author(s):  
MAHMOOD Yaseen HACHIM ◽  
Ibrahim Hachim ◽  
Kashif Naeem ◽  
Haifa Hannawi ◽  
Issa Al Salmi ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
In Silico Analysis ◽  
Cell Recruitment ◽  
Beneficial Effects ◽  
Increased Risk ◽  
Patient Groups ◽  
Chemotactic Factors

Abstract Patients with rheumatoid arthritis (RA) represent one of the fragile patient groups that might be susceptible to the critical form of the coronavirus disease -19 (COVID-19) . On the other side, RA patients have been found not to have an increased risk of COVID-19 infection. Moreover, some of the Disease-Modifying Anti-Rheumatic Drugs (DMARDS) commonly used to treat rheumatic diseases like Hydroxychloroquine (HCQ) were proposed as a potential therapy for COVID-19 with a lack of full understanding of their molecular mechanisms. This highlights the need for the discovery of common pathways that may link both diseases at the molecular side. In this research, we used the in silico approach to investigate the transcriptomic profile of RA synovium to identify shared molecular pathways with that of severe acute respiratory syndrome-corona virus-2 (SARS-COV-2) infected lung tissue. Our results showed upregulation of chemotactic factors, including CCL4, CCL8, and CCL11, that all shared CCR5 as their receptor, as a common derangement observed in both diseases; RA and COVID-19. Moreover, our results also highlighted a possible mechanism through which HCQ, which can be used as a monotherapy in mild RA or as one of the triple-DMARDs therapy (tDMARDs; methotrexate, sulphasalazine, and HCQ), might interfere with the COVID-19 infection. This might be achieved through the ability of HCQ to upregulate specific immune cell populations like activated natural killer (NK) cells, which were found to be significantly reduced in COVID-19 infection. In addition to its ability to block CCR5 rich immune cell recruitment that also was upregulated in the SARS-COV-2 infected lungs. This might explain some of the reports that showed beneficial effects.

scholarly journals In Silico Analysis and Molecular Docking Studies of Plumbagin and Piperine Ligands as Potential Inhibitors of Alpha-Glucosidase Receptor

2020 ◽  
Vol 11 (2) ◽  
pp. 9629-9637
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Docking Studies ◽  
The Body ◽  
Insufficient Amount ◽  
In Silico Studies ◽  
Optimization Simulation ◽  
Alpha Glucosidase

In ’today’s generation, Diabetes mellitus is a very common lifestyle-based disease in which an insufficient amount of insulin is produced, which results in a rise of glucose level in the body with frequent urination and patient feels thirsty and hungry. In our present work, we have used the alpha-glucosidase receptor against the natural plant product as a ligand for docking studies. For this in silico studies, various online tools, databases, and software were used. The proposed approaches were PDB, Molinspiration, Chemsketch, PyRx software, and many more. The binding scores were retrieved by PyRx software and no tumorigenicity, mutagenicity was there, and all parameters were in the desired range. The compounds used as ligands have shown energy minimization up to -6.7 to -8.7 kcal and can be further used as optimization, simulation, and in vitro and in vivo experimental validation.

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