Association between IL6 gene polymorphism and the risk of chronic obstructive pulmonary disease in the north Indian population
Nikhil
Kirtipal
Department of Biotechnology, Panjab University, Chandigarh-160014, India
author
Hitender
Thakur
Department of Biotechnology, Panjab University, Chandigarh-160014, India
author
Ranbir Chander
Sobti
Department of Biotechnology, Panjab University, Chandigarh-160014, India
author
Ashok Kumar
Janmeja
Respiratory Medicine, MMCH, Solan, Himachal Pradesh, India
author
text
article
2020
eng
Interleukin-6 (IL6) is encoded by the IL6 gene in human and acts as pro-inflammatory cytokine and an anti-inflammatory cytokine. Recent studies established that IL6 substantially contribute in the diagnosed of systemic inflammation for the patients suffering from lung diseases such as chronic obstructive pulmonary disease (COPD). Thereof, this work aimed to investigate the protagonist of IL6 (-174 G/C) genotypes as an essential risk factor for COPD in north Indian population. In the study, a total of 200 clinically diagnosed patients with COPD were selected against 200 patients. Statistical analysis reveleaed that there was no significant association between the IL6 -174 G/C genetic polymorphism and the risk of COPD (P>0.05).
Molecular Biology Research Communications
Shiraz University Press
2322-181X
9
v.
2
no.
2020
41
43
https://mbrc.shirazu.ac.ir/article_5645_9edcce68ca1f47b64aa73a27480aea49.pdf
dx.doi.org/10.22099/mbrc.2019.34594.1431
Molecular characterization and DNA methylation profile of Libyodrilus violaceous from oil polluted soil
Aemere
Ogunlaja
Department of Biological Sciences, Redeemer’s University, Ede Osun state, Nigeria
author
Vikas
Sharma
School of Life Sciences, Discipline of Microbiology, University of Kwazulu-Natal, Durban, South Africa
author
Meenu
Ghai
School of Life Sciences, Discipline of Genetics, University of Kwazulu-Natal, Durban, South Africa
author
Johnson
Lin
School of Life Sciences, Discipline of Microbiology, University of Kwazulu-Natal, Durban, South Africa
author
text
article
2020
eng
Studies on earthworms using molecular markers are rare in Africa except a handful from South Africa. Reports on Libyodrilus violaceous,an earthworm found in West Africaare available including their metal tolerance and bioaccumulation capacity but their molecular characterization and ecotoxicology studies are scarce. In this study, triplicate L. violaceous specimens were collected from four locations within a petroleum polluted site and one in a control site, ≃1Km away from point of spill. DNA was extracted and 18S rRNA and 16S rRNA genes were amplified and sequenced. DNA methylation of their 18S rRNA gene was determined using Methylation specific PCR (MSP) method. Phylogenetic trees generated for 18S rRNA and 16S rRNA genes grouped L. violaceous within the Eudrilidae family concurrent with its conventional grouping and MSP results indicate no methylation in L. violaceous population from this site.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
9
v.
2
no.
2020
45
53
https://mbrc.shirazu.ac.ir/article_5646_831c67f9bf035267795eea9201f52f8a.pdf
dx.doi.org/10.22099/mbrc.2019.35242.1449
Production of transgenic Paulownia tomentosa (Thunb.) steud. using chitosan nanoparticles to express antimicrobial genes resistant to bacterial infection
Eman Tawfik
Hussien
Lecturer of Genetics and Genetic Engineering, Faculty of Science, Helwan University, Egypt
author
text
article
2020
eng
Paulownia tomentosa (Thunb.) Steud. is a very important hard woody plant, an extremely fast-growing tree and produce timber. Therefore, there is a demand to produce transgenic Paulownia plant resistant to bacterial infection. Microbial infection (especially bacterial one) is serious sever and cause a loss in plant productivity as they bear upon the character and amount of plant product. Two phytopathogenic bacteria were chosen to consider their effect on Paulownia tomentosa. These two bacterial species were Erwinia carotovora and Pseudomonas aeruginosa. Two thionin genes (AT1G12660 and AT1G12663) were selected. They produce antimicrobial peptides to resist this bacterial infection. Chitosan nanoparticle is a novel technology in genetic transformation into plant tissues. Chitosan nanoparticles were used in a ratio of 1:1 with the plasmid DNA carrying thionin genes independently. Characterization for chitosan nanoparticles was applied to determine the conditions of genetic transformation. The new transgenic P. tomentosa lines produced are partially resistant to these two bacterial infections compared to non-transgenic lines. The inhibitory percentage in the transgenic lines ranged from 8 to 21% wherein the non-transgenic the inhibitory percentage of P. tomentosa leaves ranged from 53-24%. Likewise, it is noticed that is Paulownia tomentosa less infectious than Erwinia carotovora. In conclusion, I recommend using chitosan nanoparticle is an excellent way for gene transformation into plant tissues. Also, manipulate the idea of using thionin as antimicrobial genes to resist bacterial infection for different plant species.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
9
v.
2
no.
2020
55
62
https://mbrc.shirazu.ac.ir/article_5647_3bdbd3aba458be5f26e07f1a5da5012b.pdf
dx.doi.org/10.22099/mbrc.2019.35331.1454
Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta
Narendra
Shivani
Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
author
Aseervatham Selvi
Smiline-Girija
Department of Microbiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, 162, Poonamallee High Road, Chennai 600077, Tamil Nadu, India
author
Arumugam
Paramasivam
Biomedical Research Unit and Laboratory Animal Centre-Dental Research Cell, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
author
Jayaseelan
Vijayashree-Priyadharsini
Biomedical Research Unit and Laboratory Animal Centre-Dental Research Cell, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
author
text
article
2020
eng
Amelogenin gene (AMEL-X) encodes an enamel protein called amelogenin, which plays a vital role in tooth development. Any mutations in this gene or the associated pathway lead to developmental abnormalities of the tooth. The present study aims to analyze functional missense mutations in AMEL-X genes and derive an association with amelogenesis imperfecta. The information on missense mutations of human AMEL-X gene was collected from Ensembl database (https://asia.ensembl.org). Three different computational tools viz., SIFT, PolyPhen and PROVEAN were used to identify the deleterious or pathogenic forms of mutations in the gene studied. I-Mutant Suit was used to identify the stability of the proteins identified as deleterious by the three tools. Further, MutPred analysis revealed the pathogenicity of these mutations. Among 96 missense variants reported in AMEL-X gene, 18 were found to be deleterious using the three prediction tools (SIFT, PolyPhen and PROVEAN). When these variants were subjected to protein stability analysis, about 14 missense variants showed decreased stability whereas the other 8 variants showed increased stability. Further, these variants were analyzed using MutPred which identified 9 variants to be highly pathogenic. ExAC database revealed that all the pathogenic mutations had a minor allele frequency less than 0.01. The in silico analysis revealed highly pathogenic mutations in amelogenin gene which could have a putative association with amelogenesis imperfecta. These mutations should be screened in patients for early diagnosis of susceptibility to AI.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
9
v.
2
no.
2020
63
69
https://mbrc.shirazu.ac.ir/article_5648_9c6b50e874fa48a337da4a68b104faa6.pdf
dx.doi.org/10.22099/mbrc.2020.35413.1456
In silico analyzing the molecular interactions of plant-derived inhibitors against E6AP, p53, and c-Myc binding sites of HPV type 16 E6 oncoprotein
Farzan
Nabati
Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
author
Mohammad
Moradi
Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
author
Hassan
Mohabatkar
Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
author
text
article
2020
eng
Human papillomaviruses (HPV) are a group of strong human carcinogen viruses considered to be the fourth leading cause of mortality among women in the world. HPV is the most important cause of cervical cancer, which is the second most common cancer in women living in low and middle-income countries. To date, there is no effective cure for an ongoing HPV infection; therefore, it is required to investigate anticancer drugs against this life-threatening infection. In this study, we collected more than 100 plant-derivedcompounds with anti-cancer and antiviral potentials from a variety of papers. Smile formats of these compounds (ligand), were harvested from PubChem database and examined based on the absorption, distribution, metabolism, excretion, and toxicity properties by programs such as Swiss ADME, admetSAR, and pkCSM. Twenty compounds, which were likely to be the HPV16E6 inhibitor, were selected for docking calculations. We examined these natural inhibitors against the HPV16 E6 oncogenic protein. Eventually, three of these compounds were used as the most potent inhibitors (Ginkgetin (peculiarly), Hypericin and Apigetrin) were probably used as the possible source of cancer treatment caused by E6 oncoprotein. In this research, we conducted the docking calculations by Autodock 4.2.6 software. Docking analysis showed the interaction of these plant-originated inhibitors with E6AP, p53, and Myc binding sites on the E6 oncoprotein which support the normal function of E6AP, p53, and Myc.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
9
v.
2
no.
2020
71
82
https://mbrc.shirazu.ac.ir/article_5663_5e191b11f832694e762a8d3d86bebfa8.pdf
dx.doi.org/10.22099/mbrc.2020.36522.1483
Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunity
Sandeep
Saini
Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
author
Avneet
Saini
Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
author
Chander
Jyoti Thakur
Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
author
Varinder
Kumar
Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
author
Rishabh Dilip
Gupta
Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
author
Jogesh
Sharma
Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
author
text
article
2020
eng
The current outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)in China threatened humankind worldwide. The coronaviruses contains the largest RNA genome among all other known RNA viruses, therefore the disease etiology can be understood by analyzing the genome sequence of SARS-CoV-2. In this study, we used an ab-intio based computational tool VMir to scan the complete genome of SARS-CoV-2 to predict pre-miRNAs. The potential pre-miRNAs were identified by ViralMir and mature miRNAs were recognized by Mature Bayes. Additionally, predicted mature miRNAs were analysed against human genome by miRDB server to retrieve target genes. Besides that we also retrieved GO (Gene Ontology) terms for pathways, functions and cellular components. We predicted 26 mature miRNAs from genome of SARS-CoV-2 that targets human genes involved in pathways like EGF receptor signaling, apoptosis signaling, VEGF signaling, FGF receptor signaling. Gene enrichment tool analysis and substantial literature evidences suggests role of genes like BMPR2 and p53 in pulmonary vasculature and antiviral innate immunity respectively. Our findings may help research community to understand virus pathogenesis.
Molecular Biology Research Communications
Shiraz University Press
2322-181X
9
v.
2
no.
2020
83
91
https://mbrc.shirazu.ac.ir/article_5664_a9257a2cb727028b2164e71e6eaf9734.pdf
dx.doi.org/10.22099/mbrc.2020.36507.1487