ISSN (Print): 2328-3947

ISSN (Online): 2328-3955

Editor-in-Chief: Hari K. Koul

Website: http://www.sciepub.com/journal/AJBR

   

Article

Highly Conserved Epitopes of ZIKA Envelope Glycoprotein May Act as a Novel Peptide Vaccine with High Coverage: Immunoinformatics Approach

1Department of Biotechnology, Africa city of Technology- Khartoum, Sudan

2Al Neelain University, Faculty of Medical Laboratory Sciences

3Department of Microbiology, Soba University Hospital, Khartoum-Sudan


American Journal of Biomedical Research. 2016, 4(3), 46-60
doi: 10.12691/ajbr-4-3-1
Copyright © 2016 Science and Education Publishing

Cite this paper:
Marwan Mustafa Badawi, Marwa Mohamed Osman, Afra AbdElhamid Fadl Alla, Ammar Mohammed Ahmedani, Mohamed hamed Abdalla, Mosab Mohamed Gasemelseed, Ahmed Abubakar Elsayed, Mohamed Ahmed Salih. Highly Conserved Epitopes of ZIKA Envelope Glycoprotein May Act as a Novel Peptide Vaccine with High Coverage: Immunoinformatics Approach. American Journal of Biomedical Research. 2016; 4(3):46-60. doi: 10.12691/ajbr-4-3-1.

Correspondence to: Marwan  Mustafa Badawi, Department of Biotechnology, Africa city of Technology- Khartoum, Sudan. Email: mmbadwi44new@gmail.com

Abstract

Zika virus (ZIKV) is positive sense single stranded RNA of Flavivirus genus belonging to the Flaviviridae family. It has neither drug nor protective vaccine, and considered to be in relatedness to neurological abnormalities such as Guillain Barre Syndrome and microcephaly of neonates. The aim of this study is to analyze envelope glycoprotein E of all Zika strains using in silico approaches looking for conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine. A total of 50 Zikavirusvariants’(include 12from South America) polyproteins retrieved from NCBI database were aligned, and the conserved regions of Envelope Glycoprotein-E were selected for epitopes prediction. IEDB analysis resource was used to predict B and T cell epitopes and to calculate the population coverage. Epitopes with high scores in both B cell and T cell epitopes predicting tools were suggested. Three epitopes were proposed for international therapeutic peptide vaccine for B cell (AQDKP, TPNSPRAE and TPHWNNK) and two other epitopes designed especially for South America strains (LDKQSDTQYV and EVQYAGTDGPCK). For T cell epitopes, MMLELDPPF epitope was highly recommended as therapeutic peptide vaccine to interact with MHC class I along with three other epitopes (MAVLGDTAW, KEWFHDIPL and DTAWDFGSV) which showed very good population coverage against the whole world population. Three epitopes showed high affinity to interact with MHC class II alleles (FKSLFGGMS, LITANPVIT and VHTALAGAL) with excellent population coverage throughout the world and South America region. Herd immunity protocols can be achieved in countries with low population coverage percentage to minimize the active transmission of the virus, especially among pregnant women and other groups at risk.We recommendin vitro and in vivo proving the effectiveness of these proposed epitopes as a vaccine, as well as to be used as a diagnostic screening test.

Keywords

References

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Article

Computational Analysis of Single Nucleotide Polymorphism (SNPs) in Human GRM4 Gene

1Department of Bioinformatics, Africa city of technology, Sudan

2Alneelain University Faculty of Medical Laboratory Sciences, Sudan

3Department of haeatology, Elnehoud teaching Hospital, Sudan

4Medical Lab Manager, Tyba Hospital, Sudan

5Institute of Endemic Diseases, Khartoum University, Sudan

6Head Department of Biotechnology, Biotechnology Park, Africa city of technology, Sudan


American Journal of Biomedical Research. 2016, 4(3), 61-73
doi: 10.12691/ajbr-4-3-2
Copyright © 2016 Science and Education Publishing

Cite this paper:
Afra Abd Elhamid Fadlalla Elshaikh, Mosab Mohamed Ismaiel, Marwa Mohamed Osman, Samah Ahmed Ibrahim Shokri, Samia Othman massad, Nahid Ebrahim Merghani Fadl, Arafa Habiballa Ibrahim, Selma Shiekh Idris, Maab Mohamed Abdalla, Mohamed Ahmed Salih. Computational Analysis of Single Nucleotide Polymorphism (SNPs) in Human GRM4 Gene. American Journal of Biomedical Research. 2016; 4(3):61-73. doi: 10.12691/ajbr-4-3-2.

Correspondence to: Afra  Abd Elhamid Fadlalla Elshaikh, Department of Bioinformatics, Africa city of technology, Sudan. Email: afrahamid@outlook.com

Abstract

Background: L-glutamate is one of the most common amino acid in nature and it acts as excitatory neurotransmitter in the central nervous system. GRM4 is a large gene located in chromosome 6 and consists of 7217 bp (NCBI) divided into 10 exons. The location of GRM4 (chromosomal segment 6p21.3) is tentative susceptibility loci for Juvenile Myoclonic Epilepsy so many studies investigate the association of GRM4 polymorphism with myoclonic epilepsy juvenile. Design and methods: GRM4 gene was investigated in dbSNP/NCBI database NCBI and we used computational analysis approach. Deleterious nsSNPs were predicted by SIFT and Polyphen soft wares then the damaging nsSNPs were submitted to I mutant tool. Protein structural analysis of amino acid variants was performed by Chimera 1.8 and Project Hope. Results: We analyze 29854 SNPs from NCBI; 8561 of them found on homosapiens; of which 330 were missense, of which 208 were in the coding region, 334 were non-synonymous SNPs (nsSNPs), 232 were in the 3'un-translated region. These SNPs were analyzed using different soft wares; SIFT, Polyphen-2, Imutant3.0, PhD-SNP, PolymiRTs, Project Hope and GENEMAIA to investigate the effect of SNPs mutations on GRM4 protein structure and function. Conclusions: Computational tools were used to analyze deleterious SNPs in GRM4 gene. Out of 8561 SNPs, the SNPs (rs184636998), (rs199744441), (rs199744441), (rs149277708), (rs144660534), (rs139236496) were identified as highly damaging in coding region confirmed by using bioinformatics tools . In 3'un-translated region two SNPs (rs188406833) and (rs192860479) contained (C) allele had 4 miRSite as target binding site can be disrupts a conserved miRNA and one SNPs (rs77415386) contained (D) allele had 6 miRSite as derived allele that disrupts a conserved miRNA site. Further study must be done to detect the effect of these SNPs on the protein structure and function.

Keywords

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Article

Methylenetetrahydrofolate Reductase C677T and Platelet Glycoprotein IIb/IIIa Genes Polymorphism in Myocardial Infarction Egyptian Patients

1Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egyp

2Cardiology Departments, Faculty of Medicine, Suez Canal University, Ismailia, Egypt


American Journal of Biomedical Research. 2016, 4(3), 74-79
doi: 10.12691/ajbr-4-3-3
Copyright © 2016 Science and Education Publishing

Cite this paper:
Kefah H Ali, Nagwan A Sabek, Loaa A Tag Eldeen, Emad F Ismail, Gamela Nasr. Methylenetetrahydrofolate Reductase C677T and Platelet Glycoprotein IIb/IIIa Genes Polymorphism in Myocardial Infarction Egyptian Patients. American Journal of Biomedical Research. 2016; 4(3):74-79. doi: 10.12691/ajbr-4-3-3.

Correspondence to: Nagwan  A Sabek, Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egyp. Email: Nagwan_yasser@yahoo.com

Abstract

Background: Hyperhomocysteinemia and platelet glycoprotein GpIIIa polymorphism had been identified as risk factors for coronary atherosclerosis. The methylenetetrahydrofolate reductase MTHFR C677T variant has been shown to influence homocysteine metabolism, the interaction of plasma tHcy with other conventional risk factors remain uncertain in the clinical setting of acute myocardial infarction (AMI). The present study aimed to examine whether the MTHFR and platelet glycoprotein IIIa polymorphisms were associated with increased risk of (MI) in Egyptian patients. Subjects and Method: 150 newly diagnosed MI patients and 50 healthy matched subjects were recruited into this study, genotyping of the MTHFR C677T and GpIIIa 1565 A1/A2 polymorphisms were carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique, plasma tHcy, and folic acid levels were estimated. Results: Fasting plasma total Hcy levels were significantly higher in MI patients than controls (P <0.05), folate levels were significantly lower in MI patients than controls (P <0.05), no significant differences were observed in the MTHFR C677T and GpIIIa genotypes frequencies between MI patients and controls (P > 0.05). The frequency of the MTHFR C allele was 80.6 % and 76 % in MI patients and controls respectively and did not differ significantly between the two groups (P > 0.05). The frequency of risk allele, GpIIIa, PIA2 was significantly higher in MI patients compared to controls (p<0.05), plasma tHcy level was significantly higher and folate level was significantly lower in MI patients carrying MTHFR CC and GPIIIa PIA2A2genotypes. Conclusions: In this population, the both risk alleles of MTHFR and GpIIb/IIIa polymorphisms had no major effect on the MI incidence, they were associated with higher homocysteine levels. A gene-environment interaction might increase the risk indirectly by elevating tHcy, especially when folate intake was low, our findings might support that MTHFR and GpIIb/IIIa polymorphisms as risk factors for MI.

Keywords

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