Browsing by Author "Tabrejee, Shamira"

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In silico B-cell and T-cell epitope-based vaccine designing against Chikungunya virus
(BRAC University, 2018-05) Anushe, Sheikh; Tabrejee, Shamira
Chikungunya virus (CHIKV) is an arthropod-borne alphavirus, belonging to the Togavirus family. There is no commercial treatment or vaccine against CHIKV, despite the acute epidemics taking place in several events distributed among wide areas. In this study, we employed various computational methods to identify B-cell and T-cell epitopes from the envelope protein E1, which have the potential for vaccine development against CHIKV. By analyzing the immune parameters of the conserved sequences of E1 glycoprotein using various databases and bioinformatics tools, we identified one potential B-cell and another T-cell epitope which may be used as epitope-based peptide vaccines. Using two different B-cell epitope prediction servers, five highly similar B cell epitopes were identified from the E1 protein. Immunoinformatics analyses revealed that NTQLSEAHVEKS is a highly conserved, antigenic, surface accessible, flexible and hydrophilic B-cell epitope. Two highly conserved, non- allergenic, non-cytotoxic putative T-cell epitopes having high world population coverages were analyzed for their binding with the HLA-C 12*03 molecule. Docking simulation assay revealed that SASAKLRVL has significantly lower binding energy, which strengthened its potential as being a T-cell epitope for the epitope-based vaccine against CHIKV. This study needs more in vivo investigation. However, mindful of the stability and reproducibility of the immune system at choosing and acting against peptide epitopes, this study allows us to claim a B-cell and a T-cell epitope for the epitope-based peptide vaccine against the E1 protein of CHIKV with good confidence.
In Silico Epitope based peptide vaccine designing against yellow fever virus
(BRAC University, 2017-08) Raffi, Hasanul Karim; Tabrejee, Shamira
The most widely used vaccine for treatment of Yellow Fever patients is YF 17D. It is a live attenuated vaccine derived from Asibi strain. It is administered widely to patients throughout the world but it has few problems such as low immune response and it may cause allergic reactions. The aim of this study is todesign an epitope-based peptide vaccine by targeting E protein of Yellow Fever Virus which may induce a stronger immune response.30 sequences of E protein of Yellow Fever Virus strainswere retrieved from NCBI database. E protein was found to be mostly conserved among all the sequences with little variability. Our conserved E region was found to be a probable antigen with a value of 0.4588 in Vaxijen sever.4 epitopes were found to be common in BepiPred and BCPREDS. Three of those epitopes were found to be antigenic. A peptide VKNPTDTGHGT were predicted to have surface accessibility. So the whole epitope VKNPTDTGHGTwas taken for analyzing conservancy and was found to be 96.67% conserved in all sequences. VKNPTDTGHGTepitope also possesses flexibility and accessibility as most of the residues of the peptide were found above the threshold level. Here we suggest in vivo study of our novel peptide antigen in E protein for universal vaccine which may be used to prevent Yellow Fever virus.
In silico T-cell epitopebased vaccine designing against Mycobacterium tuberculosis
(BRAC University, 2018-09) Mondol, Winifred Claire; Tabrejee, Shamira
Mycobacterium tuberculosis is an obligate pathogenic bacterial species in the family Mycobacteriaceae and the causative agent of tuberculosis. At present BCG, an attenuated strain of Mycobacterium bovis is used as a vaccine against tuberculosis. However, the overall success of BCG is arguable as it has some serious limitations. Some of these include BCG’s inability to protect against TB in adults and also in immunosuppressed patients. Thus, it is necessary to develop vaccines that can replace BCG. In this study, various computational methods were employed to identify T-cell epitopes from the ESX-2 secretion-associated protein EspG2, which has the potential for vaccine development against Mycobacterium tuberculosis. After analyzing the immune parameters of ESX-2 secretion-associated protein EspG2 using various databases and bioinformatics tools which included IEBD, PEP-FOLD, PyRx, PyMol, etc. One T cell epitope was identified which may be used as epitope-based peptide vaccine. Five highly conserved, non- allergenic, non-cytotoxic putative T-cell epitopes were analyzed for their binding with the HLA-C 12*03 molecule. Amongst them one epitope was chosen which interacted with the maximum number of MHC alleles with satisfactory world population coverage. Docking simulation assay further revealed that SGQRRYQVL has significantly lower binding energy, which verifies that the binding cleft epitope interaction to HLA molecule will occur when it will be applied in vivo. Additional in vivo investigation can further provide concrete evidence that SGQRRYQVL be used as a peptide vaccine to effectively promote immunity against TB.
Isolation of Salmonella spp. from raw meat, elucidation of their antibiotic susceptibility pattern and evaluation of the antimicrobial efficacy of Oregano (Origanum vulgare) and Black Sesame (Sesamum indicum)
(BRAC University, 2018-04) Moumi, Sunayna Hossain; Tabrejee, Shamira
With the increasing consumption of beef all over the world, the prospect of Salmonella spp. as a potential reservoir of antibiotic resistance was investigated. As plants are considered new sources of antimicrobial agents against antibiotic resistant bacteria, the antibacterial activity of Oregano (Origanum vulgare) and Black Sesame (Sesamum indicum) were evaluated against the Salmonella spp. isolates. A total of 14 Salmonella spp. isolates were obtained from 20 raw beef samples collected from different areas of Dhaka city. Antibiotic susceptibility test of these isolates was done using 24 antibiotics belonging to eight groups – Aminoglycoside, Beta–Lactam, Lincosamide, Macrolide, Nitroimidazole, Quinolone, Sulfonamide and Tetracycline. The antibiotic susceptibility test reported that all the isolates were resistant to Oxacillin, Erythromycin, Tetracycline, Clindamycin, Co-Trimoxazole, Metronidazole, Sulfamethoxazole, Norflaxacin, and Azithromycin. The results also revealed that the isolates exhibited resistance to Cephalexin and Ceftriaxone (86%), Levofloxacin and Penicillin (79%), Kanamycin (71%), Ceftazidime (64%), Amikacin (43%) and Ciprofloxacin (7%) respectively. In addition, the results revealed that the isolates were intermediately resistant to Streptomycin (71%), Amoxicillin and Ampicillin (64%), Imipenen (43%), Ceftazidime (36%), Penicillin (21%), Cephalexin and Ceftriazone (14%), and Kanamycin (7%). No isolate was resistant to two antibiotics which were Chloramphenicol and Cefixime. As an alternative, the Methanolic, Ethanolic and Aqueous extracts of Oregano and Sesame respectively were subjected against the isolates to evaluate the antimicrobial activity. Remarkable antimicrobial activity was observed by the Methanolic extract of Oregano with average zone of inhibition of 23.6 mm, followed by the Ethanolic extract of Oregano with average zone of inhibition of 17.6 mm and least by the Aqueous extract of Sesame with average zone of inhibition of 10.6 mm. The Aqueous extract of Oregano and the Methanolic and Ethanolic extracts of Sesame did not show any antibacterial activity. This study showed that the Salmonella spp. isolates are becoming resistant to 17 antibiotics that are commonly used for Salmonella spp. illness – Amoxicillin, Levofloxacin, Cephalexin, Ampicillin, Ciprofloxacin, Ceftazidime, Ceftriazone, Nalidixic Acid, Sulfamethoxazole, Imipenen, Amikacin, Clindamycin, Norflaxacin, Azithromycin, Co-Trimoxazole, and Metronidazole. However, commonly used Cefizime and Chloramphenicol were reported to be effective antibiotics in this study. Lastly, the presence specific components responsible for the efficacy displayed by Oregano could yield in the formulation and research of an effective drug to treat highly antibiotic resistant bacteria.
Seqdev: an algorithm for constructing genetic elements using comparative assembly
(© 2016 Bangladesh Association for Plant Tissue, 2016) Rahman, Tasnim; Heickal, Hasnain; Tabrejee, Shamira; Chowdhury, Md Miraj Kobad; Sarwar, Sheikh Muhammad; Shoyaib, Mohammad
With the availability of recent next generation sequencing technologies and their low cost, genomes of different organisms are being sequenced frequently. Therefore, quick assembly of genome, transcriptome, and target contigs from the raw data generated through the sequencing technologies has become necessary for better understanding of different biological systems. This article proposes an algorithm, namely SeqDev (Sequence Developer) for constructing contigs from raw reads using reference sequences. For this, we considered a weighted frequency‐based consensus mechanism named BlastAssemb for primary construction of a sequence with gaps. Then, we adopted suffix array and proposed a gap filling search (GFS) algorithm for searching the missing sequences in the primary construct. For evaluating our algorithm, we have chosen Pokkali (rice) raw genome and Japonica (rice) as our reference data. Experimental results demonstrated that our proposed algorithm accurately constructs promoter sequences of Pokkali from its raw genome data. These constructed promoter sequences were 93 ‐ 100% identical with the reference and also aligned with 96 ‐ 100% of corresponding reference sequences with eValue ranging from 0.0 ‐ 2e-14. All these results indicated that our proposed method could be a potential algorithm to construct target contigs from raw sequences with the help of reference sequences. Further wet lab validation with specific Pokkali promoter sequence will boost this method as a robust algorithm for target contig assembly.