PREDICTION OF B-CELL EPITOPE ON FRAGMENTED GENE ENCODING FUSION PROTEIN OF NEWCASTLE DISEASE VIRUS FROM NON-VACCINATED NATIVE CHICKEN (Gallus gallus domesticus) IN SURABAYA
The aim of this research was to analyze prediction of B-cell epitopes from fragmented gene encoding Fusion (F) protein of Newcastle Disease virus in nonvaccinated native chicken (Gallus gallus domesticus) in Surabaya. A non-vaccinated native chicken that suspected of being infected with ND virus...
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| Format: | Theses and Dissertations NonPeerReviewed |
| Language: | English English |
| Published: |
2018
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| Subjects: | |
| Online Access: | http://repository.unair.ac.id/77072/1/KKC%20KK%20KH.168-18%20Fah%20p%20ABSTRAK.pdf http://repository.unair.ac.id/77072/2/KKC%20KK%20KH.168-18%20Fah%20p%20SKRIPSI.pdf http://repository.unair.ac.id/77072/ http://lib.unair.ac.id |
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| Institution: | Universitas Airlangga |
| Language: | English English |
| Summary: | The aim of this research was to analyze prediction of B-cell epitopes from
fragmented gene encoding Fusion (F) protein of Newcastle Disease virus in nonvaccinated
native chicken (Gallus gallus domesticus) in Surabaya. A non-vaccinated
native chicken that suspected of being infected with ND virus was collected from
Wonokromo poultry market in Surabaya, Indonesia. The organ sample was collected
from brain, intestine, proventriculus, lung, pharynx, and hepar and named by “F1-
D1/IND/2017” for the sample. Organ sample was shattered and centrifuged to collect
the supernatant and continued with RNA extraction. DNA amplification with two-step of
RT-PCR was using Thermoscript ™ kit. During the PCR process, electrophoresis gel was
prepared using Agarose-LE with 1% gel. The results of PCR on DNA bands was 976 bp
long, similar with expected viewed, then purified for sequencing materials preparation.
The sequencing of PCR products (cDNA) aims to confirm the primary used of Fusion
protein. The obtained nucleotides result from sequence were aligned using the existing
Clustal W in BioEdit ver. 8.0 software, then to be translated into amino acid from 976
nucleotides to be 325 amino acids also with BioEdit ver. 8.0 software. B-cell epitope
prediction on Newcastle Disease virus was analyzed using Epitope Prediction
Tools/IEDB online software with Bepipred Linear Epitope Prediction method. The result
showed that F1-D1/IND/2017 sample has 20 epitopes based on epitope affinity of
cell B on Fusion protein, more than the epitope that possessed by data from
GenBank which only have 15-17 epitopes. |
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