Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin

Helicobacter pylori is a gram-negative and a microaerophilic bacterium. It has a shape of a spiral. It primarily lives in the human stomach as it requires acidic environment to survive. As a result of living in the human stomach, it causes gastric and duodenal ulcer including as a precursor of gastr...

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Main Author:	Zainal Abidin, Nurah
Format:	Thesis
Language:	English
Published:	2008
Subjects:	Data processing Bioinformatics RS Pharmacy and materia medica
Online Access:	https://ir.uitm.edu.my/id/eprint/100894/1/100894.PDF
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id	my-uitm-ir.100894
record_format	uketd_dc
spelling	my-uitm-ir.1008942024-08-26T05:05:35Z Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin 2008 Zainal Abidin, Nurah Data processing. Bioinformatics RM Therapeutics. Pharmacology RS Pharmacy and materia medica Helicobacter pylori is a gram-negative and a microaerophilic bacterium. It has a shape of a spiral. It primarily lives in the human stomach as it requires acidic environment to survive. As a result of living in the human stomach, it causes gastric and duodenal ulcer including as a precursor of gastric carcinoma.Vaccine, a preparation of special antigenic material that is able to stimulate the production of antibodies against the infection caused by Helicobacter pylori is required. Conventional method of preparing vaccine requires the cultivation and dissection of the bacteria's main component before testing their ability to trigger the immune system. However Reverse Vaccinology searches the immunogenic antigens from in silica analyses from the genome pathway instead of culturing the microorganism. To yield a vaccine that has high selectivity against Helicobacter pylori, specific target of antigenic sequence need to be selected. The target should not have any well conserved homolog in the human host. In this study, we focus on recognizing the toxin-like outer membrane protein (ID:025331) in Helicobacter pylori including its secondary structure and predicting the antigen's epitopes that is able to bind to Major Histocompatibility Class-II molecules using a-TEPITOPE-based algorithm. The infection caused by the bacteria is widely spreading in developing countries including Malaysia. A target antigenic sequence using bioinformatic tools need to developed in order to fight against the pathogen. The physicochemical characteristic of the sequence includes its molecular weight was 30893, while it is slightly basic due the theoretical pl being 8.97; the sequence had the highest amount of leucine. It was characterise as hydrophobic due to its GRAVY value which was less than 1 as determined by ProtParam tool. The motif region predicted by SCAN PROSITE tool was from the ABC _TMl family. PSIPRED found that its secondary structure consists of 77.86 % of a-helix and 22.14 % of coil. Region "IVLLLVICA" has binding affinity for most alleles used in the query entered in the ProPred tool, as a result it can be a potential candidate for vaccine development. "IVLLL VICA" can be utilized as a potential sequence for the vaccine against Helicobacter pylori. This research is an essential work in the fields of bioinformatic analysis and helps to put forward a new way for bioinformatic analysis of other genes. 2008 Thesis https://ir.uitm.edu.my/id/eprint/100894/ https://ir.uitm.edu.my/id/eprint/100894/1/100894.PDF text en public degree Universiti Teknologi MARA (Kampus Puncak Alam) Faculty of Pharmacy Yee, Leow Chiuan
institution	Universiti Teknologi MARA
collection	UiTM Institutional Repository
language	English
advisor	Yee, Leow Chiuan
topic	Data processing Bioinformatics Data processing Bioinformatics RS Pharmacy and materia medica
spellingShingle	Data processing Bioinformatics Data processing Bioinformatics RS Pharmacy and materia medica Zainal Abidin, Nurah Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin
description	Helicobacter pylori is a gram-negative and a microaerophilic bacterium. It has a shape of a spiral. It primarily lives in the human stomach as it requires acidic environment to survive. As a result of living in the human stomach, it causes gastric and duodenal ulcer including as a precursor of gastric carcinoma.Vaccine, a preparation of special antigenic material that is able to stimulate the production of antibodies against the infection caused by Helicobacter pylori is required. Conventional method of preparing vaccine requires the cultivation and dissection of the bacteria's main component before testing their ability to trigger the immune system. However Reverse Vaccinology searches the immunogenic antigens from in silica analyses from the genome pathway instead of culturing the microorganism. To yield a vaccine that has high selectivity against Helicobacter pylori, specific target of antigenic sequence need to be selected. The target should not have any well conserved homolog in the human host. In this study, we focus on recognizing the toxin-like outer membrane protein (ID:025331) in Helicobacter pylori including its secondary structure and predicting the antigen's epitopes that is able to bind to Major Histocompatibility Class-II molecules using a-TEPITOPE-based algorithm. The infection caused by the bacteria is widely spreading in developing countries including Malaysia. A target antigenic sequence using bioinformatic tools need to developed in order to fight against the pathogen. The physicochemical characteristic of the sequence includes its molecular weight was 30893, while it is slightly basic due the theoretical pl being 8.97; the sequence had the highest amount of leucine. It was characterise as hydrophobic due to its GRAVY value which was less than 1 as determined by ProtParam tool. The motif region predicted by SCAN PROSITE tool was from the ABC _TMl family. PSIPRED found that its secondary structure consists of 77.86 % of a-helix and 22.14 % of coil. Region "IVLLLVICA" has binding affinity for most alleles used in the query entered in the ProPred tool, as a result it can be a potential candidate for vaccine development. "IVLLL VICA" can be utilized as a potential sequence for the vaccine against Helicobacter pylori. This research is an essential work in the fields of bioinformatic analysis and helps to put forward a new way for bioinformatic analysis of other genes.
format	Thesis
qualification_level	Bachelor degree
author	Zainal Abidin, Nurah
author_facet	Zainal Abidin, Nurah
author_sort	Zainal Abidin, Nurah
title	Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin
title_short	Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin
title_full	Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin
title_fullStr	Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin
title_full_unstemmed	Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin
title_sort	application of bioinformatics to helicobacter pylori vaccinology / nurah zainal abidin
granting_institution	Universiti Teknologi MARA (Kampus Puncak Alam)
granting_department	Faculty of Pharmacy
publishDate	2008
url	https://ir.uitm.edu.my/id/eprint/100894/1/100894.PDF
_version_	1811769106360172544

Application of bioinformatics to Helicobacter pylori vaccinology / Nurah Zainal Abidin

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