JIOMICS

JIOMICS | VOL 5 | ISSUE 2 | DECEMBER 2015 | 1-62
JOURNAL OF INTEGRATED OMICS
Journal of Integrated Omics
A METHODOLOGICAL JOURNAL
HTTP://WWW.JIOMICS.COM
Special Issue: Proceeding Abstracts of the 4 th International Congress on Analytical Proteomics (ICAP 2015)
Rice Proteomics: Method Development of 2D-PAGE for Malaysian Upland
Rice
Arif, S. M.* 1 , Rahmat, Z. 1 , Ma, N. L. 2
1
Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia,
81310, Johor Bahru, Johor, Malaysia. 2 Department of Biological Science, Faculty of Science and Technology, Universiti Malaysia Terengganu,
21030 Kuala Terengganu, Terengganu, Malaysia. *Corresponding author: syakila.arif@gmail.com ; zaidah@utm.my
Available Online: 31 December 2015
Abstract
Purpose: Method development is the establishment of analytical method that will be applicable and copacetic for the target analysis. It is
one of the critical determinants to ensure the successful of the experiment being carried out. The aim of this study is to develop a suitable 2D-
PAGE method that could help in the proteomics analysis of Malaysian upland rice. Although 2D-PAGE for rice proteomics has been established
for more than a decade ago, none has been reported for Malaysian upland rice and it is acknowledged no universal protocol ever exists
as each plant behaves differently.
Experimental description: In this study, a cultivar of Malaysian upland rice named Wai with age ranging from 4-16 weeks were extracted
by using modified TCA/Acetone based method. The isoelectric focusing (IEF) was performed using 18cm immobiline pH gradient strip, pH
range 4-7 with the protocol: 1 h at 100 V (linear), 2h at 500 V (gradient), 12h at 8000 V (gradient), 2h at 8000 V (linear) and 10h at 100 V
(slow). The strip was loaded on 12% acrylamide gel for the second phase and electrophoresis was carried out at 100 V for 16 hours and stained
with comassie brilliant blue red 250. The protein spot was analyzed using PDQuest software version 8.0.
Results: The suitability of the method developed is determined based on the resolution of the protein spot on the gel and its pattern. The
result shows that it is feasible to visualize numbers of protein spot with good intensity for all age range (4-16 weeks) of Wai cultivar which
indicates the suitable method for 2D-PAGE analysis of Malaysian upland rice is developed.
Conclusions: This study accommodates new insights for upland rice protein separation, serving as platform that boosts the relevance and
importance of the developed 2D-PAGE for further Malaysian upland rice proteomics analysis.
Keywords: Development, Proteomics, Upland Rice, 2D-PAGE.
Acknowledgements: We thank the Universiti Teknologi Malaysia (UTM) and Ministry of Education (MOE) for funding this project
(Fundamental Research Grant Scheme, Vote: 4F366 and Research University Grant, Vote: 10J16) and Zamalah for sponsoring the graduate
student scholarship.
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