Achievements
report for Graduate Student Researcher Development Grant by Taikichiro Mori Memorial Research Fund for the academic
year 2009
Student
name: Mohamed Helmy Mahmoud Attia Shehata
Student
number: 80725860
Student
grade: Ph.D., 1st grade.
Affiliation: Gradute School for Media and Governance
Research
project: Rice Proteogenomics project
Introduction
Using
the Graduate Student Researcher Development Grant by Taikichiro Mori Memorial Research Fund, I was able to
improve my research environment and therefore, achieve better results in my
research. This resulted in the contribution in three international conferences.
The details of the achievements are mentioned below.
The research grant helped me to upgrade my workspace by adding powerful hardware
e.g. monitor and memory. Add new mobile workstation by purchasing new powerful
Mac Book Pro and some peripheral. Moreover, I used the grant to cover some of
the traveling expenses while traveling for the conference.
International
Conferences Contributions
1-
The
10th international conference on Systems Biology
(ICSB2008).
Stanford University, CA, USA 2009.
Date
and Venue: August 2009, Stanford University, USA.
Title:
Novel
genomic features of the rice genome revealed by proteogenomic
analysis
Abstract:
Rice,
considered as one of the world’s most important plants. Almost half of the world
population are relaying on rice either totally or partially. Moreover, it’s one of the plant model organisms because of its
relatively small genome (12 chromosomes and 430 Mbp).
Thus, research projects concerning the rice plant are currently running such as
genome sequencing and genome annotation projects. Although, the rice whole
genome sequence and annotation were published and updated several time (6 builds
to date), there was no attempt to include the whole proteome data in genome the
annotation. Here, we followed systems biology approach, integrating experimental
data and bioinformatics tools, to improve the rice genome annotation using whole
proteome data. We performed mass spectrometry shotgun analysis (LC-MS/MS) on
digested peptides extracted from undifferentiated cultured cells in our lab. The
peptides were extracted in-gel and in-solution, and fractionated using different
fractionation methods (SCX and IEF) to broaden our coverage range. Next, Mascot
search against the database of The Institute for Genomic Research (TIGR) was used to perform proteins/peptides identification. Through
these steps 5,989 proteins were identified including
69,876 peptides. The raw data files were then compared
against the identification results and the identified MS/MS spectra were
excluded. Mascot was used to search the remaining
spectra against the gene database and transcript database available from TIGR
DB. This identification resulted in 577 and 1347 peptides identified from the
gene and the transcript databases, respectively. These numbers were reduced through the peptide’s score, identification
confidence and minimum length. Thus, we finally got 177 and 697 peptides form
the genes and mRNA respectively, indicating existence of miss-annotated regions.
The identified peptides from the gene database were
blasted against the corresponding transcripts. The blasting results in 80
peptides aligned to regions previously considered non-coding regions. Similarly,
the transcript identified peptides will be aligned to
the gene database hoping to find more significant genomic features.
2-
The 32nd Annual Meeting of the Molecular Biology Society of Japan
(MBSJ2009).Yokohama, Japan.
Date
and Venue: December 2009, Yokohama, Japan.
Title:
Novel
Abstract:
The
LC-MS/MS-
3
- The 20th International Conference on Genome Informatics
(GIW2009).
Yokohama, Japan.
Date
and Venue: December 2009, Yokohama, Japan.
Title:
PGFeval:
Abstract:
Utilization
of the
Here
we present PGFeval (
Analyzing
our LC-MS/MS