Assignment6
Deadline: Feb 7,2003 at 16.30
Please notify instructor once you complete
this assigment uisng this e-mail address: assign6@learnbioinfo.org
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Study E-cell simulation system and answer
the following questions
1. What’s E-cell simulation system
2. Design one experiment for using with E-cell simulation system.
E-cell simulation system or E-cell simulation environment is sofware program for cellular and biochemical modeling and simulation. The developed software attemped to mimic real cell. It provide an convenion in study of cellular metabolism and also higher-order cellular phenomena such as gene regulation networks, DNA replication, and the other occurences in the cell cycle.
E-CELL, a modeling and simulation
environment for biochemical and genetic processes, has been developed.
The E-CELL system allows a user to define functions of proteins, protein-protein
interactions, protein-DNA interactions, regulation of gene expression
and other features of cellular metabolism, as a set of reaction rules.
E-CELL simulates cell behavior by numerically integrating the differential
equations described implicitly in these reaction rules. The user can
observe, through a computer display, dynamic changes in concentrations
of proteins, protein complexes and other chemical compounds in the cell.
Using this software, we constructed a model of a hypothetical cell with
only 127 genes sufficient for transcription, translation, energy production
and phospholipid synthesis. Most of the genes are taken from Mycoplasma
genitalium, the organism having the smallest known chromosome, whose
complete 580 kb genome sequence was determined at TIGR in 1995. We discuss
future applications of the E-CELL system with special respect to genome
engineering.
Design experiment using E-cell simulation system.
Molecular control of iron(Fe) metabolism.
Iron metabolism in cellular level are study in
many detail. The knowledge of iron is well know but it still be question
about molecular mechanism to control iron kinetic in different cell
type. A significant component
of the means by which cellular iron metabolism is controlled in mammalsoccurs
through directed changes in the use of specific messenger RNA (mRNA).
Iron regulatory proteins (IRPs) are critical components of a sensory
and regulatory system that coordinates the use of mRNA-encoding proteins
that are required to maintain cellular and organismal iron homeostasis
in a variety of circumstances.Hence, mammals use a combination of transcriptional
and post-transcriptional mechanisms to control the abundance of proteins
that modulate the transport, cellular uptake, and metabolic fate of
iron. This study will focuses on the molecular control of cellular iron
homeostasis, and prefer the reader to referred to other reviews for
more extensive analysis of the molecular or physiological aspects of
whole-body
iron metabolism. The difficult of cultture technique eoend upon type
of cell and also animal model is really hard toperform under more constrict
of ethical cammittee. E-cell simulation system are then comfortable
and easy way to try some condition for sure to perform futher wet-laboratory.
Figure: show IRP-IRE model control synthesis of proteins involve in cellular iron metabolism.
E-cell will be used for analysis ....
- Study contration of labile intracellular iron pool that can turn on IRP gene.
- Substitution study.
Use other divalent or trivalent cation to sustitute for iron such as Cu2+ Mn2+Zn2+. And study molecular effect on transferrin, trasferrin receptor and ferritin gene expression by that elements.
- Study other gene expression.
Other gene involve in IRP-IRE model and cellular iron metabolism.
- Study free iron effect.
Free iron can generate harmful hydroxy radical. So, if increase intracellular iron over capacity of sequestrate molecule such as ferritin, the overwhem iron may acculmulate at membrane or somewhere in cytoplasm and may induce toxic in cell that resulting effect on gene and enzymatic function.
Intracellular iron will be vary by e-cell available fuction for analysis of IRP gene product at each condition. Include pathologic effect such as iron overload and iron deficiancy stage.
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