Meghan, Jack, Callie, Noah, and Peyton
2.12.12
3
Arabidopis Proposal
Arabidopsis columbia is the research organism being used in this test. Arabidopsis
has many interesting characteristics that make it ideal for this kind of experiment. Because
of Arabidopsis’ size and short life cycle (2-3 months) many tests can be done with many
plants in a limited space with limited time. This is perfect for confirming the effects of a
variable by testing many plants at once and getting significant data in a relatively short
amount of time. The growth conditions are simple for Arabidopsis, which leaves little room
for unintended variables due to complicated care processes. Also, the entire genome of
Arabidopsis has been sequenced, meaning that the plant’s genetic makeup is known, if not
understood. These characteristics make Arabidopsis easy to test and maintain in a
classroom environment.
RNA interference, or RNAi, is both a natural and simulated processes by, which small
lengths of RNA 20-24 nucleotides long (miRNA) are used to affect gene expression. In the
process of RNAi double-stranded RNA is introduced and binds to Dicer, a double-strandedRNA-specific ribonuclease. Dicer cleaves the RNA into miRNA and selects one strand of the
RNA to be used by the RNA-induced silencing complex (RISC). RISC uses the selected miRNA
and binds to a strand of mRNA bound for protein synthesis that matches the miRNA’s
nucleotide sequence. Once bound, RISC splits apart the mRNA effectively making it
impossible to synthesize the mRNA strand’s respective protein. RISC also has the ability to
remain attached to the mRNA strand and thus block all transcription machinery, making
protein synthesis impossible. RNAi can be used by scientists today to possibly silence faulty
genes in humans with genetic disorders, a treatment called RNAi therapy. RNAi therapy can
also be used in the agricultural community to extinguish unwanted genes from crops and
livestock.
The specific aims for our research group are to gain an understanding and to educate
others in the roll of RNA interference in the Arabidopsis plant. We will be using three forms
of Arabidopsis including, a wild type (non mutant) which serves as a control, and two
mutants. One with three out of the four genes removed that code for the Dicer protein. The
deleted sequences are as follows DCL 2, 3, and 4. The second plant will have three out of
six genes coding for the Risc Complex removed. Those genes are RCL 2, 5, and 6. With our
genetically diverse population of Arabidopsis we plan to see the effect of RNAi on plants that
are subject to drought. By observing the presence or absence of phenotypic change we will
hopefully be able to understand more about RNA interference and its effect on the
Arabidopsis plant. Furthermore we will be able to understand the importance of the
mechanisms of RNAi, which includes the Dicer polypeptide and the Risc Complex.
For these Arabidopsis experimental trials our group plans to measure the
phenotypic response when the experimental plant group's watering time is reduced.
We chose this variable because of the real-world implications climate change
(drought in this case) imposes on the environment: the well being of different types of
plant species as one of them. At the time of watering one set of plants (the control
group) will receive twenty minutes of water, while the other group of plants (the
experimental group) will receive ten minutes of water. The phenotypic measurement
recorded on the Arabidopsis plants will consist of the height of the plant, the distance
from the soil to the tallest part of the plant, and the largest diameter of the plant,
measured in centimeters. These two phenotypic variables measured will provide an
accurate depiction on the well being of the plants and how our variable implemented,
drought, affects them.
This experiment shows how the changes in water will affect the growth of the
plant and how that growth will affect overall health of the plant. Very often the
environment will change the amount of moisture a plant will be able to obtain so by
testing the effects of a drought on a plant we can see what DNA changes are made to
make the plant capable of surviving in such conditions.