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Now featuring the PREP Handbook with activities using Arabidopsis thaliana.
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Nadja Anderson, Ph.D
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Department of Molecular and Cellular Biology
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Meet Arabidopsis thaliana, a member of the mustard family which includes broccoli, cauliflower, cabbage, brussel sprouts, kohlrabi, radish, turnips, leeks and onion, as well as some 3000 other species.
Arabidopsis is the plant of choice for the study of DNA and genes in plants. The entire genome has been sequenced since the end of the year 2000 (Arabidopsis sequencing project), this means that scientist know where the genes are on the chromosomes and how to "spell" the genes. But do the scientists know the functions of the genes? For a few yes, approximately 1,000 of the 26,000 Arabidopsis genes. The task at hand now is to figure out the function of the other 25,000 genes.
What
is the function of a gene
Scientist have systematically deleted individual genes in Arabidopsis
and asked what is the effect on the organism, therefore what is the function
of the gene.
Why study gene function in plants?
Let us follow their reasoning using the scientific method:
Observation: Previous research--sequencing
of the Arabidopsis genome, possible comparison to other "known"
genes, and a speculative (putative) function.
Question: What are the functions of the 25,000 unknown genes in
Arabidopsis; more realistically-what is the function of gene X?
Hypothesis: If gene X is deleted from Arabidopsis then we
should see a change in the physical characteristics of the plants.
Explanation: If gene X happened to control flower development,
then the plant with gene X deleted would have no flowers…..
assumption--that you will see an external characteristic effect.
The Experimental setup for observations of Arabidopsis during its life cycle:
The normal Arabidopsis life cycle is about 8 weeks from planting the seed back to seeds on the mature plant. Arabidopsis is a winter annual, and requires a few days of cold to signal the seed that it is time to germinate.
1. Moisten soil completely with water and
miracle grow fertilizer and fill pots 7/8th to the top.
2. Sprinkle 10-20 seeds onto soil and cover with saran wrap.
3. Place in refrigerator for 3-4 days.
4. Place seeds in pots under grow lights, keep covered let the seeds germinate.
After a few days the cotyledons
of the seedling should be apparent in the pots.
click on image for larger view
5. Slice several holes into the saran wrap and let plants grow a few more
days before removing the cover.
6. After removing the cover, water by adding miracle grow in the tray
about 1/4 inch deep, every 3-4 days.
7. Two-three weeks should result in a rosette structure of leaves (called
the rosette leaves).
click on image for larger view
8. About four weeks you will see the plant begin to "bolt" which
is the structure that will eventually produce the
flowers.
Click on image for larger view
9. Arabidopsis self pollinates,
a couple weeks later you will see the plant covered with the fruit (called
siliques). You will notice the plant is looking like it is dying, in doing
so the siliques and seeds will dry out and allow the seed to be spread
(in nature) and stored (indefinetely in the lab and in nature).
click on image for larger view
Below are a few analyses of characteristic differences found in plants
that have one gene deleted when compared
to wild type (wt) which does not have a gene deletions (what is the significance
of wt presence in this experiment?).
.
click on images for larger view
dwarf and wt: Mutant plant is deleted in a gene that controls cell elongation.
Click on image for larger view
erecta and wt: Mutant plant is deleted in a gene that is involved in organ
specification.
gene X and wt: Many deletions result in no apparent effect. There are
many reasons why a gene may not have a visible effect.
--Perhaps the gene has a duplicate gene that is taking care of its function.
Check by looking for duplicity in the Arabidopsis sequences. Possible
Error: May still have a duplicity in function that is not apparent by
the sequence information
--Perhaps the gene product is used during a specific environmental condition
(i.e. stress), and researchers would not see the characteristic effect
grown in the laboratory under ideal conditions.
Your project will consist of deciding on a testable hypothesis and designing
an experiment for that hypothesis that will evaluate whether gene X has
a function under an environmental condition that you will manipulate.
Some links to help you with the project
General Arabidopsis research information:
TAIR--The Arabidopsis Information Resources
Lab protocol working with Arabidopsis and plants:
Information about the DNA sequences, comparison of sequences, publication database
NCBI--National Center for Biotechnology Information