Science Buddies: "Ask an Expert"

I discovered this website only one week ago and started to search for a good science project idea for the science symposium organized every year in my region. I never participated in such events but this time I really want to try my best and, hopefully, win the competition.
School has not even started yet but I think that I should already prepare myself ahead of time. I am really interested in the project: "Investigate Native Plant Evolution with Chloroplast Sequencing"
I plan to start with a plant that has medical properties and then, following the indication given on this website, eventually find the DNA sequence of it's rubisco enzyme. I will then use BLAST to find matching sequences in other species of plants and then build a realistic cladogram.
However, the first step should be to find the correct plant. I am trying to find a plant with the following characteristics:
-has medical properties
-is not common (rare or difficult to grow)
-is not already listed on NCBI (I would like to find a new rubisco-coding DNA sequence to help future research)

This is because I would like to find, thanks to the cladogram, related species to the tested plant and hopefully easier to grow. Those species would then have a high probability of containing medical properties similar to the tested plant ones.

Could you help me finding that sort of plant? Should I contact a botanical garden?
Thank you very much for everything you are going to post!

22sonst,

If you could provide me with more information on what exactly you wish to accomplish and your methods that would be great. If I understand correctly you would like to find a rare medicinal plant that you determine the sequence of its' RuBisCO enzyme.

The RuBisCO enzyme should generally have the same DNA sequence in every plant. Although there are slight differences depending whether you are looking at the long chain within the DNA of the chloroplast molecule or the small chain found within the nucleus of the plant cell.

To genetically engineer a plant to have a greater amount of the RuBisCO enzyme would allow more glucose for the plant to consume creating a better crop. This type of research is being done especially with crop plants. You are interested in medicinal plant properties, I know this isn't a rare plant but have you considered using Aloe vera plants. I think that would be a great plant to possibly research as increased amounts of the RuBisCO enzyme may allow more effective medicinal properties of the Aloe vera gel produced by the plant. http://en.wikipedia.org/wiki/Aloe_vera

If you were determine the specific structure of the enzyme in Aloe vera plants that may be a good route to take. I would suggest letting us know more specifically what you would like to accomplish. Also, what kind of equipment will you have available for your project? Do you have a biology teacher that will be helping you?

I am sorry that I can't be more help, please provide a little bit more information for us. I am sure that another expert on here may be able to provide more assistance.

-Travis Sigafoos

Thank you very much for your reply!
I plan to follow the indications of the science fair project "Investigate Native Plant Evolution with Chloroplast Sequencing" with a slight change: investigating the evolution of medicinal plants. A fairly recent article on Scientific American
http://blogs.scientificamerican.com/ext ... xtinction/
states that 93 percent of all the medicinal plants used in Ayurveda Indian medicine are endangered. I believe that by finding the RuBisCO-coding DNA-sequence of some of those species could help to find other species closely related (using a cladogram) that are not endangered. Further researches on those species could lead to the discovery of similar medicinal properties to the endangered specie's ones. However i wasn't able to find the list of those endangered species it would be very helpful!
Other plants with medicinal properties that seem to me a very good subject to study are:
Oenocarpus bataua a difficult plant to cultivate (palm tree with very specific soil and pH requirements and a very long lifecycle, also altitude-sensitive)
Croton lechleri (which produces Sangre de Drago, a tropical panaceum)
Alas those plants are not available in my area (Belgium) and are not in the collection of the botanical garden where I planned to go (National botanical garden of Belgium)
Do you have any other suggestions and advice to help me in my project?

The project that you suggested me about studying the structure of Aloe Vera RuBisCO protein would rather relate of "Computational Exploration of Protein Function" project, that would also be a very interesting project to conduct. However I can't be sure the structure of that protein has not already been discovered.
I probably will have the help of my biology teacher but I can not be 100% sure about it, when school will start I am going to ask her. I was planning to ask some help to university laboratories or contact the National botanical garden (has PCR and electrophoresis instruments in it's laboratories).

I look forward to your (or someone else's) reply



I hope the aim of my project is now clear!

Sorry for the double post but I have just found out that Aloe vera's RuBisCO-coding DNA-sequence has not been inserted in the GeneBank. (Double check from another person would be helpful though ). I could follow the protocol written in "Native plant evolution..." until I find the DNA sequence of the protein and then start following the indications listed in "Computational Exploration of Protein Function" to discover the 3D (quaternary) structure of this protein.
Could you give me some more explanations about your idea on Aloe vera?

Thank you really really much!
P.S: I still need some advice for the medicinal plant project

Hi,

I believe you are interested in doing this project:

https://www.sciencebuddies.org/science- ... p012.shtml

Travis has given you some excellent background information on this topic. This is an extremely challenging project. It would definitely be worthwhile to be able to sequence a plant that is not already registered on NCBI, and your idea to select an endangered, medicinal herb is excellent. However, before you start, here are some issues that you should carefully consider:

1. The process to extract and amplify the DNA and verify the purity of the sample is very time consuming. Working in a high school lab, you would probably have to schedule the experiment in steps over a period of time. You would not find out if the experiment was successful until the end. So you could possibly do a lot of work without good results. Do you have enough time available to do the experiment, and possibly repeat it?

2. The reagents to do the experiment are very expensive. Have you made a list of everything that would be required and checked for local availability? Because of the possibility of failure of the experiment, you should plan to repeat the experiment at least twice.

3. Do you have access to all of the equipment required? Is there someone who is familiar with DNA extraction who can help you with the specific techniques involved in the process?

4. You would learn a lot in doing this project. However, does your grade on this project depend on actually getting results, or would results be evaluated on how well you designed and documented the experiment? It is very exciting and rewarding to be able to have a perfect DNA gel at the end, verifying the purity of the PCR products. Obtaining the RUBISCO sequence of new plants to the database would be a significant accomplishment. However, unless you have access to the required equipment, there is a high possibility of obtaining less than ideal results. The DNA extraction and amplification process requires using absolutely perfect sterile technique and avoiding any possible DNA contamination of the sample. Most high school labs do are not ideal for this type of work. If your grade will depend on obtaining perfect results, I would encourage you to pick a “safer” project.

I hope that my comments will be helpful and I do not mean to be discouraging at all. I just want you to be able to carefully consider all of the problems and risks before you proceed. If you are willing to work very hard, and if perhaps you can obtain access to a molecular biology lab at a university, then I would absolutely encourage you to proceed.

Obtaining one of more plants for this project is the first challenge. You definitely do not want to try collecting plants from the wild, since almost all are endangered. Why don’t you contact local plant nurseries, botanical gardens, or write the government agency that is involved in saving this important group of plants? Once you can identify plants that might be available, you can check to see if they are in the NCBI database. That might be an easier compared to identifying plants that aren’t in the database and then looking for them. Fortunately, getting a good DNA sample does not require a lot of plant material.

Please do let us know if you need additional information. We can help with the details if you do decide to proceed with this project.


Donna Hardy

Hi,

I found the thread from a previous student who attempted the chloroplast sequencing project and it should be very helpful for you to see the details required to complete this project. Also, if you decide to proceed, you will know what potential problems you will need to avoid.

https://www.sciencebuddies.org/science- ... A6+Rubisco


I hope this helps.

Donna Hardy

Hi,

There is a partial chloroplast sequence for Aloe vera in Genbank:

http://www.ncbi.nlm.nih.gov/nuccore?term=aloe%20vera


Donna Hardy