Genetics and Genomics

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Genetics and Genomics

Postby Magali6 » Mon Oct 08, 2012 8:09 pm

Hello, Iv'e always been interested in plants and the health benefits they can provide. I was able to find a project involving the sequencing of the chloroplast genome on a native plant in order to determine its evolutionary relationship to other plant species. My question is what native plant would be good to sequence its genome and if there are native plants out there that are not well studied. Any other suggestions would be of great help.
Thanks,
Magali Padilla
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Re: Genetics and Genomics

Postby VSegarra » Tue Oct 09, 2012 4:53 pm

This sounds like a very cool project Magali! You'd be using chloroplast DNA as an "evolutionary clock"!! Are you working with already-annotated sequence data? If you are not, this sounds like a very ambitious project!! A sequencing project like this done from scratch can be expensive and require a research lab setting. For example, you would need access to a sequencing facility and the materials to isolate DNA from chloroplasts. Could you provide more information about the project you were thinking about doing? Nowadays there are sequencing data repositories that are accessible to the public for free that you can use as tools to carry out computer-based or analysis-based "experiments" (see here: http://www.ncbi.nlm.nih.gov/genome). If you want to do something like this you would need to see what sequences are available and think about what hypothesis you would like to test. Once you provide me with more information about what you want to do, I would be glad to help you further! Looking forward to hearing back from you!
Veronica
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Re: Genetics and Genomics

Postby Magali6 » Tue Oct 16, 2012 9:16 am

Thank you so much for your feedback. I have decided to change the topic of the project and hope you can assist me. My question is how can sorghum inhibit cancer tumor growth specifically when dealing with human colon cancer cells.
Magali6
 
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Joined: Fri Oct 05, 2012 9:08 am
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Project Question: What kind of mutation matter?
Project Due Date: January 18
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Re: Genetics and Genomics

Postby VSegarra » Thu Oct 18, 2012 6:20 pm

Hi Magali,
Wow, that is quite a change in research focus! While this is a very interesting research question, as you describe it now, at the very least, you will probably need access to a research laboratory that works with a human colon cancer cell line. Do you have access to such a lab? Why the interest in sorghum? Do you have any indications to think sorghum will have an effect on these types of cells?
Looking forward to hearing back from you,
Veronica
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Re: Genetics and Genomics

Postby Magali6 » Sun Oct 21, 2012 10:05 am

While I viewed the link that you sent me I saw which plants had their genome completely sequenced and I saw that sorghum was one of them. I was curious to find out what it was and as I researched it I found out that it is not only a plant high in fiber and consumed as a starch in developing countries but it is found to have therapeutic benefits such as anti-cancer and chemo protective uses. I was really interested and found this assay about an experiment conducted in the University of Missouri were scientist tested three sorghum extracts rich in 3-Deoxyanthonins and found that all three extracts had strong antiproliferative activity against human colon cancer cells. I don't have current access to a research lab that works with human a colon cancer cell line but just across the street from our school is a John Muir Lab and they work with colon cancer screening so me and my partner will have to contact them. Either than that we have most of the equipment that we will need in our classroom lab. If you can provide use with other suggestions it would be useful.
Thanks,
Magali
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Posts: 6
Joined: Fri Oct 05, 2012 9:08 am
Occupation: Student
Project Question: What kind of mutation matter?
Project Due Date: January 18
Project Status: Not applicable

Re: Genetics and Genomics

Postby Magali6 » Sun Oct 21, 2012 10:08 am

While I viewed the link that you sent me I saw which plants had their genome completely sequenced and I saw that sorghum was one of them. I was curious to find out what it was and as I researched it I found out that it is not only a plant high in fiber and consumed as a starch in developing countries but it is found to have therapeutic benefits such as anti-cancer and chemo protective uses. I was really interested and found this assay about an experiment conducted in the University of Missouri were scientist tested three sorghum extracts rich in 3-Deoxyanthonins and found that all three extracts had strong antiproliferative activity against human colon cancer cells. I don't have current access to a research lab that works with human a colon cancer cell line but just across the street from our school is a John Muir Lab and they work with colon cancer screening so me and my partner will have to contact them. Either than that we have most of the equipment that we will need in our classroom lab. If you can provide use with other suggestions it would be useful.
Thanks,
Magali
Magali6
 
Posts: 6
Joined: Fri Oct 05, 2012 9:08 am
Occupation: Student
Project Question: What kind of mutation matter?
Project Due Date: January 18
Project Status: Not applicable

Re: Genetics and Genomics

Postby VSegarra » Sun Oct 21, 2012 4:13 pm

Sounds good! It will be interesting to see what kind of help and feedback you will get from your John Muir Lab neighbors. I think contacting them should be high in your priority list. You may also want to find out if there are any academic research labs (at a nearby university or college) that has similar research interests to yours. They might also be willing to help. Let me know if there is anything else we can do to help.
Veronica
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Re: Genetics and Genomics

Postby Magali6 » Wed Oct 24, 2012 8:58 am

Thank you.
It would be appreciated if you can advise us and give us precautions on how to maintain a cell cuture and what are the differences between a cell cutlure v.s a cancer cell culture.
-Magali and Veronica
Magali6
 
Posts: 6
Joined: Fri Oct 05, 2012 9:08 am
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Project Question: What kind of mutation matter?
Project Due Date: January 18
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Re: Genetics and Genomics

Postby VSegarra » Tue Nov 20, 2012 1:36 pm

Hi Magali and Veronica!
Cell culture is something that you most probably will do in the context of a research lab alongside experienced scientists. It is best if you get this type of advice from the people that are actively helping you to culture cells in the lab. Best wishes for your research! Be sure to keep us posted!
Veronica
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Re: Genetics and Genomics

Postby Magali6 » Tue Dec 04, 2012 11:13 am

Thank you for your help we were fortunate to get a mentor for our project. His name is Gary Firestone and he is a scientist that currently works in U.C. Berkley. Our concern is getting the red sorghum bran for our experiment. We were wondering if you know any contacts that could supply or donate us with red sorghum bran.
Thank you,
Magali and Veronica
Magali6
 
Posts: 6
Joined: Fri Oct 05, 2012 9:08 am
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Project Question: What kind of mutation matter?
Project Due Date: January 18
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