Help with Gel Electrophoresis?

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Help with Gel Electrophoresis?

Postby beccan15 » Tue Oct 09, 2012 4:57 pm

So here's the project I want to modify:
http://www.sciencebuddies.org/science-f ... eityourown
It's the 'Building your own tool for identifying DNA' one.

What I want to do is modify this project to involve different fruits/plants/vegetables. Is there any way I could do this? I don't know what I could compare, and I'm having trouble finding anything on the internet. Please help!

Just a note, this project should be able to be done at home or in my high school lab (which is not preferred, it's super hard to get lab time) and I would be willing to use stains if need be. Please make your suggestions as simple as possible!

Thank you!
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Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
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Re: Help with Gel Electrophoresis?

Postby sunmoonstars » Wed Oct 10, 2012 5:53 am

Hi,

From the link you gave - in the "Make it your own" section, you mention two ideas:

1.
Use your gel electrophoresis chamber to determine if two different types of plants use the same molecule for pigment. To prepare your samples, take the flowers from a plant, grind up the flower, add a little bit of isopropyl alcohol, and continue grinding. Once the solids settle, pour the pigment-tinted alcohol into a separate container. Let most of the alcohol evaporate and then add a drop or two of your buffer solution to reconstitute the pigment.


For the first, you could use the pigmented part of different green vegetables and test if they use the same molecules for pigment. Use the same method as mentioned for the flower petals.


2.
Try combining this experiment with one of the DNA extraction science projects like the Do-It-Yourself DNA or the Extracting Onion DNA Science Buddies project ideas. Can you see the DNA you extracted on your gel? Are there different bands? Note: you will need to use a stain to visualize the DNA. DNA stains are available from online science supply companies, like Science Kit catalog #WW6488701 or Wards Natural Science catalog #38 V 9014.


For the second, You can use the vegetables as the source of your DNA extraction, then run the DNA on the gel. Here you could compare if the DNA band(s) run the same in each vegatable sample. If not, what would that tell you about the DNA samples and the vegetables they came from?


Let me know if you have more questions.
Tonya
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Re: Help with Gel Electrophoresis?

Postby beccan15 » Wed Oct 10, 2012 11:56 am

Thank you!

But I have another question: for either of those experiments, what would the control be? (It's a requirement to have a control group) And would I have to use a stain to see the DNA from the second idea?
beccan15
 
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Occupation: Student: 10th grade
Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
Project Due Date: February, Early March 2013
Project Status: I am conducting my research

Re: Help with Gel Electrophoresis?

Postby sunmoonstars » Fri Oct 12, 2012 12:44 pm

beccan15 wrote:Thank you!

But I have another question: for either of those experiments, what would the control be? (It's a requirement to have a control group) And would I have to use a stain to see the DNA from the second idea?


Yes, you need a stain to see the DNA. The pigments you can see without staining them.

Before you can determine the controls, you need to ask a question. What is the question you would like to answer? Start here in the Project Guide for some ideas:
http://www.sciencebuddies.org/science-fair-projects/project_question.shtml
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Re: Help with Gel Electrophoresis?

Postby beccan15 » Fri Oct 12, 2012 12:51 pm

Thank you so much for all the help, but my teacher told me that I'm not allowed to do a project that involves gel electrophoresis because it's too complicated.

So instead, I'm going to determine which detergent (shampoo, dishwashing soap, or laundry detergent) can extract the most DNA from a fruit, but again I'm having trouble with finding the control.

My question is: Which detergent will produce the most DNA?

Also, I thought about doing the control as no detergent, but that wouldn't make sense, would it? I mean, you need the detergent to actually extract the DNA.
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Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
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Project Status: I am conducting my research

Re: Help with Gel Electrophoresis?

Postby microkts » Sat Oct 13, 2012 10:11 pm

Hi,

In order to determine what your control will be you need to determine your variables. What will your independent and dependent variables be? Once you have figured out your variables your control will be the initial condition of your independent variable. In other words it will be the condition that you compare your test conditions to. Here is the Science Buddies page on variables to help you get started:

http://www.sciencebuddies.org/science-f ... bles.shtml

Let us know if you have any more questions.

Kierstyn
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Re: Help with Gel Electrophoresis?

Postby beccan15 » Sun Oct 14, 2012 7:46 am

My independent variable will be the detergent I use (like shampoo, dishwashing liquid, or laundry detergent) and my dependent variable would be the amount of DNA collected. I don't know what the initial condition of the independent variable is! I'm guessing its no detergent...but then the control wouldn't work and I'd get no DNA...
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Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
Project Due Date: February, Early March 2013
Project Status: I am conducting my research

Re: Help with Gel Electrophoresis?

Postby microkts » Mon Oct 15, 2012 5:46 pm

Hi,

Great job identifying your variables. I agree with you about the no detergent. You will likely get little or no DNA. No detergent could be your control group. Then you would compare how much better each detergent is at extracting DNA than no detergent.

Alternatively you could choose one of the three detergents to serve as the control group. Then you would be comparing if the other two detergents extra DNA better or worse than your control detergent. In this case I would select the detergent that was used in the original protocol as the control.

Whichever control you choose just make sure to state your hypothesis in such a manner that makes it clear what you are testing. What would be your hypothesis statement if you used no detergent as the control? What would it be if you used dish soap as the control?

Let me know if you have any more questions.

Kierstyn
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Re: Help with Gel Electrophoresis?

Postby beccan15 » Tue Oct 16, 2012 2:43 pm

Just so I'm clear:

For control being no detergent:
My question could be: Which detergent will produce the most DNA?
My hypothesis could be: _______ will produce the most DNA.

For dish soap being the control:
Question: Which detergent will produce more DNA than dish soap?
Hypothesis: _______ will produce more DNA than dish soap.

I'll probably go with the control being no detergent, but I still have to ask my teacher.

Thanks for all your help!
beccan15
 
Posts: 27
Joined: Tue Oct 09, 2012 4:34 pm
Occupation: Student: 10th grade
Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
Project Due Date: February, Early March 2013
Project Status: I am conducting my research

Re: Help with Gel Electrophoresis?

Postby microkts » Tue Oct 16, 2012 7:47 pm

You have the right idea about your questions and hypothesis. Just make sure that you state your hypothesis as an If/then statement. Here is an example:

http://www.sciencebuddies.org/science-f ... bles.shtml

Kierstyn
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Re: Help with Gel Electrophoresis?

Postby beccan15 » Wed Oct 17, 2012 12:41 pm

Oh my gosh! I completely forgot about that!

So it would be: If I use dish soap to extract DNA, then I will get the most DNA.
Or: If I use laundry detergent to extract DNA, then I will get more DNA than if I used dish soap.
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Occupation: Student: 10th grade
Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
Project Due Date: February, Early March 2013
Project Status: I am conducting my research

Re: Help with Gel Electrophoresis?

Postby microkts » Thu Oct 18, 2012 11:41 am

Beccan15,

Those are good hypotheses. Post here again you have any more questions as you continue your project.

Kierstyn
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Re: Help with Gel Electrophoresis?

Postby beccan15 » Thu Nov 08, 2012 5:36 pm

So I'm changing things up (again)..and now I want to do something like determining the optimal concentration of SDS for the most DNA, but does it seem too obvious that the higher concentration of the chemical will yield more DNA?
beccan15
 
Posts: 27
Joined: Tue Oct 09, 2012 4:34 pm
Occupation: Student: 10th grade
Project Question: electrophoresis with different plants/fruits/vegetables, haven't decided yet
Project Due Date: February, Early March 2013
Project Status: I am conducting my research

Re: Help with Gel Electrophoresis?

Postby heatherL » Thu Nov 15, 2012 8:19 am

Hi beccan15,

You have been getting some excellent advice from Kierstyn, and I liked your idea of comparing different detergents. That said, SDS is a common detergent used for DNA extraction, and learning how to do an optimization experiment is a very good skill!

It is not necessarily true that the highest concentration of SDS will yield the most DNA. If you use too much, for example, the SDS could get in the way of your purification of the DNA. That is why the amounts are often optimized for DNA extraction protocols. So your experiment would still be interesting and relevant if you decided to optimize the concentration of SDS instead of comparing different detergents.

Please keep us posted on your progress!

Heather
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