In look for ideas: organelle study

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In look for ideas: organelle study

Postby karel5_98 » Dec 16 2011 10:01 am

Hi, I am less than a year ahead of finishing my Ph.D and I am looking for some ideas on performing new experiments on my subject. As of now, it's about characterization of protein, lipids, pigments, and if possible, subcomponents of a plant plastid. As far as characterization is concerned, I ask myself what else could be done with reasonable effort. What else could we be asking ourselves at a characterizational level?

So, I am looking for a collection of biotechnologic, biochemical, or other techniques that can hypothetically be applied to the study of (in my case) an organelle.
This of course doesn't exist as such a specific thing, but I wondered if a more general compillation of techniques, explaining pros, cons, and possible application fields exists somewhere, online or in print.
Anyway, any other advise will be greatly appreciated.

My supervisor is extremely busy nowadays, so discussing this matter is not that easy.
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Re: In look for ideas: organelle study

Postby CrowSan » Dec 16 2011 10:49 am

Hi - this is quite a difficult request to answer (for myself anyway) as
a) I am not a plant biologist
b) I do not know what charaterisations you have alreay performed
c) do not know what facilities you lab has for your research.

However I have noticed that from your list of charaterisations you fail to mention DNA/RNA work.
People appear to be doing this research on Plastids. The link below is to a paper published this year on sense/anti-sense RNA's. (http://nar.oxfordjournals.org/content/e ... 3.abstract)
If you have access to a qPCR facility you might want to look at specific RNA levels in various plastid populations.
Also it appears that RNAi (RNA interference - a technique where a specific RNA in a cell can be down-regulated/destroyed) can be done in Plastids/plants. Here is a good example from 2005:
http://www.pnas.org/content/102/23/8216.full

Just a thought to get the discussion started. Also (although we do not want to know the specifics of you research) it would help a little if you could expand on the techiques you have done and the devices/machines you have access to.
Hope this helps
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Re: In look for ideas: organelle study

Postby karel5_98 » Dec 24 2011 2:50 pm

Hi CrowSan, and thanks for the reply.

As of now, we have done some proteomic analysis on some of the components of the organelle which we have been able to separate by a methodology adapted from published papers.
We have analyzed some of the contents of several pigments and/or lipids present in the different sub-fractions we have been able to isolate.
The techniques potentially within reach are most of the more usual chemical, analytical, biochemical or biotechnological techs. generally available in reasonably well-equipped labs in research center environments with shared facilities. Most things one could come up with, I guess.

As I see it, we are trying to find some differences regarding lipid and pigment handling (i.e. storage, synthesis, or whatever) in the fractions we are able to isolate. Regarding this, it is very clear that we have to relate hypothetical differential lipid, pigment, and/or protein traits of the different subcomponents we have been able to isolate, and then relate this information to make a bigger picture to make up "our story".
I think making "the picture" bigger will likely be necessary to yield something interesting enough to present. In fact, that is the point of my post.

I am not sure whether I have been both informative and discrete enough; also, I understand the question really wasn't an easy one to answer, but thanks to take some minutes to reply! :)
And please accept my apologies about my delay to reply, since you seemed willing to extend the discussion at least a little more. If you come up with some more ideas, you're of course most welcome! :)

Greetings from in Spain,

K

P.S. About the specific suggestions you made, I am not very familiar with sense/antisense and RNAi techniques; are they very time consuming?
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Re: In look for ideas: organelle study

Postby CrowSan » Jan 05 2012 6:12 am

Hi - it is now my turn to apologise for the delay in my reply (just back to work following an extended christmas break).
From what you said I am not sure if RNAi would tie into what you are doing (as it seems to be mostly chemical/biochemical).
RNAi is not very time consuming but the RNAi needs to be synthesised and then delivered to the plant/plastid (in a mechanism I am not familar with).
Excluding the RNAi/DNA aspect of the work, could it be possible that you can use the techniques that you have used already in your plastids to extend your observations? For example by examining changes in plastid composition that occur with changing environmental conditions (i.e. plants growing in the dark, growing in the cold etc). This may be easiest as you already have the techniques available and you could even link the research to climate change (for example if the plant you are studying is from Spain you might want to examine plastid composition changes in response to increased temperature or reduced moisture).
Just a thought - my knowledge of plant biology is about the same as my knowledge of lunar rocks (zero).
Greatings from the (cold) UK!
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