[Arabidopsis] A question about biotin treatment to plant seedlings

[Matthew Hudson]

Dear Xi

This study showed very strong transcriptional responses to mechanical  
stress can occur within 5 minutes:
Walley JW, Coughlan S, Hudson ME, Covington MF, Kaspi R, et al. 2007  
Mechanical Stress Induces Biotic and Abiotic Stress Responses via a  
Novel cis-Element. PLoS Genet 3(10): e172. doi:10.1371/journal.pgen. 
0030172

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0030172

My guess is that heat shock responses could be similarly fast, and  
that most transcriptional responses can thus happen very rapidly.  
However, in your experiment it sounds like you need to wait for  
exogenously applied biotin to get into the majority of the plant's  
cells, which is probably the limiting factor in timing your experiment  
(note that heat or mechanical stress reach the target cells more or  
less instantly). How long this takes will depend on your method of  
applying the biotin (sprayed or added to media), the age and size of  
your plants, the type of media used and possibly several other  
variables. My feeling would be that you should either do a time-course  
experiment with a known rapidly-responsive gene, or if none exists, do  
an array at a reasonably delayed time point (could be as little as 1  
hour or as much as 24 hours) and then use qPCR with a robustly  
responding gene to find out how rapid the response actually is.

Hope this helps

Matt

Matthew Hudson
Associate Professor
University of Illinois


On Mar 17, 2011, at 7:49 PM, Ann Loraine wrote:

> Hello,
>
> My lab has observed a dramatic change in transcript accumulation  
> patterns 3
> hours after a heat shock. We also observed dramatic changes in  
> splicing
> patterns for some genes.
>
> We haven't tested earlier times points via RNA-Seq, but publicly- 
> available
> microarray data sets reveal mRNA abundance differences only 1/2 hour  
> after
> comparable treatments.
>
> If you can find a microarray experiment that resembles your  
> experimental
> design, I would recommend looking at that first because it can give  
> you an
> idea of what to expect.
>
> Very best wishes,
>
> Ann Loraine
>
>
> On 3/17/11 4:55 PM, "Xi Chen" <cxde from iastate.edu> wrote:
>
>> Sorry for bothering. I want to clarify my question again, due to some
>> unclear description in my first e-mail.
>>
>> I have a general question about how soon after a mechanical or  
>> chemical
>>> perturbation Arabidopsis seedlings will have a transcriptional   
>>> response
>>> detectable by a deep seq method.
>>
>>
>>
>>> If you have conducted a dose response experiment to a stimuli  
>>> using deep
>>> seq methods, could you let me know when you began to get a  
>>> detectable shift
>>> in transcript accumulation .
>>
>>
>> PS: In my case, I am using biotin as chemical perturbation.
>>
>>
>>> Thank you so much!
>>
>>
>> Xi
>>
>>
>> On Thu, Mar 17, 2011 at 12:58 PM, Xi Chen <cxde from iastate.edu> wrote:
>>
>>> Hello researchers,
>>>
>>> Sorry to bother you, I have a question about how soon Arabidopsis  
>>> seedlings
>>> will respond to the biotin treatment. For example, I will treat my
>>> Arabidopsis seedling samples with biotin starvation for a while,  
>>> and add
>>> biotin into it to see how the transcriptional profile changes. But  
>>> I don't
>>> know how to pick the treatment timing, 30 min or 1 hr. Do you have  
>>> any
>>> suggestion or comments for this. Thank you so much!
>>>
>>> Best,
>>>
>>> Xi
>>>
>>>
>>>
>> _______________________________________________
>> Arab-gen mailing list
>> Arab-gen from net.bio.net
>> http://www.bio.net/biomail/listinfo/arab-gen
>
> -- 
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
>
>
> _______________________________________________
> Arab-gen mailing list
> Arab-gen from net.bio.net
> http://www.bio.net/biomail/listinfo/arab-gen