[Arabidopsis] vertical growth

Matthew Hudson via arab-gen%40net.bio.net (by mhudson from illinois.edu)
Sun Nov 21 18:01:10 EST 2010


Hi everyone

I wanted to add some more suggestions / cautions to the below.

1) Roots (of wild type Arabidopsis) will be negatively phototrophic  
(grow away from light) ONLY if the light contains blue wavelengths  
(can be white or blue but not red or far-red), and of course if the  
roots are free to grow in that direction (see below).

2) Seedlings grown under far-red light will show reduced root growth,  
this is probably also true of decreased R:FR ratio light in many cases  
but this will depend on other factors.

3) Usually a medium is used that has too high a percentage of agar or  
agarose for the roots to penetrate, and they grow across the surface  
of the media. Root growth on this type of media will be strongly  
affected by contact with the media on one side (thigmatropism). While  
they are the easiest way to measure root growth in Arabidopsis,  
vertical plates must be used carefully in terms of interpretation for  
this reason.

4) The presence / absence of sucrose in the media will have a strong  
effect on all light and environmental responses of seedlings (tending  
to decrease all of them). If replicating previous experiments it is  
important to use the exact same media composition.

5) Light on the roots will influence not only root growth but also  
shoot growth. In fact, to see reproducible effects of R:FR on shoots,  
it is necessary to use a root medium that blocks light. Sometimes soot  
agar (a very low percentage agar that allows roots to penetrate and  
contains powdered carbon) is used for this, more usually experiments  
are done on soil in black pots.

Despite all the above, most work in this area concerns the role of  
genes in the cell biology of root development. Thus, if a mutant shows  
a different root development / growth pattern to "wild type" in your  
conditions, however unlike the natural environment they are, you  
generally have a sound scientific conclusion that the gene is involved  
in root growth or development somehow. That is, as long as all the  
conditions (media, orientation, light, temperature, seed treatment)  
are the same for both genotypes.

If, however, your research concerns the physiology of roots in the  
natural environment, or you are trying to extrapolate from Arabidopsis  
to crop plants, then you will have serious problems interpreting your  
data in the light of what really happens in real soil.

Much of the controversy about this type of experiment is between cell  
biologists and root physiologists, for the above reasons.

Hope this helps!

Matt Hudson

Associate Professor
Dept. of Crop Sciences
University of Illinois, Urbana
IL 61801

On Nov 20, 2010, at 12:08 AM, Rosemary White wrote:

> Dear all,
>
> Root growth is certainly affected by light - inhibited by white  
> light, not
> sure if promoted/affected by dim light and/or with certain R/FR  
> ratio.  If
> you grow Arabidopsis vertically with white light coming from one  
> side of the
> petri dish, the roots will grow away from the light.  And yes, you get
> autofluorescent plastids in light-grown roots.  Light effects can be  
> seen in
> expression of certain genes - on a couple of occasions, we could  
> only see
> GFP-tagged protein expression in dark-grown roots, or in light-grown  
> roots
> that were kept in the dark for 24-48 h before imaging.
>
> When people here want to follow root growth over time, they grow  
> roots down
> into a dark rhizobox,  illuminate with green light when imaging,  
> then have
> lights off the rest of the time, with the shoots growing up into the  
> light
> past a light barrier at the shoot-root interface.  Note that this is  
> in
> cereals, not Arabidopsis...
>
> cheers,
> Rosemary
>
> Rosemary White
> CSIRO Plant Industry
> GPO Box 1600
> Canberra, ACT 2601
> Australia
>
> T 61 2 6246 5475
> F 61 2 6246 5334
> E rosemary.white from csiro.au
>
>
> On 19/11/10 9:43 AM, "Turner John Prof (BIO)" <J.G.Turner from uea.ac.uk>  
> wrote:
>
>> Dear Brian and others posting on this,
>>
>> These are wonderfully inventive solutions, but I throw in a couple  
>> of cautions
>> to think about.
>>
>> It is important that light intensity and light quality (spectrum)  
>> are uniform
>> for the plants you grow: intensity is important for photosynthesis,  
>> but also
>> light reflected from neighbouring seedlings alters the Red:FR  
>> ratio, and this
>> does alter growth.
>>
>> Light on roots is generally "unnatural", but most of us grow plants  
>> in axenic
>> culture which exposes roots to light, and I am told that this  
>> promotes
>> development of proplastids in the roots.
>>
>> It would be really useful if someone can confirm that root growth  
>> in roots
>> exposed to the light is not different from root growth in roots not  
>> exposed to
>> the light.
>>
>> JOHN
>>
>>
>>
>>
>> John Turner
>> Professor of Plant Science
>> Chair of the Centre for Contemporary Agriculture
>> Norwich Research Park Professor for Biosciences
>> Associate Dean for Enterprise and Engagement
>> Honorary Faculty Member, John Innes Centre
>> School of Biological Sciences
>> University of East Anglia
>> Norwich Research Park NR4 7TJ
>>
>> 01603 592192
>> 07767668146
>>
>> http://www.contemporaryagriculture.com
>>
>> http://www.uea.ac.uk/bio/
>>
>>
>> -----Original Message-----
>> From: arab-gen-bounces from oat.bio.indiana.edu
>> [mailto:arab-gen-bounces from oat.bio.indiana.edu] On Behalf Of Brian Cady
>> Sent: 18 November 2010 17:11
>> To: arab-gen from oat.bio.indiana.edu
>> Subject: [Arabidopsis] vertical growth
>>
>> Here at Adan Colon-Carmona's lab we wrap bundles of 3-6 square  
>> plates with a
>> rubber band. When banded together, the unit will sit in the  
>> incubator with
>> each
>> plate vertically aligned.
>>
>> Brian Cady
>>
>>
>>
>>
>>
>> ________________________________
>> From: "arab-gen-request from oat.bio.indiana.edu"
>> <arab-gen-request from oat.bio.indiana.edu>
>> To: arab-gen from magpie.bio.indiana.edu
>> Sent: Thu, November 18, 2010 12:03:51 PM
>> Subject: Arab-gen Digest, Vol 67, Issue 7
>>
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>> Today's Topics:
>>
>> 1. Re: Petri Dish Racks (Tobias Baskin)
>> 2. Re: Petri Dish Racks (Holt, Ben F. III)
>> 3. Re: Petri Dish Racks (Rosemary White)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 17 Nov 2010 08:19:57 -0500
>> From: Tobias Baskin <baskin from bio.umass.edu>
>> Subject: Re: [Arabidopsis] Petri Dish Racks
>> To: SaraN <passiflora42 from yahoo.com>
>> Cc: arab-gen from magpie.bio.indiana.edu
>> Message-ID: <p06240504c90985ad185f@[10.0.1.2]>
>> Content-Type: text/plain; charset="us-ascii" ; format="flowed"
>>
>> Hi,
>> We made our own by hand, lots of little strips of plexi
>> glass. Its a pain. Its a bit easier to make them from wood, but still
>> tedious. I have since learned that some baking cooling racks have
>> spacings that are just right. You will have an amusing trip to the
>> local supermarket or home-stuff store with your petri dish to find a
>> product with optimal spacing. I have also seen plates placed all
>> together in small boxes. This doesn't give space between each plate
>> but if the boxes have shallow sides (like pipette tip boxes) it can
>> be ok. Hope this helps.
>>         Tobias Baskin
>>
>>> Does anyone know of a product that would hold petri dish racks
>>> vertically?  We are growing Arabadopsis on plates in various  
>>> solutions
>>> and need them to be vertical so they grow upright.  Thanks in  
>>> advance.
>>>
>>> _______________________________________________
>>> Arab-gen mailing list
>>> Arab-gen from net.bio.net
>>
>>
>> --
>>    _      ____          __   ____
>>   /  \   /          / \    /   \ \        Tobias I. Baskin
>>  /   /  /          /   \   \      \         Biology Department
>> /_ /   __      /__ \   \       \__    611 N. Pleasant St.
>> /      /          /       \   \       \        University of  
>> Massachusetts
>> /      /          /         \   \       \        Amherst, MA, 01003
>> /      / ___   /           \   \__/  \ ____
>> www.bio.umass.edu/biology/baskin
>> Voice: 413 - 545 - 1533 Fax: 413 - 545 - 3243
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 17 Nov 2010 20:36:27 +0000
>> From: "Holt, Ben F. III" <benholt from ou.edu>
>> Subject: Re: [Arabidopsis] Petri Dish Racks
>> To: Arabidopsis Listserv <arab-gen from magpie.bio.indiana.edu>
>> Message-ID: <C90998EA.9C3E%benholt from ou.edu>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> I sent Sara a reply earlier, but just realized I didn't reply to the
>> listserv. Basically we use similar approaches to what Tobias  
>> described - my
>> reply to Sara is below.
>>
>> Hi Sara,
>>
>> We use three cheap methods and all work fine. First - the two super  
>> cheap,
>> probably don't have to buy anything options:
>> 1) If you have some of those flats that are split up into multiple  
>> wells
>> (like 6X6 or something along those lines), you can flip it upside  
>> down and
>> wedge the plates in the cracks on the bottom - sounds pretty low  
>> rent, but
>> it works like a charm and only requires the effort of a flipping  
>> motion.
>> 2) If you have an extra metal rack from the standard light shelving  
>> used in
>> most labs, just place it on top of your existing shelving and put  
>> the plates
>> in the cracks - this is my favorite option. We have one old piece of
>> shelving from who knows where and it holds many plates in our  
>> standard
>> growth room. [The baking supply store racks idea from Tobias sounds  
>> like a
>> great solution if you don't have any old shelving lying around]
>> 3) Costs a few bucks option: If you are handy or have a handy  
>> person in your
>> department, just take a 4" tall piece of flat plexiglass sheet cut  
>> to your
>> preferred length (we have one that is 2.5-3 feet long) and find a  
>> few square
>> wood blocks that can be attached to the back (like a scrap piece  
>> from the
>> end of a 2"X4"). Cut one side of the block to get the desired angle  
>> of the
>> sheet once it is attached. For each block, drill a couple of holes  
>> through
>> the plexiglass and attach the block to the back of the sheet with  
>> wood
>> screws. To keep the plates sitting on the front side of the  
>> plexiglass sheet
>> you can epoxy a strip of plexiglass dowel at the bottom edge. If  
>> you don't
>> have any wood scraps, you can also cut a thin strip of plexiglass  
>> and use
>> heat to bend it to your desired angle and then epoxy 2-3 such  
>> strips to the
>> back of the flat sheet.
>>
>> Ben
>>
>> ========
>> Ben Holt
>> Assistant Professor
>> University of Oklahoma
>> Department of Botany and Microbiology
>> GLCH Rm 219
>> 770 Van Vleet Oval
>> Norman, OK  73019
>> Phone (405)325-9018
>> FAX   (405)325-7619
>> http://www.ou.edu/cas/botany-micro/faculty/holt.html
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 18 Nov 2010 08:06:01 +1100
>> From: Rosemary White <rosemary.white from csiro.au>
>> Subject: Re: [Arabidopsis] Petri Dish Racks
>> To: Tobias Baskin <baskin from bio.umass.edu>, SaraN
>> <passiflora42 from yahoo.com>
>> Cc: "arab-gen from magpie.bio.indiana.edu"
>> <arab-gen from magpie.bio.indiana.edu>
>> Message-ID: <C90A8EE9.1F4D7%rosemary.white from csiro.au>
>> Content-Type: text/plain; charset="US-ASCII"
>>
>> And if you only need to hold a few plates vertically, another  
>> option is an
>> old-fashioned toast rack.  We source these from our local two  
>> dollar shop
>> (which is actually $USD2 now!)  You need to rummage around, petri  
>> dishes in
>> hand, to find one with the right spacing - for thick toast.
>> cheers,
>> Roseamry White
>>
>>
>> On 18/11/10 12:19 AM, "Tobias Baskin" <baskin from bio.umass.edu> wrote:
>>
>>> Hi,
>>> We made our own by hand, lots of little strips of plexi
>>> glass. Its a pain. Its a bit easier to make them from wood, but  
>>> still
>>> tedious. I have since learned that some baking cooling racks have
>>> spacings that are just right. You will have an amusing trip to the
>>> local supermarket or home-stuff store with your petri dish to find a
>>> product with optimal spacing. I have also seen plates placed all
>>> together in small boxes. This doesn't give space between each plate
>>> but if the boxes have shallow sides (like pipette tip boxes) it can
>>> be ok. Hope this helps.
>>> Tobias Baskin
>>>
>>>> Does anyone know of a product that would hold petri dish racks
>>>> vertically?  We are growing Arabadopsis on plates in various  
>>>> solutions
>>>> and need them to be vertical so they grow upright.  Thanks in  
>>>> advance.
>>>>
>>>> _______________________________________________
>>>> Arab-gen mailing list
>>>> Arab-gen from net.bio.net
>>>
>>
>>
>>
>>
>> ------------------------------
>>
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