[Arabidopsis] vertical growth

Tobias Baskin via arab-gen%40net.bio.net (by baskin from bio.umass.edu)
Sun Nov 21 10:30:52 EST 2010


Dear All,
	Caution! We need to be careful. First, there are almost 
certainly differences between species. The kind of rhizotron growth 
experiment is used for cereals because those roots are strongly and 
pervasively sensitive to light. Growing maize on an agar plate as in 
one of the many "toaster rack" setups being discussed, in a lighted 
chamber,  will give slow growing roots, at least compared to the 
rhizotron set up. Arabidopsis roots are not that light sensitive. It 
is true that shining unilateral light on them will produce a negative 
tropism, but it is a weak response (the angle is not large) and it 
does not invovle the inhibition of elongation. In thinking about 
this, I have speculated that it might reflect arabidopsis's growing 
in disturbed habitats with shallow roots, often exposed to 
significant light intensities. If so, it suggests that the clutch of 
vertical plates is plausible, with the shoots in bright light and the 
roots in dimmer light but not darkness.  Be that as it may, 
arabidopsis roots on vertical plates in lighted chambers grow 
vigorously, with at least certain parameters (max elemental 
elongation, cell division rate) comparable to those measured for, 
say, maize, with the most minimal dim green safe light for 
photography.

	Second, considering roots in the light vs dark is different 
than plants in the light in the dark. It is comparatively easy to put 
the whole arabidopsis seedling in the dark, and the roots of 
etioloated arabidopsis certainly grow more slowly than when the whole 
seedling is in the light (as on a vertical plate). However, 
experimentally it is difficult to allow the shoot to be in the light 
and the roots to be in the dark (for a small plant like arabidopsis) 
so that root growth can be measured.  I think this was the thrust of 
John Turner's question. Difficult to assess. Obviously, differences 
between light grown and dark grown *plants* cannot be safely 
extraplolated to differences between roots in the light and dark (of 
plants whose shoots are in the light).

	My few millimeters,
			Tobias


At 5:08 PM +1100 11/20/10, 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
>>>
>>
>>
>>
>  >
>>  ------------------------------
>>
>>  _______________________________________________
>>  Arab-gen mailing list
>>  Arab-gen from net.bio.net
>>  http://www.bio.net/biomail/listinfo/arab-gen
>>
>>  End of Arab-gen Digest, Vol 67, Issue 7
>>  ***************************************
>>
>>
>>
>>
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-- 
       _      ____          __   ____   
      /  \   /          / \    /   \ \        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



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