From dhowe at cs.uoregon.edu  Wed Oct 26 11:53:13 2005
From: dhowe at cs.uoregon.edu (Doug Howe)
Date: Wed, 26 Oct 2005 11:53:13 -0700
Subject: axon regeneration as part of differentiation?
Message-ID: <435FD099.5020504@cs.uoregon.edu>

I wanted to see if anyone else in the Neuro interest group thought there 
was an issue here before I posted a SF tracker item on it. 

The term GO:0031103 'axon regeneration' has 'neuron morphogenesis during 
differentiation' in it's path to root. This means that the process of 
'axon regeneration' in GO is implicitly restricted to occur during 
neuron differentiation.   This doesn't seem correct to me.  It seems to 
me that 'axon regeneration' is the extenstion of an axon by a mature 
neuron (ie not a differentiating neuron) after loss of the axon for some 
reason.  This process doesn't involve de-differentiation and 
re-differentiation of the neuron.

 Does anyone else see it that way?

I'm not in tune with the current biology on this, so I could be incorrect.

-Doug

-- 
* * * * * * * * * * * * * * * *
Doug Howe, Ph.D.
ZFIN Scientific Curator
Zebrafish Information Network
5291 University of Oregon
Eugene, OR 97403-5291

Phone: (541) 346-5733
* * * * * * * * * * * * * * * *



From erika at cribi.unipd.it  Fri Oct 28 05:43:08 2005
From: erika at cribi.unipd.it (erika at cribi.unipd.it)
Date: Fri, 28 Oct 2005 14:43:08 +0200 (CEST)
Subject: axon regeneration as part of differentiation?
In-Reply-To: <435FD099.5020504@cs.uoregon.edu>
References: <435FD099.5020504@cs.uoregon.edu>
Message-ID: <1130503388.43621cdcd277f@webmail.cribi.unipd.it>

Hi Doug, 
I agree with you about axon regeneration.
I think that this mechanism is in response to injury.
Regeneration requires a multistep processes. First, the injured neuron must
survive, and then the damaged axon must extend its cut processes to is original
neuronal targets.Once, contact is made, the axon needs to be remyelinated and
functional synapses need to form on the surface of the targeted neurons.
I think that it would be possible to talk about to aspects of regeneration:
functional regeneration and morphological regeneration.
The last one is about the regeneration of the tipical structure of a neuron in
the damaged tissue.
The first pertains to the re-establishment of neuronal function (functional
synaptic connection and re-myelination.
What do you think about it?

Erika


Quoting Doug Howe <dhowe at cs.uoregon.edu>:

> I wanted to see if anyone else in the Neuro interest group thought there
> 
> was an issue here before I posted a SF tracker item on it. 
> 
> The term GO:0031103 'axon regeneration' has 'neuron morphogenesis during
> 
> differentiation' in it's path to root. This means that the process of 
> 'axon regeneration' in GO is implicitly restricted to occur during 
> neuron differentiation.   This doesn't seem correct to me.  It seems to
> 
> me that 'axon regeneration' is the extenstion of an axon by a mature 
> neuron (ie not a differentiating neuron) after loss of the axon for some
> 
> reason.  This process doesn't involve de-differentiation and 
> re-differentiation of the neuron.
> 
>  Does anyone else see it that way?
> 
> I'm not in tune with the current biology on this, so I could be
> incorrect.
> 
> -Doug
> 
> -- 
> * * * * * * * * * * * * * * * *
> Doug Howe, Ph.D.
> ZFIN Scientific Curator
> Zebrafish Information Network
> 5291 University of Oregon
> Eugene, OR 97403-5291
> 
> Phone: (541) 346-5733
> * * * * * * * * * * * * * * * *
> 



Erika Feltrin, PhD Student
Bioinformatics Lab c/o CRIBI
Padua University
via U. Bassi, 58/b 35131

erika at cribi.unipd.it
+ 39.049.827.6165
+ 39.049.827.6159


From gillespm at cshl.edu  Mon Oct 31 13:34:40 2005
From: gillespm at cshl.edu (Marc Gillespie)
Date: Mon, 31 Oct 2005 16:34:40 -0500
Subject: axon regeneration as part of differentiation?
In-Reply-To: <435FD099.5020504@cs.uoregon.edu>
References: <435FD099.5020504@cs.uoregon.edu>
Message-ID: <FEF3957F-E52B-4095-B09A-129B7A789AC6@cshl.edu>

Hi All,

I am sure this will only muddy the water, but here are my thoughts  
below.

Marc

Marc Gillespie
Reactome
Stein Lab
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

email: gillespm at cshl.org
telephone: (718) 990-5249

http://www.reactome.org


On Oct 26, 2005, at 2:53 PM, Doug Howe wrote:

> I wanted to see if anyone else in the Neuro interest group thought  
> there was an issue here before I posted a SF tracker item on it.
> The term GO:0031103 'axon regeneration' has 'neuron morphogenesis  
> during differentiation' in it's path to root. This means that the  
> process of 'axon regeneration' in GO is implicitly restricted to  
> occur during neuron differentiation.   This doesn't seem correct to  
> me.  It seems to me that 'axon regeneration' is the extenstion of  
> an axon by a mature neuron (ie not a differentiating neuron) after  
> loss of the axon for some reason.

Depends on what happens at the molecular level, which I am interested  
to find out if we know one way or the other. Does regeneration  
involve the same process, albeit locally within the axon, that would  
be occurring during the original differentiation? Somehow I remember  
way back when reading that in some peripheral cases schwann cells act  
as a guide, but there is no guarantee that the axon will return to  
its previous precise location, and that the growing axon repeats the  
process that occurred in differentiation, though now, because of  
physical constraints it has a limited number of choices.

> This process doesn't involve de-differentiation and re- 
> differentiation of the neuron.

Isn't the fact that it is an extending axon, a form of "de- 
differentiation? Differentiated axons don't extend?

>
> Does anyone else see it that way?

I have to say though that I see what you are saying as well. What do  
we do with the observation that the soma of the cell is probably not  
undergoing all of the changes that are involved in 'neuron  
morphogenesis during differentiation'?

Maybe the root of the question; Is it ok for  'neuron morphogenesis  
during differentiation' to refer to just the axon of a neuron?


>
> I'm not in tune with the current biology on this, so I could be  
> incorrect.
>
> -Doug
>
> -- 
> * * * * * * * * * * * * * * * *
> Doug Howe, Ph.D.
> ZFIN Scientific Curator
> Zebrafish Information Network
> 5291 University of Oregon
> Eugene, OR 97403-5291
>
> Phone: (541) 346-5733
> * * * * * * * * * * * * * * * *
>
>



From lenov at ebi.ac.uk  Mon Oct 31 14:00:48 2005
From: lenov at ebi.ac.uk (Nicolas Le =?iso-8859-1?Q?Nov=E8re?=)
Date: Mon, 31 Oct 2005 22:00:48 -0000 (GMT)
Subject: axon regeneration as part of differentiation?
In-Reply-To: <FEF3957F-E52B-4095-B09A-129B7A789AC6@cshl.edu>
References: <435FD099.5020504@cs.uoregon.edu>
    <FEF3957F-E52B-4095-B09A-129B7A789AC6@cshl.edu>
Message-ID: <32816.81.103.19.87.1130796048.squirrel@webmail.ebi.ac.uk>


>> I wanted to see if anyone else in the Neuro interest group thought
>> there was an issue here before I posted a SF tracker item on it.
>> The term GO:0031103 'axon regeneration' has 'neuron morphogenesis
>> during differentiation' in it's path to root. This means that the
>> process of 'axon regeneration' in GO is implicitly restricted to
>> occur during neuron differentiation.   This doesn't seem correct to
>> me.  It seems to me that 'axon regeneration' is the extenstion of
>> an axon by a mature neuron (ie not a differentiating neuron) after
>> loss of the axon for some reason.
>
> Depends on what happens at the molecular level, which I am interested
> to find out if we know one way or the other. Does regeneration
> involve the same process, albeit locally within the axon, that would
> be occurring during the original differentiation?

Even if the molecular processes are different (and they're not) it is
still axon regeneration, so the concern is sound.

> Somehow I remember
> way back when reading that in some peripheral cases schwann cells act
> as a guide, but there is no guarantee that the axon will return to
> its previous precise location, and that the growing axon repeats the
> process that occurred in differentiation, though now, because of
> physical constraints it has a limited number of choices.

Yep, and since the growth factors and ephrin gradients are not there, the
guidance would be different. But the axonal bit is the same.

>> This process doesn't involve de-differentiation and re-
>> differentiation of the neuron.
>
> Isn't the fact that it is an extending axon, a form of "de-
> differentiation? Differentiated axons don't extend?

No, no. Differentiated axons extend. They grow collaterals. It is one of
the form of long-term plasticity.


-- 
Nicolas LE NOV?RE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521,  Fax: +44(0)1223 494 468,  Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov