nucleus and ganglion

[Jyl Boline]

Hello again All,

Our next terms are nucleus and ganglion, for which we have several
potential definitions. Please share your thoughts on what these
definitions should be. Thanks much!

Nucleus:
1) Group of cells that have commonality of cytoarchitecture
chemoarchitecture and connections
2) A subcortical part of the nervous system consisting of a
relatively compact group of cells that is distinguishable
histologically that share a commonality of cytoarchitecture,
chemoarchitecturel and connectivity.
3) A neural nucleus is an anatomical structure consisting of a
discrete aggregate of neuronal soma.
4) Nucleus of brain is a subcortical gray matter which has as its
direct proper parts predominantly discrete aggregate of somas of
neurons.

Ganglion:
1) A collection of neurons in the peripheral nervous system
2) Any of a number of aggregations of neurons, glial cells and their
processes, surrounded by a glial cell and connective tissue sheath
(plural: ganglia).
3) Segment of neural tree (organ) which primarily consists of cell
bodies of neurons located outside the neuraxis (brain and spinal
cord); together with a nucleus and its associated nerve, it
constitutes a neural tree (organ).

Best,
Jyl

[Mihail Bota]

In BAMS Thesaurus we have the following entries:

1. Cell nucleus ( Brown, 1833 ) : A rounded organelle in the cells (Hooke, 1665) of all organisms except bacteria and similar forms that is enclosed in a double membrane and contains the genetic material of the cell; see Oxford English Dictionary (1989). Not to be confused with gray matter nucleus. Clearly described and named by Brown (1833, p. 709).

2. Gray matter nucleus : A term applied to many gray matter regions in the cerebrospinal axis (Meckel, 1817), usually though not always (e.g., the human dorsal lateral geniculate nucleus) when they have relatively clear borders and are nonlaminated. The first use of the term in this way was by Ludwig (1779, Fig. 2b, p. 36); the cell nucleus, a cytological feature, was named by Brown (1833, p. 710).

3. Ganglia ( G ; Galen, c173 ) : A ganglion is a recognizable aggregation of neurons (Waldeyer, 1891). There are marginal ganglia associated with invertebrate nerve nets, central ganglia associated with invertebrate central nerve cords, and peripheral ganglia in the invertebrate and vertebrate peripheral nervous system (Meckel, 1817). For vertebrates it has long been best practice to restrict the term ganglion (and terms derived from ganglion) to structures of the peripheral nervous system (Meckel, 1817). As Herrick wrote, "The term ‘ganglion' is also sometimes used for nuclei or centers within the brain…but this usage is objectionable, for the use of the word ganglion in vertebrate neurology should be restricted to collections of neurons outside the central nervous system, such as the ganglia of the cranial and spinal nerves and the sympathetic [autonomic] ganglia." (1915, p. 108). A prime example is the use of "basal ganglia" for cerebral nuclei (Swanson, 2000). Discovered and named in macrodissected adult mammals by Galen (c173; see translation by May , 1968, pp. 695-696).

I take advantage of this opportunity to announce that the BAMS Thesaurus, which includes most general terms for an ontology, is a part of a paper just published in PNAS:
http://www.ncbi.nlm.nih.gov/pubmed/21078980
The Thesaurus itself can be downloaded from PNAS in Word format.

The searchable and editable version of the Thesaurus will be released in a week or so.

Sincerely,

Mihai

On Mon, Nov 22, 2010 at 10:50 AM, <csa...@bidmc.harvard.edu> wrote:

This requires a little history, otherwise the concept of "basal ganglia" will not make sense.
The word ganglion was used in the older literature (1800's) to mean any collection of nerve cell bodies, either within or outside the CNS.  Thus, if you read the old literature, the basal ganglia were the gray matter structures (caudate, putamen, nucleus accumbens, globus pallidus, and variably depending upon the context perhaps the thalamus, amygdala, or subthalamic nucleus) in the forebrain.  The basal nucleus of Meynert was also sometimes referred to as the basal ganglion of Meynert.  This changed with time, so that now we typically mean only collections of nerve cells outside the CNS as ganglia.
The term nucleus ("kern" in the old German literature, where for example the "mandelkern" mean the "almond nucleus" and referred to the amygdala) meant a collection of nerve cell bodies in a subcortical structure in the brain, but occasionally also in the spinal cord (as in Clarke's nucleus or Onuf's nucleus).  The modern usage typically includes other information beyond spatial aggregation, such as chemoarchitecture and connectivity.  In general, when there is a collection of cells with common chemical phenotype and connections (e.g., the orexin neurons in the lateral hypothalamus) but no clear aggregation, they are not called a nucleus but instead an "area".  So the aggregation is still a part of the definition.  But cells that are outside the aggregate, but share the same chemoarchitecture and connections are usually considered to be part of the same nucleus.  Also, some aggregates may consist of several cell types with different connections or neurotransmitters (e.g., the arcuate nucleus contains both NPY-AgRP neurons that promote feeding and POMC neurons that inhibit feeding).  Sometimes these are called subnuclei, if they separate out spatially, as they do in the paraventricular hypothalamic nucleus.
So, this is complicated!
I would go for nucleus along the following lines: a spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype and connections.
For ganglion, I would say: a spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections.

Clifford B. Saper, MD, PhD
James Jackson Putnam Professor of Neurology and Neuroscience, Harvard Medical School
Chairman, Department of Neurology
Beth Israel Deaconess Medical Center
330 Brookline Avenue, Boston, MA 02215 USA
Phone: 617-667-2622; Fax: 617-975-5161
Email: csa...@bidmc.harvard.edu

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[Maryann Martone]

I think the only confusion is that we don't tend to call the cerebellar cortex or cerebral cortex a nucleus.  Non-laminated is certainly a differentia, although some nuclei, e.g., the LGN and superior colliculus are laminated.  So, sub-cortical and non-laminar would both be defining.

Maryann Martone

Professor-In-Residence

Dept of Neurosciences

University of California, San Diego

San Diego, CA  92093-0446

Tel:  858 822 0745

Fax:  858 246 0644

[Jyl Boline]

Hello All,

Unless there are any major objections, we will add the following
definitions to CUMBO:

Nucleus:
A spatially aggregated collection of nerve cell bodies in the CNS,

consisting of one or more subpopulations that share cell type,
chemical phenotype, and connections, and including nearby cells that

share the same cell type, chemical phenotype, and connections.

Ganglion:
A spatially aggregated collection of nerve cell bodies in the PNS,

consisting of one or more subpopulations that share cell type,
chemical phenotype, and connections.

Cell nucleus:

A rounded organelle in the cells (Hooke, 1665) of all organisms except
bacteria and similar forms that is enclosed in a double membrane and
contains the genetic material of the cell; see Oxford English

Dictionary (1989). (Brown, 1833, BAMS Thesaurus).

The next set of definitions have to do with nerves/tracts etc. This
is what we have so far, but we're probably missing terms, and some of
these may be synonyms. Please let me know your thoughts on these as
well.

Nerve:
1) Bundles of axons located in the peripheral nervous system
2) Segment of neural tree organ which has as its direct proper parts a
nerve trunk and its branches; together with other nerves of the same
tree it constitutes a neural tree.

Nerve fiber bundle:
A fasciculated bundle of neuron projections largely or completely
lacking synapses.

Tract:
A collection of axons that largely arises from one central nervous
system part and terminates in another. Tracts are generally named by
their region or origin followed by their region of primary
termination, e.g., mammillothalamic tract contains axons that arise
from neurons in the mammillary bodies and terminate in the thalamus.

Pathway:
A collection of nerve fibers

Thanks and have a great weekend!

Best,
Jyl

[Maryann Martone]

Why are we definiing cell nucleus for an upper level brain anatomy
term? We can visit gene ontology's definition and revise it, but I
wouldn't include it in CUMBO.

[Mihail Bota]

The mistake is on my side. I just copied the relevant definitions from FMC. I put it there just to make the difference between the gray matter nucleus and nucleus of a cell. The word "nucleus" appears in both cases with very different meanings.

Mihai

neurotransmitters (e.g., the arcuate nucleus contains both NPY-AgRP neurons

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Maryann Martone
Professor-In-Residence
Dept of Neurosciences
University of California, San Diego
San Diego, CA  92093-0446
Tel:  858 822 0745
Fax:  858 246 0644

Maryann Martone
Professor-In-Residence
Dept of Neurosciences
University of California, San Diego
San Diego, CA  92093-0446
Tel:  858 822 0745
Fax:  858 246 0644

[Maryann Martone]

Thanks Mihail.  For best practices, we should give an unambiguous label to each.  Brain nucleus is not right, because nuclei are found in the spinal cord.  CNS nucleus?

Fax:  858 822 3610

[Mihail Bota]

I think we use gray matter nucleus. So, it can be found anywhere there is a gray matter, and that part fulfills the criteria for "nucleus". "CNS" has the "system" included, and FMC is topographical.

If PONS would prefer CNS nucleus, then a bridge from and to "gray matter nucleus" can be done by the following definitions:

Central nervous system (CNS; Meckel, 1817): In animals with bilateral symmetry, a topographic division that is an obvious condensation of the nervous system (Monro, 1783) in the longitudinal plane (Henle, 1855), lying on or near the median plane (Henle, 1855). For invertebrates this longitudinal division consists of one or more nerve cords, whereas for vertebrates it consists of a single, hollow, and dorsal (Barckay, 1803) cerebrospinal axis (Meckel, 1817). In adult Echinoderms, which are radially symmetrical, a presumptive CNS is formed by a circular cord with associated radial cords, but there is no dominant ganglion (Galen, c173) that could be considered an invertebrate brain; see Bullock & Horridge (1965, pp. 9-14), Heinzeller & Welsch (2001, p. 41). When a CNS is present, its obligate companion topographic division is a peripheral nervous system (Meckel, 1817). While a continuous brain (Edwin Smith Surgical Papyrus, c1700 BC) and spinal cord (Galen, c162-c166) were known to Hippocrates in On the Sacred Disease and Fleshes (see translations by Adams, 1972, p. 351; and Potter, 1995, p. 139, respectively), the term central nervous system as currently understood for vertebrates was first used by Meckel (1817; see English translation, 1832, vol. 1, p. 152).

Gray matter (GM; Meckel, 1817): Since the 16th century the nervous system (Monro, 1783) has been divided more and more precisely into gray matter and white matter (Meckel, 1817) based on their appearance in freshly dissected material observed with the naked eye—topographic macroarchitecture of nervous system; since the 19th century this differentiation has been made at the histological (subsystems microarchitecture of nervous system) level. Gray matter is the nervous system compartment that consists of the cell bodies (Deiters, 1865) of neurons (Waldeyer, 1891); the cytoplasmic neuron extensions: axons (Kölliker, 1896), dendrites (His, 1889), and amacrine extensions; and synapses (Foster & Sherrington, 1897) between the neuron extensions—as well as glia (Virchow, 1846) and parts of the circulatory system: vascular cells. Neuropil (Waldeyer, 1891) refers to the gray matter compartment exclusive of cell bodies and vascular cells (blood vessels) and thus consists of the cytoplasmic extensions of neurons and glia, including synapses. There is often a fuzzy border of variable and difficult to measure width between white matter and gray matter. For early history see Clarke & O’Malley (1996, Ch. 10); for modern histological interpretation see Peters et al. (1991), Swanson (2003, pp. 60-66). The general term nervous system gray matter as defined here was probably first used by Meckel for macrodissected adult humans (1817, see English translation, 1832 vol. 2, pp. 152-154, 166-167); also see Herrick (1915, p. 108).

[Mihail Bota]

Hi Jyl,

We just made publicly available the online version of the FMC Thesaurus. Please see below the text I've just sent to the BAMS users (it includes links, etc.). I  think this Thesaurus may help the PONS CUMBO as well as the pan-mammalian ontology.

Mihai
-------------------
Dear BAMS user,

We are happy to announce the public release of the Foundational Model of Connectivity (FMC) Thesaurus. This online version implemented in BAMS 2.0 (direct link: http://brancusi1.usc.edu/thesaurus/principles/) is the Thesaurus published in Swanson & Bota, PNAS, 2010 (http://www.ncbi.nlm.nih.gov/pubmed/21078980). The Thesaurus follows rigorously the recommendations of the first INCF Neuroanatomy Workshop.

The online version is freely available, and users can view the alphabetical lists of defined standard terms of FMC (concepts), related terms and references, as well as synonyms of concepts. The online version also includes a simple and powerful search form that allows users to search by terms, abbreviations, and references. We highly recommend users to read the notations rules of FMC, before starting to use the Thesaurus. Each page of the Thesaurus includes a link to these rules.

The online version of the Thesaurus also includes the options of adding comments by the registered users. If you would like to register in BAMS2, please email Dr. Larry Swanson or reply to this message. Registered users can take advantage of the comments forms and suggest improvements to the present online version of the Thesaurus (1.0).
We implemented a versioning system that will take into account all useful comments, and thus each suggestion that improved in any way the future releases of the online Thesaurus will be associated with its author.

Please feel free to forward this message to anybody who might be interested.

We also announce that BAMS reached the 10,000 names of brain regions and fiber tracts landmark. These names are both in BAMS2 (http://brancusi1.usc.edu) and "BAMS Classical" (http://brancusi.usc.edu/bkms).

[Jyl Boline]

Hello again All,

So far we haven't had any feedback on our set of definitions having to

do with nerves/tracts etc. This is what we have so far, but we're
probably missing terms, and some of these may be synonyms. Please let

me know your thoughts on these.

Nerve:
1) Bundles of axons located in the peripheral nervous system
2) Segment of neural tree organ which has as its direct proper
parts a nerve trunk and its branches; together with other nerves of
the same tree it constitutes a neural tree.

Nerve fiber bundle:
A fasciculated bundle of neuron projections largely or completely
lacking synapses.

Tract:
A collection of axons that largely arises from one central nervous
system part and terminates in another. Tracts are generally named by
their region or origin followed by their region of primary
termination, e.g., mammillothalamic tract contains axons that arise
from neurons in the mammillary bodies and terminate in the thalamus.

Pathway:
A collection of nerve fibers

Thanks much!

Best,
Jyl

[Mihail Bota]

Very good questions!
Please see below some of my answers.

On Wed, Dec 15, 2010 at 5:25 PM, Chris Mungall <cjmu...@lbl.gov> wrote:

No answers, only questions and some exercises to help improve these

* can we list examples of each of these? E.g the cranial nerves.

 --the list: http://brancusi.usc.edu/bkms/brain/ontology-details.php?id=852

Also, FMC definition for nerves:

http://brancusi1.usc.edu/thesaurus/definition/nerves/

and for tracts

http://brancusi1.usc.edu/thesaurus/definition/white-matter-tract/ -- this one answers, at least partially, to some of your questions.

See also the definitions of the vomeronasal nerve:
http://brancusi.usc.edu/bkms/brain/ontology-details.php?id=855

of the optic nerve:

http://brancusi.usc.edu/bkms/brain/ontology-details.php?id=859

As you'll see, some subparts of them have "tract" in their names.

Optic nerve and olfactory nerve are in CNS.

I'll think at the remaining questions.

Mihai
 

* what are the relationships between these classes? Is NFB a superclass of both nerve and tract? If not, are they all mutually disjoint classes? I presume not, but it's good to make all assumptions explicit

* are tract and nerve disjoint classes? I presume so based on the CNS/PNS distinction. Again, it's good to make this explicit

* can we avoid weasel-words like "largely"? Is there a tract that does not go from one CNS location to another? If so, mention it. If not, remove "largely"

* Are nerves always part_of the nervous system, or can they overlap with the CNS? Is there a name for the structure that is a continuous nerve+tract?

* Many AOs have a class "peripheral nerve" but treatment is inconsistent. Can we come up with a good shared definition for this?

* FMA divides things into neural tree organs and segments of neural tree organs. For example, cranial nerve II is not a subclass of cranial nerve - it's a subclass of nerve trunk, which is a subclass of segment of neural tree organ. Do we want to adopt their definitions?

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[Mihail Bota]

On Wed, Dec 15, 2010 at 5:25 PM, Chris Mungall <cjmu...@lbl.gov> wrote:

* Are nerves always part_of the nervous system, or can they overlap with the CNS? Is there a name for the structure that is a continuous nerve+tract?

--yes. Optic nerve-->optic chiasm-->optic tract. The bundled axons from retinal ganglion cells are initially called "nerve", then where they decussate that portion is called "chiasm", and then the set of axons and their branches are called "tracts" (I think that everybody agrees that retina is CNS).

I think we have here two problems: one that is ontology-specific - classes and one that is terminology used by neuroanatomists. To avoid confusions, ontological classes should be named differently than the terms used by neuroanatomists.

We (BAMS) use the following terminology: the most general class is white matter tract (http://brancusi1.usc.edu/thesaurus/definition/white-matter-tract/).
If you think is good enough, feel free to use it.

Mihai
 

[Mihail Bota]

Thank you for correction Dr. Saper.

So, the criterion to dissociate a nerve from a tract is actually a structural one, not only a positional one - it is the type of the cell that produces myelin.

Can I ask for references regarding the myelinization of cranial nerves? If we get this, then we can better answer the questions of Chris Mungall.

Mihai

On Thu, Dec 16, 2010 at 4:27 AM, <csa...@bidmc.harvard.edu> wrote:

Mihail, the optic nerve is not a nerve.  It is a misnomer, because it is a CNS tract (it has central myelin).  Nerves are PNS structures and have peripheral myelin.

As for the olfactory nerve, this is a misnomer as well, but of a different kind, because there really is no olfactory nerve.  There are olfactor nerve rootlets, which run from the olfactory epithelium, through the cribiform plate, into the olfactory bulb, but then never form a distinct nerve bundle.  The thing that most neuroanatomy teachers point to when they teach the cranial nerves is actually the olfactory tract, from the olfactory bulb (which is already part of the CNS) to the basal forebrain.  

Clif

 

 

Clifford B. Saper, MD, PhD

James Jackson Putnam Professor of Neurology and Neuroscience, Harvard Medical School

Chairman, Department of Neurology

Beth Israel Deaconess Medical Center

330 Brookline Avenue, Boston, MA 02215 USA

Phone: 617-667-2622; Fax: 617-975-5161

Email: csa...@bidmc.harvard.edu

 

Note: This message is confidential and may be legally privileged. It is intended solely for the addressee. If you receive it in error, please delete this message and notify the sender immediately. Any use by an unintended recipient is prohibited.