POC Conf. Call 5-10-11

POC meeting, Webex Conference Call; Date: Tuesday May 10th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_5-03-11?

Conductive cells and tissues for vascular and non-vascular plants

THIS PART IS STILL UNDER CONSTRUCTION

conductive and related cell types for bryophytes and vascular plants

Current parent: axial cell

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]

Comment: These cells make up the axial system, also known as vertical or longitudinal system.

Existing descendents of axial cell:

sieve tube member (PO:0000289, alt: PO:0000286)

phloem fiber (PO:0004519)

xylem element (PO:0000273)

>tracheary element (PO:0000273)

>>tracheid (PO:0000301)

>>vessel member (PO:0002003)

>xylem fiber (PO:0000274)

>>fiber tracheid (PO:0000355)

>>libriform fiber (PO:0004520)

>>septate fiber (PO:0004521)

The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system

At the bryophyte term meeting on 4-25-2011 (RW and MAG present), we decided that axial cell was not the correct term to use to describe all of the elongated cells associated with conducting tissue in plants. They are different cell types and have different origins, so they should not all be grouped together.

New proposed hierarchy (children of plant cell):

plant cell

>hydroid

>leptoid

>vascular cell (new term)

>>sieve tube member

>>tracheary element

>>>tracheid

>>>vessel member

>>phloem fiber cell

>>xylem fiber cell

>>other kinds of fiber cells

>ground tissue cell (PO:0025030)

>>stereid

>>collenchyma cell

>>sclerenchyma cell (PO:0000077)

>>>fiber cell (new term)

>>>sclerid (new term)

Proposed definitions:

fiber cell:

vascular cell:

conductive tissue for bryophytes and vascular plants

trace as possible name for category for veins, central strands, and costas

vascular tissue

For vascular plants, we have the class:

portion of vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]

Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.

part_of vascular bundle (which is part_of vascular system)

This is okay, but suggest that we make it a child of the new class portion of axial tissue (see below), and also change definition to include xylem or phloem.

Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve tube members.

Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or may occur as scattered vascular bundles. May include other types of tissue, such as fibers.

part_of vascular system (should add vascular system participates_in sporophytic phase)

currently part_of vascular bundle. Removed this relation, because it is not true for all plants. Also vascular bundle is now a portion of vascular tissue, so it can't be part_of.

children of vascular tissue:

hydathode (PO:0005660) - A structural modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis. [GR:pj, ISBN:0080374913]

Should be is_a cardinal organ part. Do hydathodes ever occur on stems or branches, or are they always part of phyllomes?

proposed definition: A cardinal organ part that releases water through a pore.

Comment: Usually found on leaves. Hydathodes may have one or more pores that appear to be incompletely developed stomata that lack the ability to open and close. Generally, hydathodes are located at the end of a minor vein. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.

leaf vein (PO:0005417) - see more below details below

phloem (PO:0005417): A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]

proposed definition: A portion of vascular tissue that has as parts sieve tube members.

Comment: Functions in the conduction of organic substances in vascular plants.

metaphloem (PO:0006076): Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

proposed definition: A portion of phloem tissue that is the part of a primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

protophloem (PO:0006077): The first-formed elements of the primary phloem.

proposed definition: A portion of phloem tissue that has as parts the first-formed elements of the primary phloem.

tracheid bar (PO:0019026): A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]

-should be is_a xylem

xylem (PO:0005352): A portion of vascular tissue composed of (that has as parts) xylem elements.

vascular bundle (PO:0005020): A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]

This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.

proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.

Comment: Usually contains both xylem or phloem. May also contain other types of tissue such as plant fibers or vascular cambium. May also contain portions of ground tissue.

part_of vascular system

New children of plant tissue:

hydrome: A portion of axial tissue that has as parts hyrdoids.

Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in water conduction and support, similar to xylem in vascular plants.

Synonyms: hydrom, leptoxylem (Hebant)

leptome: A portion of axial tissue that has as parts leptoids.

Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.

Synonyms: leptom, leptophloem (Hebant)

central strand: A unit strand of axial tissue that has as part hydrome or leptome.

Comment: Often contains both hydrome and leptome. Found in bryophytes located in the center of non-vascular shoot axes such as a gametophore axis or seta, or in the costa of a non-vascular leaf.

synonyms: conducting strand, central cylinder

stereome: A portion of axial tissue that has as parts stereids.

Comment: Found in bryophytes.

From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.

portion of plant fiber: Currently fibers are plant cell types, but they should also be a tissue type.

Proposed definition: A portion axial tissue that has as parts fiber cells.

Comment: Contains elongated, lignified fiber cells that are dead at maturity.

phloem fiber: A portion of plant fiber that has as parts phloem fiber cells.

xylem fiber: A portion of plant fiber that has as parts xylem fiber cells.

leaf vein, midrib, costa

• leaf vein (PO:0020138): A strand of vascular tissue in the leaf blade.

is_a portion of vascular tissue; part_of leaf vascular system

This term only applies to vascular leaves, and should be renamed vascular leaf vein.

proposed definition, vascular leaf vein (PO:0020138): A strand of vascular tissue that is part of a leaf lamina in a vascular leaf.

part_of leaf vascular system, part_of leaf lamina

• Suggest new term primary leaf vein: A vascular leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.

Comment: A leaf may have more than one primary vein. The central primary vein is the midvein.

• midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]

Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ". Suggest we rename it vascular leaf midvein to distinguish it from costa.

proposed definition of vascular leaf midvein: A primary leaf vein that is the central vein of a leaf lamina in a vascular leaf.

Comment: Often the most prominent vein of a vascular leaf.

broad synonyms: mid rib, midrib, mid-rib

related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128

• Moss Ontology has requested the term midrib for bryophytes. It is often called a costa.

Proposed definition for costa:' A central strand that is part of a non-vascular leaf.

Comment: Found in bryophytes, especially mosses.

part_of non-vascular leaf

broad synonyms: mid rib, midrib, mid-rib

Refs:

Sperry 2003, IJPS; Hebant 1977;

Continuing User requests: for PSO

- Deal with and complete the list of user requests on SourceForge-

root terms

submitted by Rich Zobel (Nov 2009)

gametophytic phase and sporophytic phase

sporophytic phase (PO:0028002)

Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with fertilization or the division of a non-fertilized embryogenic cell.

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy or in vitro culture of haploid embryos.

gametophytic phase (PO:0028003)

Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]

Comment: During the gametophytic phase, a plant may produce gametes by mitosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with meiosis.

Comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory. This usually occurs when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.