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Glossary - F




F1     First generation of offspring after a mating (first filial generation).
F2     Second generation of offspring after a mating (second filial generation).
F actin    

Filamentous actin. One of the most common macromolecular assemblies in all animal cells, found in cytoskeletal structures such as stress fibers, microvilli and muscle sarcomeres. In these structures, actin coassembles with actin-binding proteins to form long filamentous bundles which are often attached to the plasma membrane and/or associated with myosin motors.

See G actin
See Myosin

F cell

F ectoblast (S)


A rectal epithelial cell in the hermaphrodite tail. This cell acts as a blast cell in the male tail.

See Y cell
See Rectal epithelium

f neuron     ADF cell
Facultative developmental stage    

An optional larval or juvenile stage which an animal may choose to follow under certain conditions. The male adult can also be considered a facultative stage in C. elegans, since it is not required for propagation of the species.

See Dauer

Facultative parasite    

An organism that is capable of independent existence but which under certain conditions may become parasitic. For instance, some otherwise free-living nematodes can enter the body of a insect, invade its tissues and kill the animal, and then feed upon bacteria within the dead insect gut. Converse condition is an obligate parasite.

See Parasite

Fan     Part of the male copulatory apparatus. A complex flattened structure extending laterally at the extreme tip of the adult male consisting of nine pairs of sensory rays that lie within a web-like cuticle. On the ventral surface of the fan, the gubernaculum presents the cloacal opening, spicules, phasmids, hook and post-cloacal sensilla. The fan replaces the simple pointed tail tip of the hermaphrodite and of the juvenile male, during the end of the L4 stage, during a morphogenetic process called fan formation or tail tip remodeling.
Fan formation    

Reshaping of the male tail during late larval development in which the tail tip cells fuse together and change shape. The posterior hyp cells (hyp 8,9,10,11) move forward (retraction of the previous tail spike) while a late round of cell divisions in posterior blast cells produce new sensilla including the rays which spread laterally to form a fan-shaped tail covered with new cuticle (Sulston et al., 1980; Nguyen et al., 1999).

See Retraction


A bundle of neuron processes. Alternately, it can refer to a bundle of intracellular filaments.


This term can have multiple meanings, generally concerning the behavior of networks of groups of animals, cells, cell parts, or molecules. Positive feedback generally acts to increase the outcome of the original signal, whereas negative feedback acts to decrease that outcome over time.

In neuroscience, feedback can refer to a set of synapses that connect back directly onto the original neuron in a circuit.

In biochemistry, feedback inhibition can refer to circumstances in which the product of a reaction acts to reduce the activity of the enzyme.

See Reciprocal synapse


A mutant phenotype where FEMinization of the hermaphrodite (XX) and male (XO) animals occurs. In these mutants, both XO and XX animals become fertile females. Maternal effect may be seen.


This sexual form does not normally exist in C. elegans. Some viable female strains have been created as mutant alleles in which production of sperm has been suppressed (e.g. fem or fog mutants). These adults generate only female gametes and can mate successfully with males.

See Fem
See Feminization
See Fog

Feminization     Conversion of XX (normally wild type hermaphrodite) and X0 (normally wild type male) animals to females in C. elegans. Occurs as a result of certain mutations in the sex determination pathway which block spermatogenesis in the germline as well as development of the male somatic gonad (Doniach and Hodgkin, 1984; Meyer, 1997; Meyer, 2005).
Fenestration     The presence of holes (“windows”) in a membrane or cell process that allow the passage of large molecules, macromolecular structures, or fluids between two sides of the barrier. Some biological structures display natural fenestrations, such as the “pores” in the nuclear membrane, or the holes in the somatic sheath of the gonad (Hall et al., 1999). Fenestrations can sometimes be induced experimentally; for instance by laser surgery on the eggshell or the vitelline membrane of the embryo (Schierenberg and Junkersdorf, 1992).
Fertilization     The event in which a sperm and an oocyte (haploid germ cells) fuse together to form one diploid embryo (See Greenstein, 2005 and Wormatlas) .
Fertilization membrane Dense vitelline layer (S)  

A temporary structure known to form in some nematode species at the moment of fertilization in order to physically block subsequent spermatocytes from entering the egg; e.g. blocking polyspermy. This evanescent structure is apparently secreted by the oocyte from pre-positioned vesicles and remains in place until a permanent eggshell can replace it. It has been seen only after fast freezing fixations in C. elegans (Hall and Greenstein, unpublished) but has also been noted in Ascaris (Fairbairn, 1957; Foor, 1967; Anya 1976) .

See Glycocalyx

Feulgen stain     A specific stain for nuclear DNA which labels all cell nuclei and can be viewed by light microscopy. It contains fuchsin, a colorless dye which has a strong affinity for DNA and produces red color in its presence. A fixed animal can be stained with Feulgen to highlight the DNA content of all nuclei. Larval stages give the most dramatic results (Sulston and Horvitz, 1977).

Term used to refer to various long thin extended objects. It can refer to a subcellular structure such as a thick filament of the internal cytoskeleton, or to an extracellular object lying in the basal lamina or cuticle layers. More often the term has been used to refer to either a cellular process (for instance a “nerve fiber” or “muscle fiber”) or to a structure made up from a group of cell processes, or even a whole groups of cells.

Fiber layers    

Three (or possibly just two) of the innermost layers of the cuticle (corresponding to layers 6, 7, 8 of Ascaris cuticle) which display tightly woven fibers that run coherently in helical or circumferential orientations around the body. Two of these layers appear to run at 65° angle to the longitudinal body axis, but in opposite directions to each other (Kramer, 1997). These layers lie between the boundary zone and the basal layer. Together they comprise the basal zone (Bs) of the cuticle (Bird and Bird, 1991).

Some roller and dumpy mutations of collagen genes may disrupt this helical organization, causing the entire animal to adopt a helical twist to the outer cuticle and forcing the animal to move helically in a rolling motion, rather than in a sinusoidal path. The fiber layers can show visible lamination between themselves, and may be visualized as striated bands by various imaging modalities, including polarized light, TEM, and freeze etching.

See Basal layer
See Basal zone
See Boundary zone
See Cortical layer
See Fibril layer
See Matrix layer
See Median zone
See Roller
See Locomotion


This term may refer to any of a number of long thin objects, just as the word “fiber” has been used rather widely. Fibrils (as opposed to “fibers”) have most often been identified with a class of extracellular macromolecules (perhaps extended collagens) lying within the medial zone of the cuticle.  When clustered macromolecules lie in register side by side, the resulting fibrils may present a distinctive striated appearance.

See Fiber
See Fibril layer

Fibril layer Fibrillar layer(S)  

A portion of the medial zone of the cuticle, lying just beneath the cortical zone and above the matrix layer. This thin layer contains a more densely arrayed set of fibrils than the spongy-looking matrix layers above and below it.

See Basal layer
See Cortical layer
See Fiber layers
See Matrix layer
See Median zone

Fibrous body FB  

A specialized organelle that develops inside the spermatocyte and spermatid, containing a distinctive bundle of parallel fibers (5 nm diameter). The fibrous body initially is surrounded by a complete double membrane and may be fed by sequential fusions of special vesicles derived from the cis Golgi region, within the spermatocyte cytoplasm. As the spermatocyte develops into the spermatid, the fibrous bodies enlarge and dominate the cytoplasm. Fenestrations develop in their surrounding membrane. In late spermatids the fibrous bodies disappear, while the “special vesicles” transform into membranous organelles (also called “special membrane structures” by Wolf et al., 1978) and come to lie at the cell periphery. It is unclear whether the contents of the fibrous body (the fibers) contribute somehow to the membranous organelle.

See Membranous organelle
See Special vesicle

Fibrous organelle    

A complex structure located in hypodermal cells underlying the bodywall muscle that generally includes two hemi-adherens junctions (or hemidesmosomes) facing outward from the organelle and is responsible for securing these muscles to the cuticle (Hresko et al., 1999). They may also occur in more scattered locales away from muscles, with a secondary concentration where touch dendrites fasten to the cuticle.

In the embryo, they seem to be restricted to narrow stripes underlying muscles during muscle morphogenesis. Their initial localization is organized by a hypodermal protein, myotactin (Hresko et al., 1999). These appositions generally span the hypodermis, forming symmetrical pairs of hemi-adherens junctions on both faces of the thin hypodermal layer that separates muscle from cuticle. While one hemi-junction faces the muscle border (binding to the thick basal lamina separating these two tissues), the second hemi-junction faces the cuticle, often linked to a dense structure lying within the cuticle itself. Intermediate filaments span the hypodermal layer to link the two hemi-junctions. Thus, the components of one fibrous organelle include the two hemi-junctions and the filaments that secure them in parallel.

Fibrous organelles often occur in regularly-spaced stripes along the bodywall, in registration with the annuli of the cuticle. In some nematode species these organelles often lie in register with dense body-like structures in the muscle cells to form a larger complex, termed the desmo-osmoid. This relationship is less commonly seen in C. elegans.

See Adherens junction

FIF Formaldehyde induced fluorescence  

A staining technique in which exposure of fixed animals to formaldehyde vapors localizes serotonin and dopamine histochemically in C. elegans (Horvitz et al., 1982; Sulston et al., 1975).


A term that has been used most often in reference to certain classes of cytoskeletal macromolecules that form extremely long thin uniform structures, including actin (thin filaments), myosin (thick filaments), and intermediate filaments (whose diameter is in between those of actin and myosin).

See Actin
See Intermediate filament
See Myosin

Filopodium/Filopodia (/pl)    

Long, thin, finger-like processes created during process extension. Seen in neuronal growth cones and in distal edge of somatic gonad sheath (Chalfie et al, 1994; Hall et al., 1999).

See Growth cone
See Pseudopodium / Pseudopod / Pseudopodia


Long, thin extensions of the dendrite of the AFD neuron. These fingers have also been called villi or microvilli, although no one has yet proven a molecular homology to villi of other cell types. These fingers are probably stationary, and each lies embedded in a narrow separate channel formed by the amphid sheath.

Other cells may also extend long thin finger-like processes, including the DTC, the somatic sheath cell (pair #1), the neuron growth cone, and the hypodermis during embryonic closure. All of these examples involve apparently motile cells, where the fingers may either lead the active outgrowth, or trail behind the cell as it moves.
Some portions of the cuticle are specialized to form long thin fingers at the sieve and the flaps within the pharyngeal lumen.

See Filopodium / Filopodia
See Flaps
See Sieve

Finger cell    

AFD neuron of the amphid sensillum.

Finger-like projections     The narrow structures that are formed by interdigitations of the plasma membrane and cytoplasm at the junction of the special vesicle and the fibrous body inside developing spermatocytes (Wolf et al., 1978). The plasma membrane becomes highly folded, more regular in shape and more electron dense, suggesting some structural reinforcement stabilizes these finger-like projections. Some authors suggest that the fingers correspond to microvilli (Bird and Bird, 1991).
FITC Fluorescein isothiocyanate   A commonly used fluorescent stain for light microscopy that produces a bright yellow-green label. The absorption maximum of FITC is about 495 nm and the peak emission wavelength is about 530 nm.

A chemical mixture used to preserve the tissue structures of an animal for histological study. Common fixatives used for C. elegans include aldehydes which fix protein, osmium tetroxide which fixes and stains lipids, and methanol/acetic acid which both fixes and clears tissue.

See also Anatomical methods

Flaccid Floppy (S)   A semi-paralysed body phenotype in which muscle tone is lost and the animal fails to actively control its body shape.

A whip-like appendage used for motility by certain cells and small organisms. It is found in sperm, bacteria, fungi, and protozoans. There are no flagella in C. elegans spermatozoon which only has a lamellipodium and no thinner “non-motile flagellum” (Qin et al., 2001). This portion of chemosensory and mechanosensory dendrites, often featuring an axoneme, a striated rootlet and a distal cluster of extended microtubules, shares many molecular constituents with true flagella and other forms of cilia in species ranging from bacteria to sea urchin, fruit fly, and the mouse (Rosenbaum and Witman, 2003).

See Cilium/ Cilia
See Lamellipodium


Metarhabdion (S)
Glottid apparatus (S)

  Three cuticle extensions, or fingers, which extend inward into the anterior buccal cavity. They may act to filter the contents of the lumen while separating the buccal cavity from the pharynx lumen proper. They are probably formed by the pm1 pharyngeal muscles, also known as the metastom.

A characteristic behavior seen in the late stage of lethargus, just prior to the molt, in which the animal executes rapid 180° rotations about its longitudinal axis. This movement is thought to help in loosening the old cuticle from the new cuticle, in preparation for the molt (Singh and Sulston, 1978).

See Lethargus
See Molt

FLP cell



A pair of neurons with ciliated endings in the head. Have mechanosensory function.

A member of a class of short peptide molecules that can act as neurotransmitters, neurohormones, and neuromodulators. They are found in the nervous systems of a wide spectrum of animals including nematodes (Li et al., 1999).

See Neuropeptide

Focal adhesion    

Attachments that are formed by vertebrate cells in culture to the substratum. C. elegans body wall muscle cell dense bodies and M-lines are similar to focal adhesions (Lin et al., 2003).

See Adhesion plaque
See Dense body
See Dense plaque

Fog     A mutant phenotype where Feminization Of Germline occurs. XX animals (normally wild type hermaphrodites) are transformed into fertile females. Depending on the mutation, X0 animals may stay as wild type males or may be somatically male with both sperm and oocytes in the germline.
Follower axon    

An axon that does not establish a new path as it grows away from a neuron cell body along the bodywall, but closely follows a route established previously by another “pioneer axon”.  In general, a follower axon may exhibit a smaller, simpler growth cone than that of a pioneer.

See Pioneer axon
See Growth cone

Foraging     Continuous, possibly exploratory, movements of the C. elegans head. This is a complex behavior produced by the elaborate motor and sensory anatomy of the animal's head. The terms “feeding” and "foraging" are often used interchangeably though foraging behavior encompasses more extensive range of activities. These side-to-side head motions are suppressed during backwards motion (Ringstad and Horvitz, in Hart, 2006).
Formaldehyde induced fluorescence FIF   See FIF
Founder cell    

The earliest stem cells in the early embryo from which all tissues derive. There is one founder cell for the germline, P4, and five for the somatic tissues, AB, MS, E, C and D, each of which generates a stereotyped lineage (Deppe et al., 1978).

Several intermediate blast cells give rise to these founders and can also be considered as founder cells: P0 (the original cell after fertilization), P1, P2, P3, and EMS. Another synonym might be “embryonic blast cell” (see discussion in Sulston et al., 1983). Patterns of cell division for each founder cell are unique, and involve fixed lineages where many daughters arise from unequal cell divisions involving highly stereotyped planes of division.

See Gönczy and Rose, 2005 for more detail.

Fountainhead pattern     Cytoplasmic streaming seen within the newly fertilized embryo which occurs at the one cell stage. This is apparently organized by the position of the sperm pronucleus which determines the A/P axis of the embryo. Internal granules and cortical granules (as seen by DIC optics) flow in a distinctive pattern that has been termed the “fountainhead” (Hird and White., 1993; Goldstein and Hird, 1996).
Four-dimensional microscopy

Four-dimensional imaging (S)
4D video recording (S)

  The generation of time-lapse recordings of multiple image planes (X,Y coordinates) at different focal depths (Z coordinate). This technique is particularly useful for examination of the early development of the C. elegans embryo. These recordings can be used to create a “movie” to follow cell divisions and movements over time.
Four-fold stage Late pretzel stage (S)  

The final stage of embryogenesis prior to hatching, where the embryonic worm is bent in three places within the eggshell.

See Pretzel stage

Free living     Describes the life style of an animal that is not living as a parasite within the body of a host animal or plant. C. elegans is a free living soil nematode.

A method of fixation used for preparing animals for immunofluorescent staining in which the whole nematode is exposed to repeated cycles of freezing and thawing in dry ice/ethanol mixture prior to aldehyde fixation. The repeated cycle acts to break open the tough cuticle exterior to permeabilize the internal tissues to fixative and antibodies.

See Anatomical Methods-Freeze-crack and Staining Protocol


1) Process through which two cells join to make one structure. In C. elegans, many cells in the developing nematode eventually undergo fusion to form syncytial tissues (e.g. hypodermis, muscle, glands) (Podbilewicz and White, 1994). Cell fusion is also a key step in fertilization, bringing the spermatozoon inside of the oocyte (fusion of gametes).

2) Alternately, some cells can undergo self-fusion in order to produce ring-like structures; these include the sheath cells of many sensilla and some processes in gland cells.

3) Membrane fusion is involved during the release of chemical transmitters from synaptic vesicles or release of other intercellular signals from cells or glandular secretions.

Fusion pore    

An intermediate structure thought to occur during the process of membrane fusion between two cells, or membrane-bound organelles. Such structures are generally not well demonstrated by TEM as yet in C. elegans (but see Nguyen et al., 1999), although cell fusions are commonplace.

Alternately, a distinctive type of fusion pore has been described in the spermatid, in which a membranous organelle within the cell fuses with the plasma membrane (Achanzar and Ward, 1997). Here the fusion pore is reinforced by an electron dense “collar” on its cytoplasmic face that holds the pore open to allow the contents of the membranous organelle to flow through.

A persistent fusion pore, albeit much larger, is maintained between germ cells and the rachis in the syncytial gonad; here again the pore is apparently maintained in an open state, reinforced by an electron dense material on the cytoplasmic face, most likely consisting of hemicentin (Vogel and Hedgecock, 2001; Hall, unpublished).

This section should be cited as: Herndon, L.A., Lints, R. and Hall, D.H. 2010. Glossary F. In WormAtlas.  doi:10.3908/wormatlas.6.6
Edited for the web by Laura A. Herndon. Last revision: December 13, 2013.