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and the basement membrane.
Facilitated diffusion Selective diffusion based on the shape or
hydrophilicity of the diffusing molecule.
Fate map A map of an embryo showing cells or areas that are destined to
develop into speci¬c later-stage structures or adult tissues and organs.
Fertilization Fusion of the egg and the sperm and subsequently of the
maternal and paternal genetic material.
GLOSSARY 279


Fertilization envelope The layer of extracellular matrix formed upon
fertilization when the contents of the egg™s cortical granules are
exocytosed between the plasma and vitelline membranes; constitutes a
barrier to polyspermy.
Fibroblast A type of cell found in connective tissues that produces an
extracellular matrix rich in type I collagen.
Filopodium A long, thin extension of the cell surface, including
membrane and cytoplasm.
Fixed point A special solution of systems of ¬rst-order differential
equations (containing only ¬rst derivatives) at which the derivative of
each quantity simultaneously vanishes.
Flagellum (plural flagella) Long, cilium-like protrusion whose undulations
drive a cell through a ¬‚uid medium.
Fluid The collective name for phases of matter in which atoms and
molecules do not (as in solids) bind tightly to each other, such as liquids
and gases.
Follicle cell Accessory cells, not of the oogenic (i.e. egg) lineage, closely
associated with the developing ovum.
Fractal A special geometric object, with the property of being self-similar
under arbitrary magni¬cation.
Free energy The energy that can be extracted from a system to drive
reactions under speci¬c experimental conditions, which thus takes into
account changes both in energy, entropy, and other characteristic
properties (volume, enthalpy, number of molecules) speci¬ed by the
experimental conditions.
Frictional force A force acting between two surfaces moving past one
another, which is typically proportional to the velocity (as opposed to the
acceleration) of the relative motion.
Gametes The cells that participate in fertilization and jointly produce the
founding cell (zygote) of a new organism. In animals the gametes are the
ova (eggs) and the spermatozoa.
Gap genes A class of nonuniformly expressed genes (e.g., giant, Kr¨ppel)
u
involved in segmentation in long-germ-band insects such as
Drosophila. Gap genes are generally controlled by maternal gene
products; their products, in turn, are involved in the control of pair-rule
genes.
Gap junction A tubular structure consisting of several connexin protein
subunits that forms a transmembrane communication channel between
adjacent cells.
Gastrula A two-layered (in diploblasts) or three-layered (in triploblasts)
stage of embryonic development, which arises from the blastula by a
sequence of cellular and morphogenetic changes.
Gastrulation The series of developmental steps leading to the formation of
a gastrula.
Gel point The instant when a solution containing polymerizing monomers
develops a spanning network of interconnected polymers with apparent
elastic properties; at the gel point a special percolation transition (i.e., the
sol--gel transition) takes place.
Gene One or more segments of DNA that together specify the sequence of
a speci¬c RNA or protein.
Genetic code The relationship, employed in protein synthesis, of the
64 nucleic acid triplet codons to the 20 primary amino acids.
280 GLOSSARY


Genome The totality of the genetic material in the chromosomes of a
particular organism.
Genotype The speci¬c genetic makeup of a cell or organism, as contrasted
with its phenotype.
Germ cells The cells that give rise to eggs and sperm.
Germ layers The tissues of the early-stage animal embryo (in diploblasts
the ectoderm and endoderm and in triploblasts the ectoderm, mesoderm,
and endoderm) that will give rise to the animal™s de¬nitive tissues and
organs.
Germ line The cell lineage in animal embryos that includes only the germ
cells and gametes.
Glycocalyx The extracellular carbohydrate-rich coat of the cell surface,
composed of a network of glycosaminoglycans, proteoglycans, and
glycoproteins.
Glycoprotein A protein covalently linked to one or more oligosaccharides.
The oligosaccharides of transmembrane glycoproteins are located on the
extracellular domain.
Glycosaminoglycan One of several nitrogen-containing polysaccharides
(polymers of sugars) found in the extracellular matrices of animal tissues.
Examples include hyaluronan, heparan sulfate, and chondroitin sulfate.
Golgi apparatus Cell organelle, consisting of membranous sacs, involved in
the modi¬cation and packaging of secreted materials and membrane
proteins.
Gonads The reproductive organs of animals (female, ovaries; male, testes).
Gradient Continuously varying distribution of a substance as a function of
another variable, for example the concentration of a morphogen as a
function of position.
Gray crescent The region on the surface of the early frog embryo,
generated by rotation of the cortical cytoplasm, where gastrulation is
initiated.
Growth factor A secreted protein that in¬‚uences cell proliferation or
differentiation.
Haploid The state of a cell, derived from the diploid state by meiosis, that
contains only one set of chromosomes and thus only one copy of each
gene. The haploid state contains half the number of chromosomes of the
diploid state.
Haptotaxis The movement of cells in response to an insoluble extracellular
molecular gradient.
Hemidesmosome A cell junction that attaches an epithelial cell to an
underlying basal lamina. The portion adjoining the cell is
morphologically similar to one face of a desmosome.
Hensen™s node The regional thickening of cells at the anterior end of the
primitive groove on the dorsal surface of the embryos of birds, reptiles,
and mammals, through which gastrulating cells migrate anteriorily to
form tissues in the future head and neck; the functional equivalent of the
Spemann--Mangold organizer of amphibian embryos.
Heterodimer A complex of two molecules (e.g., proteins) in which the
monomers are nonidentical.
Hindgut The posterior region of the digestive tube.
Histone One of a group of ¬ve distinct low-molecular-weight, basic (i.e.,
positively charged) proteins that organize DNA into chromatin subunits
(nucleosomes) in all eukaryotic nuclei.
GLOSSARY 281


Hooke™s law The physical law that expresses the property of elastic
materials, according to which a deforming force (such as tension) is
proportional to the deformation it causes (such as elongation).
Homeobox genes Genes that specify a set of transcription factors whose
DNA-binding region is an evolutionarily conserved motif called the
homeodomain. A homeodomain contains about 60 amino acid residues and
the corresponding region of a homeobox gene, the homeobox, is therefore
(see genetic code) about 180 base pairs in length.
Homologous genes Genes that are evolutionarily related to one another
through common ancestry.
Homologous chromosomes Chromosomes containing the same sets of
genes. A homologous pair of each chromosome (other than the sex
chromosomes) is present in diploid cells. With respect to sex
chromosomes, in mammals a homologous pair of X chromosomes is
present in the cells of females; one X and one nonhomologous
Y chromosome are present in the cells of males.
Hopf bifurcation The bifurcation taking a ¬xed point into a limit cycle in
a dynamical system.
Housekeeping genes Genes that specify the proteins that perform general
cell functions; housekeeping genes are potentially transcriptionally active
in every cell.
Hox genes A subset of homeobox genes that is involved in specifying
regional identity along the body axis of vertebrates, arthropods, and
other metazoans, as well as in the limbs and other organs of these
groups.
Hydrolysis Cleavage of a molecule by the splitting of a bond with the
addition of the hydrogen and hydroxide ions of a water molecule to the
respective newly exposed sites.
Hydrophilic A molecule or portion of a molecule that has strong af¬nity
for water.
Hydrophobic A molecule or portion of a molecule that lacks af¬nity for
water.
Hypoblast The sheet of cells in early-stage avian and mammalian embryos
that lies beneath the epiblast in the blastoderm. The hypoblast gives rise
to extra-embryonic structures.
Imaginal discs Flattened epithelial sacs, on the surface of larvae of certain
insects, that give rise to adult appendages during metamorphosis.
In vitro Literally, ˜˜in glass;” in developmental biology, referring to studies
of isolated tissues or cells.
In vivo Literally, ˜˜in life;” in developmental biology, referring to studies of
tissues or cells in the intact embryo.
Induction Alteration of the composition or shape of a tissue by a second
tissue or its products.
Inertial force A force equal to the mass of an object times its acceleration.
Ingression A cell rearrangement in which a population of cells moves
from the surface of a tissue mass into an interior lumen, as in some
forms of gastrulation.
Inner cell mass Population of cells in a mammalian blastula that gives rise
to all the structures of the organism™s body.
Inositol A sugar molecule that plays several different cellular roles. In
phosphorylated forms (e.g., IP3 ) and phospholipid-linked forms (inositol
phospholipids) it is a component of signaling molecules, which regulate
282 GLOSSARY


intracellular calcium ion deployment. Its phospholipid-linked forms are
also components of the glycosylphosphatidylinositol (GPI) membrane
anchors of certain cell surface proteins.
Integral membrane protein A protein that in its functional form contains
one or more domains inserted into a membrane.
Integrin Collective name for a class of special adhesion molecules that
connect the cell to the extracellular matrix.
Intermediate filaments A family of cytoskeletal ¬laments of diameter
smaller than microtubules and larger than micro¬laments. Examples
include keratin (epithelial cells), vimentin (¬broblasts), desmin (muscle
cells), neuro¬laments (neurons).
Interfacial energy The amount of energy required to increase the contact
area between two distinct substances by one unit.
Interfacial tension The same as interfacial energy in the speci¬c case
when one or both of the contacting substances is a liquid. The
liquid--vacuum (in practice, the liquid--air) interfacial tension is called
surface tension.
Interphase Phase of the eukaryotic cell cycle in which an intact nucleus
(as opposed to mitotic chromosomes) is present.
Involution Tissue rearrangement in which a cell layer undergoes folding
at its edges.
Ion channel Con¬guration of proteins in the plasma membrane or other
cell membranes that permits the passage of speci¬c ions.
IP3 (inositol trisphosphate) An intracellular signaling molecule involved in
calcium ion deployment. (See also inositol.)
Isologous diversification Behavior of interacting copies of initially
identical dynamical systems, leading to stable diversi¬cation of the
different copies with respect to their dynamical state.
Joule Unit of energy and work equal to 1 meter — 1 newton.
Juxtacrine Type of local communication between cells involving direct
cell--cell contact.
Kinase An enzyme that links a phosphate group to another molecule. A
protein kinase links a phosphate to a protein.
Kinesin A motor protein that moves cargoes along microtubules using
energy released from the hydrolysis of ATP.
Kinetochore Portion of the chromosome centromere that serves as an
attachment site for spindle microtubules.
Knock-out The biological outcome of inactivating or deleting a speci¬c
gene; also used to refer to the organism in which this has been
accomplished.
Lamin Any of a speci¬c class of intermediate ¬lament-type proteins that
form the ¬brous nuclear lamina beneath the nuclear envelope during
interphase.
Lateral inhibition Suppression of the propagation of an activity in a
spatially extended dynamical system, either by another activity emanating
from the same locus or by the local depletion of resources required for
the initial activity.
Ligand A molecule that binds to a different molecule, its receptor.
Laplace equation The equation that expresses the equilibrium condition of
a liquid surface, a consequence of Newton™s second law.
Limit cycle A special set of solutions of a system of ¬rst-order differential
equations that is located along a closed orbit (and thus periodically
GLOSSARY 283


traversed) in the state space of the functional variables comprising the
system.
Linear stability analysis A mathematical method applied to a system of
equations to classify the spatial patterns they describe as functions of the
various parameters they contain (e.g., the diffusion coef¬cients and rate
constants in reaction--diffusion equations).
Lipid A molecule of biological origin that is insoluble in water.
Lipid bilayer Planar con¬guration of lipid-containing amphipathic
molecules.
Loss angle (δ) A quantity constructed from the loss and storage moduli,
de¬ned by tan δ = G /G ; the absolute value of δ (between 0 and π/2)
gives a measure of how liquid (sol-like) or elastic (gel-like) is the
viscoelastic material.
Loss modulus (G ) One of the physical parameters characterizing a
viscoelastic material, namely, its ability to dissipate energy.
Lumen An open space within a tissue.
Lysis The breakdown of subcellular or supracellular molecular structure.
M phase The phase of the eukaryotic cell cycle during which mitosis
occurs.
M-phase-promoting factor A regulatory molecule in the eukaryotic cell
cycle consisting of a dimeric complex of the proteins cdc2 and cyclin.
Macromere A large cell that arises as a result of unequal early cleavages.
Marginal zone The middle region of an amphibian embryo, including the
equator de¬ned in relation to the animal and vegetal poles.
Maternal gene A gene that speci¬es a protein or RNA assembled into the
egg during oogenesis (e.g., bicoid, hunchback), often in a spatially
nonuniform fashion.
Matrix-driven translocation A phenomenon identi¬ed in model
extracellular matrices constructed in vitro, in which, following the
establishment of a sharp boundary between two matrices of differing
composition (e.g., containing or lacking particles), one matrix partially
engulfs the other.
Mediolateral The axis in a bilaterally symmetric embryo or organism
de¬ned by the direction from the central axis (e.g., notochord, vertebral
column) to the sides of the body. See also convergent extension.
Mediolateral intercalation Movement of cells between one another along
the embryo™s mediolateral axis during convergent extension so as to form
a longer, narrower cell mass.
Meiosis The process of two consecutive cell divisions in the diploid germ

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