Glossary

A

Abaxial muscles Muscles derived from the lateral portions of the myotome.

Acetylation See Histone acetylation.

Achondroplasia Condition wherein chondrocytes stop proliferating earlier than usual, resulting in short limbs (achondroplasic dwarfism). Often caused by mutations that activate the FgfR3 gene prematurely.

Acron Anterior region of the body of an arthropod (including insects); in front of the mouth and includes the brain.

Acrosomal process A fingerlike process in the sperm head extended by the polymerization of actin filaments during the early stages of fertilization in sea urchins and many other species. It contains surface molecules for species-specific recognition between sperm and egg.

Acrosome (acrosomal vesicle) Caplike organelle that, together with the sperm nucleus, forms the sperm head. Contains proteolytic enzymes that can digest the extracellular coats surrounding the egg, allowing the sperm to gain access to the egg cell membrane, to which it fuses.

Acrosome reaction The Ca²⁺-dependent fusion of the acrosome with the sperm cell membrane, resulting in exocytosis and release of proteolytic enzymes that allow the sperm to penetrate the egg extracellular matrix and fertilize the egg.

Actinomyosin contractions Contractile forces within a cell caused by myosin attaching to and moving along filamentous actin. Examples: contractions of muscle cells; apical constrictions of neural plate cells at the hinge points.

Actinopterygian fishes Ray-finned fish; includes teleosts.

Activins Members of the TGF-β superfamily of proteins; with Nodal, important in specifying the different regions of the mesoderm and for distinguishing the left and right body axes of vertebrates.

Adepithelial cells Cells that migrate into the imaginal discs early in the development of the holometabolous insect larva; these cells give rise to muscles and nerves in the pupal stage.

Adhesion Attachment between cells or between a cell and its extracellular substrate. The latter provides a surface for migrating cells to travel along.

Adult pluripotent stem cells Stem cells in an adult organism capable of regenerating all cell types of the adult. Example: neoblasts of planarian flatworms.

Adult stem cell niche Niche that houses adult stem cells and regulates stem cell self-renewal, survival, and differentiation of the progeny that leave the niche.

Adult stem cells Stem cells found in the tissues of organs after the organ has matured. Adult stem cells are usually involved in replacing and repairing tissues of that particular organ, forming a subset of cell types. Compare with Adult pluripotent stem cells; Embryonic stem cells.

Afferent Carrying to, as in neurons that carry information to the central nervous system (spinal cord and brain), from sensory receptor cells (e.g., sound waves from the ear, light signals from the retina, touch sensations from the skin); or vessels that carry fluid (e.g., blood) to a structure.

Aging The time-related deterioration of the physiological functions necessary for survival and reproduction.

Allantois In amniote species, extraembryonic membrane that stores urinary wastes and helps mediate gas exchange. It is derived from splanchnopleure at the caudal end of the primitive streak. In mammals, the size of the allantois depends on how well nitrogenous wastes can be removed by the chorionic placenta. In reptiles and birds, the allantois becomes a large sac, as there is no other way to keep the toxic by-products of metabolism away from the developing embryo.

Allometry Developmental changes that occur when different parts of an organism grow at different rates.

Alternation of generations In plants, a life cycle in which a haploid multicellular gamete-producing stage (the gametophyte) alternates with a diploid multicellular spore-producing stage (the sporophyte).

Alternative pre-mRNA splicing A means of producing multiple different proteins from a single gene by splicing together different sets of exons to generate different types of mRNAs.

Amacrine neurons Neurons of the vertebrate neural retina that lack large axons. Most are inhibitory. See also Neural retina.

Ametabolous A pattern of insect development in which there is no larval stage and the insect undergoes direct development to a small adult form following a transitory pronymph stage.

Amnion “Water sac.” A membrane enclosing and protecting the embryo and its surrounding amniotic fluid. Derived from the two layers of the somatopleure: ectoderm that supplies epithelial cells, and mesoderm that generates the connective tissue.

Amniote egg Egg that develops extraembryonic membranes (the amnion, chorion, allantois, and yolk sac) that provide nourishment and other environmental needs to the developing embryo. Characteristic of the amniote vertebrates: the reptiles and birds, in which the egg typically develops in a shell outside the mother’s body; and the mammals, where the egg has become modified to develop inside the mother.

Amniotes The groups of vertebrates in which the embryo develops an amnion (water sac) that surrounds the body of the embryo. Includes reptiles, birds, and mammals. Compare with Anamniote.

Amniotic fluid A secretion that serves as a “shock absorber” for the developing embryo while preventing it from drying out.

Ampulla Latin, “flask.” The segment of the mammalian oviduct, distal to the uterus and near the ovary, where fertilization takes place.

Anagen The growth phase of a hair ollicle, during which the hair grows in length.

Analogous Structures and/or their respective components whose similarity arises from their performing a similar function rather than their arising from a common ancestor (e.g., the wing of a butterfly vs. the wing of a bird). Compare with Homologous.

Anamniotes The fish and amphibians; i.e., the vertebrate groups that do not form an amnion during embryonic development. Compare with Amniotes.

Anchor cell (AC) The cell connecting the overlying gonad to the vulval precursor cells in C. elegans. If the anchor cell is destroyed, the VPCs will not form a vulva, but instead become part of the hypodermis.

Androgen insensitivity syndrome Intersex condition in which an XY individual has a mutation in the gene encoding the androgen receptor protein that binds testosterone. This results in a female external phenotype, lack of a uterus and oviducts and presence of abdominal testes.

Androgen Masculinizing substance, usually a steroid hormone such as testosterone.

Anencephaly A congenital defect (almost always lethal) resulting from failure to close the anterior neuropore. The forebrain remains in contact with the amniotic fluid and subsequently degenerates, so the vault of the skull fails to form.

Aneuploidy Condition in which one or more chromosome(s) is either lacking or present in multiple copies.

Aneurogenic Devoid of any neural innervation.

Angioblasts From angio, blood vessel; and blast, a rapidly dividing cell (usually a stem cell). The progenitor cells of blood vessels.

Angiogenesis Process by which the primary network of blood vessels created by vasculogenesis is remodeled and pruned into a distinct capillary bed, arteries, and veins.

Angiopoietins Paracrine factors that mediate the interaction between endothelial cells and pericytes.

Animal cap In amphibians, the roof of the blastocoel (in the animal hemisphere).

Animal hemisphere The upper half of an egg containing the animal pole. In the amphibian embryo, the cells in the animal hemisphere having little yolk divide rapidly and become actively mobile (“animated”).

Animal pole The pole of the egg or embryo where the concentration of yolk is relatively low; opposite end of the egg from the vegetal pole.

Anoikis Rapid apoptosis that occurs when epithelial cells lose their attachment to the extracellular matrix.

Anorectal junction The meeting of endoderm and ectoderm at the anus in vertebrate embryos.

Antennapedia complex A region of Drosophila chromosome 3 containing the homeotic genes labial (lab), Antennapedia (Antp), sex combs reduced (scr), deformed (dfd), and proboscipedia (pb), which specify head and thoracic segment identities.

Anterior heart field Cells of the heart field forming the outflow tract (conus and truncus arteriosus, right ventricle).

Anterior intestinal portal (AIP) The posterior opening of the developing foregut region of the primitive gut tube; it opens into the future midgut region which is contiguous with the yolk sac at this stage.

Anterior necrotic zone A zone of programmed cell death on the anterior side of the developing tetrapod limb that helps shape the limb.

Anterior neuropore See Neuropore.

Anterior visceral endoderm (AVE)  Mammalian equivalent to the chick hypoblast and similar to the head portion of the amphibian organizer, it creates an anterior region by secreting antagonists of Nodal.

Anterior-posterior (anteroposterior or AP) axis The body axis defining the head versus the tail (or mouth versus anus). When referring to the limb, this refers to the thumb (anterior)-pinkie (posterior) axis.

Anther A pollen-producing organ on the stamen (male portion) of a flower.

Anti-Müllerian hormone (AMH) TGF-β family paracrine factor secreted by the embryonic testes that induces apoptosis of the epithelium and destruction of the basal lamina of the Müllerian duct, preventing formation of the uterus and oviducts. Also known as anti-Müllerian factor, or AMF. Sometimes called Müllerian-inhibiting factor (MIF).

Anticlinal divisions In plants, cell divisions in which the new cell walls are laid down perpendicular to the surface of the plant. Compare with Periclinal divisions.

Anurans Frogs and toads. Compare with Urodeles.

Aorta-gonad-mesonephros region (AGM) A mesenchymal area in the lateral plate splanchnopleure near the ventral aorta that produces the hematopoietic stem cells.

Aortic arches These begin as symmetrically arranged, paired vessels that develop within the paired pharyngeal arches and link the ascending/ventral and descending/dorsal paired aortae. Some of the aortic arches degenerate.

Aperture An opening. In plants, this is an area on the walls of a pollen grain where the wall is thinner or softer so that the expanding pollen tube can exit.

Apical At the apex, or top. Example: The apical layer of your epidermis is the outermost layer, facing the external environment.

Apical constriction Constriction of the apical end of a cell, caused by localized contraction of actinomyosin complexes at the apical border. Apical ectodermal fold (AEF) The ectoderm overlying the mesenchyme of the developing fish fin that promotes fin ray development; derived from the original apical ectodermal ridge, which becomes the AEF in ray-finned fish after the proximal patterning of the stylopod.

Apical ectodermal ridge (AER) A ridge along the distal margin of the limb bud that will become a major signaling center for the developing limb. Its roles include (1) maintaining the mesenchyme beneath it in a plastic, proliferating state that enables the linear (proximal-distal) growth of the limb; (2) maintaining the expression of those molecules that generate the anterior-posterior axis; and (3) interacting with the proteins specifying the anterior-posterior and dorsal-ventral axes so that each cell is given instructions on how to differentiate.

Apical epidermal cap (AEC) Forms in the wound epidermis of an amputated salamander limb and acts similarly to the apical ectodermal ridge during normal limb development.

Apicobasal axis Apical-to-basal axis.

Apomixis Asexual reproduction in plants, where an embryo forms from cells that did not divide meiotically.

Apoptosis Programmed cell death. Apoptosis is an active process that prunes unneeded structures (e.g., frog tails, male mammary tissue), controls the number of cells in particular tissues, and sculpts complex organs (e.g., palate, retina, digits, and heart). See also Anoikis; Necrotic zones.

Aqueous humor Nourishing fluid that bathes the lens of the vertebrate eye and supplies pressure needed to stabilize the curvature of the eye.

Archenteron The primitive gut of an embryo. In the sea urchin, it is formed by invagination of the vegetal plate into the blastocoel.

Area opaca The peripheral ring of avian blastoderm cells that have not shed their deep cells.

Area pellucida A 1-cell-thick area in the center of the avian blastoderm (following shedding of most of the deep cells) that forms most of the actual embryo.

Aromatase Enzyme that converts testosterone to estradiol (a form of estrogen). Excess aromatase in the environment is linked to herbicides and other chemicals and is believed to contribute to reproductive disorders (demasculinization and feminization, particularly in male amphibians).

Arthrotome Mesenchymal cells in the center of the somite that contribute to the sclerotome, becoming the vertebral joints, the intervertebral discs, and those portions of the ribs closest to the vertebrae.

Astrocytes See Astroglial cells.

Astroglial cells (astrocytes) A diverse class of star (astro) shaped glial cells that carry out an array of functions, including establishing the blood-brain barrier, responding to inflammation in the CNS, and supporting synapse homeostasis and neural transmission.

Autocrine interaction The same cells that secrete paracrine factors also respond to them.

Autonomous specification A mode of cell commitment in which the blastomere inherits a determinant, usually a set of transcription factors from the egg cytoplasm, and these transcription factors regulate gene expression to direct the cell into a particular path of development.

Autophagy Intracellular system that removes and replaces damaged organelles and senescent cells.

Autopod The distal bones of a vertebrate limb: carpals and metacarpals (forelimb), tarsals and metatarsals (hindlimb), and phalanges (“digits”; the fingers and toes).

Autotrophy The process found in organisms such as plants and bacteria of synthesizing complex organic compounds using inorganic substances and light or chemical energy.

Auxin A family of plant hormones that regulate the growth and shape of the embryo as well as that of organs during adult stages. The most common is indole-3-acetic acid (IAA).

Axial protocadherin A type of protocadherin expressed in the presumptive notochord cells that allow them to separate from the paraxial (somite-forming) mesoderm to form the notochord. Found in amphibian embryos. See Protocadherin.

Axis determination The developmental process whereby the major body axes of an animal or plant are specified.

Axon Thin extension of the nerve cell body. Transmits signals (action potentials) to targets in the central and peripheral nervous systems. Axonal migration is crucial to development of the vertebrate nervous system.

Axoneme The portion of a cilium or flagellum consisting of two central microtubules surrounded by a row of 9 doublet microtubules. The motor protein dynein attached to the doublet microtubules provides the force for ciliary and flagellar function.

B

Bacteroid A special state of a bacterium, which has become differentiated as part of a symbiotic complex with legume roots.

Basal At the base, or bottom. Example: The basal layer of epidermal cells is the lowest layer, which sits on the basal lamina.

Basal disc The “foot” of a hydra; enables the animal to stick to rocks or the undersides of pond plants.

Basal lamina Specialized, closely knit sheets of extracellular matrix that underlie epithelia, composed largely of laminin and type IV collagen. Epithelial cells adhere to the basal lamina in part via binding between integrins and laminin. Sometimes called the basement membrane.

Basal layer (stratum germinativum) The inner layer of both the embryonic and adult epidermis. This layer contains epidermal stem cells attached to a basement membrane.

Basal transcription factors Transcription factors that specifically bind to the CpG-rich sites, forming a “saddle” that can recruit RNA polymerase II and position it for transcription.

Basic fibroblast growth factor (Fgf2) One of three growth factors required for the generation of hemangioblasts from the splanchnic mesoderm. See also Angiopoietins; Vascular endothelial growth factors (VEGFs).

Bergmann glia Type of glial cell; extends a thin process throughout the developing neuroepithelium of the cerebellum.

bHLH proteins The basic helix-loop-helix family of transcription factors, including such proteins as scleraxis, the MRFs (MyoD, Myf5, and myogenin), and c-Myc.

Bicoid Anterior morphogen critical for establishing anterior-posterior polarity in the Drosophila embryo. Functions as a transcription factor to activate anterior-specific gap genes and as a translational repressor to suppress posterior-specific gap genes.

Bilaminar germ disc An amniote embryo prior to gastrulation; consists of epiblast and hypoblast layers.

Bilateral holoblastic cleavage Cleavage pattern, found primarily in tunicates, in which the first cleavage plane establishes the right-left axis of symmetry in the embryo and each successive division orients itself to this plane of symmetry. Thus the half-embryo formed on one side of the first cleavage plane is the mirror image of the other side.

Bilaterians (triploblasts) Those animals characterized by bilaterian body symmetry and the presence of three germ layers (endoderm, ectoderm, and mesoderm). Includes all animal groups except the sponges, cnidarians, ctenophores, and placozoans.

Bindin A 30,500-Da protein on the acrosomal process of sea urchin sperm that mediates the species-specific recognition between the sperm and the egg vitelline envelope during fertilization.

Bindin receptors Species-specific receptors on the vitelline envelope of sea urchin eggs that bind to the bindin on the acrosomal process of sperm during fertilization.

Biofilm Mats of microorganisms, such as bacteria, that generate an extracellular matrix. These regulate larval settlement of many marine invertebrate species.

Bipolar interneurons Neurons in the neural retina, positioned between the photoreceptors (rods and cones) and ganglion cells for transmitting signals from the photoreceptors to the ganglion cells.

Bipotential (indifferent) gonad Common precursor tissue derived from the genital ridge in mammals, from which the male and female gonads diverge.

Bisphenol A (BPA) Synthetic estrogenic chemical compound used in plastics and flame retardants. BPA has been associated with meiotic defects, reproductive abnormalities, and precancerous conditions in rodents.

Bithorax complex The region of Drosophila chromosome 3 containing the homeotic gene Ultrabithorax (Ubx), which is required for the identity of the third thoracic segment, and the abdominal A (abdA) and Abdominal B (AbdB) genes, which are responsible for the segmental identities of the abdominal segments.

Bivalent The four chromatids of a homologous pair of chromosomes and their synaptonemal complex during prophase of the first meiotic division. Also called a tetrad.

Blastema A group of undifferentiated progenitor cells that form in some organisms at the site of an amputation; the blastema is able to grow and differentiate to replace the amputated tissue.

Blastocoel A fluid-filled cavity of the blastula stage of an embryo.

Blastocyst A mammalian blastula. The blastocoel is expanded and the inner cell mass is positioned on one side of the ring of trophoblast cells.

Blastoderm The layer of cells formed during cleavage at the animal pole in telolecithal eggs, as in fish, reptiles, and birds. Because the yolk concentrated in the vegetal region of the egg impedes cleavage, only the small amount of yolk-free cytoplasm at the animal pole is able to divide in these eggs. During development, the blastoderm spreads around the yolk as it forms the embryo.

Blastodisc Small region at the animal pole of the telolecithal eggs of fish, birds, and reptiles, containing the yolk-free cytoplasm where cleavage can occur and that gives rise to the embryo. Following cleavage, the blastodisc becomes the blastoderm.

Blastomere A cleavage-stage cell resulting from mitosis.

Blastopore The invagination point where gastrulation begins. In deuterostomes, this marks the site of the anus. In protostomes, this marks the site of the mouth. Blastula Early-stage embryo consisting of a sphere of cells surrounding an inner fluid-filled cavity, the blastocoel.

Blood islands Aggregations of hemangioblasts in the splanchnic mesoderm. It is generally thought that the inner cells of these blood islands become blood progenitor cells, while the outer cells become angioblasts.

BMP family See Bone morphogenetic proteins.

BMP4 A protein in the BMP family, used extensively in neural development; for example, BMP4 is produced by target organs innervated by the trigeminal nerve and causes differential growth and differentiation of the neurons. Also involved in bone differentiation. See Bone morphogenetic proteins.

Bone marrow-derived stem cells (BMDCs) See Mesenchymal stem cells.

Bone morphogenetic proteins (BMPs)  Members of the TGF-β superfamily of proteins. Originally identified by their ability to induce bone formation, BMPs are extremely multifunctional, having been found to regulate cell division, apoptosis, cell migration, and differentiation.

Bottle cells Invaginating cells during amphibian gastrulation, in which the main body of each cell is displaced toward the inside of the embryo while maintaining contact with the outside surface by way of a slender neck.

Brain-derived neurotrophic factor (BDNF) A paracrine factor that regulates neural activity and appears to be critical for synapse formation by inducing local translation of neural messages in the dendrites. BDNF is required for the survival of a particular subset of neurons in the striatum (a region of the brain involved in movement).

Brainbow Genetic method used to trigger the expression of different combinations and amounts of different fluorescent proteins within cells, labeling them with a seeming “rainbow” of possible colors that can be used to identify each individual cell in a tissue, organ, or whole embryo.

Branchial arches See Pharyngeal arches.

Brown adipose cells (brown fat) Adipose cells derived from the central dermomyotome. Brown fat cells produce heat, as opposed to white adipose cells that store lipids. Brown fat cells contain numerous mitochondria and dissipate energy as heat instead of synthesizing ATP.

Bulge A region of the hair follicle that is a niche for adult stem cells.

C

Cadherins Calcium-dependent adhesion molecules. Transmembrane proteins that interact with other cadherins on adjacent cells and are critical for establishing and maintaining intercellular connections, spatial segregation of cell types, and the organization of animal form.

Cajal-Retzius cells Reelin-secreting cells in the neocortex just under the pial surface. Reelin directs the migration of newly born neurons toward the pial surface.

Callus In plants, a growing mass of unorganized and undifferentiated cells that cover a wound; these cells can be induced to form a plant meristem and develop into shoots and/or roots.

Calorie restriction Dietary restriction as a means of extending mammalian longevity (at the expense of fertility).

Cambrian explosion The rapid diversification of life in the Cambrian period (approximately 541 million years ago) during which most major animal groups appeared, including those with species living today.

Canalization model In plants, a model for explaining the polarized transport of auxin along the apical to basal axis during vascular development and regeneration. In this model, the vasculature apical to the developing tissue or healing wound serves as the auxin source, and the row of increasingly basal developing or regenerating vascular cells serve as the auxin sink.

Canalization See Robustness.

Cancer stem cell hypothesis The hypothesis that the malignant part of a tumor is either an adult stem cell that has escaped the control of its niche or a more differentiated cell that has regained stem cell properties.

Cap sequence See Transcription initiation site.

Capacitation The set of physiological changes by which mammalian sperm become capable of fertilizing an egg.

Carcinogenesis The initiation of cancer whereby a non-cancerous cell is transformed into a cancerous cell.

Cardia bifida A condition in which two separate hearts form, resulting from manipulation of the embryo or genetic defects that prevent fusion of the two endocardial tubes.

Cardiac neural crest Subregion of the cranial neural crest that extends from the otic (ear) placodes to the third somites. Cardiac neural crest cells develop into melanocytes, neurons, cartilage, and connective tissue. Cardiac neural crest also contributes to the muscular-connective tissue wall of the large arteries (the “outflow tracts”) of the heart, as well as contributing to the septum that separates pulmonary circulation from the aorta.

Cardiogenic mesoderm See Heart fields.

Cardiomyocytes Cardiac cells derived from heart field tissue that form the muscular layers of the heart and its inflow and outflow tracts.

Carpel The female reproductive organ of an angiosperm flower, containing stigma, an ovary, and often a style. Sometimes called a Pistil.

Catagen Regression phase of the hair follicle regeneration cycle.

Catenins A complex of proteins that anchor cadherins inside the cell. The cadherin-catenin complex forms the classic adherens junctions that help hold epithelial cells together and, by binding to the actin (microfilament) cytoskeleton of the cell, integrate the epithelial cells into a mechanical unit. One of them, β-catenin, can also be a transcription factor.

β-Catenin A protein that can act as an anchor for cadherins or as a transcription factor (induced by the Wnt pathway). It is important in the specification of germ layers throughout the animal phyla.

CatSper Cation (usually, Ca²⁺) channels that seem to be specific to sperm. They are critical for sperm cell locomotion and guidance.

Caudal intestinal portal (CIP) The anterior opening of the developing hindgut region of the primitive gut tube; it opens into the future midgut region, which is contiguous with the yolk sac at this stage.

Caudal progenitor zone A region in the tailbud of vertebrate embryos that is made up of multipotent neuromesoderm progenitor cells. See also Neuromesoderm progenitors.

Caudal Referring to the tail.

Cavitation In mammalian embryos, a process whereby the trophoblast cells secrete fluid into the morula to create a blastocoel. The membranes of trophoblast cells pump sodium ions (Na⁺) into the central cavity, drawing in water osmotically and thus creating and enlarging the blastocoel.

Cell adhesion molecules Adhesion molecules that hold cells together. The major group of these is the cadherins. See also Cadherins.

Cell lineage The series of cell types starting from an undifferentiated, pluripotent stem cell through stages of increasing differentiation to the terminally differentiated cell type.

Cell wall An extracellular layer outside the cell membrane and surrounding the cells of plants, fungi, and many prokaryotes. In land plants, cell walls are rigid, containing cellulose, and other polymers; they inhibit cell movement and restrict the planes of cell division.

Cellular blastoderm Stage of Drosophila development in which all the cells are arranged in a single-layered jacket around the yolky core of the egg.

Cellularization The process of creating individual cells out of a multinucleated cell (a syncytium) by separating the nuclei by cell membranes. Example: During early development in the Drosophila embryo, the syncytial blastoderm is turned into a cellular blastoderm when cell membranes grow inward between the peripheral nuclei, separating off individual cells from the inner yolky cytoplasm.

Central dogma The explanation of the transfer of information coded in DNA to make proteins: DNA is transcribed into RNA, which is then translated into proteins.

Central nervous system (CNS) The brain and spinal cord of vertebrates.

Centrolecithal Type of egg, such as those of insects, that has yolk in the center and undergoes superficial cleavage.

Centromere A region of a chromosome where sister chromatids are attached to each other by the kinetochore.

Centrosome-attracting body (CAB)  Cellular structure that, in some invertebrate blastomeres, positions the centrosomes asymmetrically and recruits particular mRNAs so that the resulting daughter cells are different sizes and have different properties.

Cephalic furrow A transverse furrow formed during gastrulation in Drosophila that separates the future head region (procephalon) from the germ band, which will form the thorax and abdomen.

Cephalic neural crest See Cranial neural crest.

Cephalic Referring to the head.

Charophytic algae A group of freshwater green algae, an ancient member of which is thought to have been the common ancestor of all terrestrial plants (embryophytes).

Chemoaffinity hypothesis Hypothesis put forth by Sperry in 1965 suggesting that nerve cells in the brain acquire individual chemical tags that distinguish them from one another and that these guide the assembly and organization of the neural circuits in the brain.

Chemoattractant A biochemical that causes cells to move toward it.

Chemotaxis Movement of a cell down a chemical gradient, such as sperm following a chemical (chemoattractant) secreted by the egg.

Chiasmata Points of attachment between homologous chromosomes during meiosis that are thought to represent regions where crossing-over is occurring.

Chimera An organism consisting of a mixture of cells from two individuals.

Chimeric embryo Embryo made from tissues of more than one genetic source.

ChIP-Seq Chromatin immunoprecipitation sequencing. A lab protocol used to identify the precise DNA sequences bound by particular transcription factors or nucleosomes containing specific modified histones.

Choanoblastaea Considered to be the ancestor of all metazoans (multicellular animals); thought to have been a sphere of choanocytes that lived in the open ocean.

Choanocyte Found in sponges, it is a type of cell that contains a central flagellum surrounded by a collar of microvilli; choanocytes power the unidirectional flow of water through the sponge and also function as multipotent stem cells during sponge regeneration.

Choanoflagellates A group of unicellular and colonial free-living eukaryotes. The cells have the same basic structure as choanocytes of sponges, with a central flagellum surrounded by a collar of microvilli. Ancient choanoflagellates are considered to have been the common ancestor of all metazoans. See Choanoblastaea.

Chondrocyte-like osteoblasts Cranial neural crest cells undergoing early stages of intramembranous ossification. These cells downregulate Runx2 and begin expressing the osteopontin gene, giving them a phenotype similar to a developing chondrocyte.

Chondrocytes Cartilage cells.

Chondrogenesis Formation of cartilage, in which chondrocytes differentiate from condensed mesenchyme.

Chordamesoderm Axial mesoderm in a chordate embryo that produces the notochord. Chordate An animal that has, at some stage of its life cycle, a notochord and a dorsal nerve cord or neural tube.

Chordin A paracrine factor with organizer activity. Chordin binds directly to BMP4 and BMP2 and prevents their complexing with their receptors, thus inducing dorsal ectoderm to form neural tissue.

Chorioallantoic membrane Forms in some amniote species, such as birds, by fusion of the mesodermal layer of the allantoic membrane with the mesodermal layer of the chorion. This extremely vascular envelope is crucial for bird development and is responsible for transporting calcium from the eggshell into the embryo for bone production.

Chorion An extraembryonic membrane essential for gas exchange in amniote embryos. It is generated from the extraembryonic somatopleure. The chorion adheres to the shell in birds and reptiles, allowing the exchange of gases between the egg and the environment. It forms the embryonic/fetal portion of the placenta in mammals.

Chorionic villus sampling Taking a sample from the placenta at 8–10 weeks of gestation to grow fetal cells to be analyzed for the presence or absence of certain chromosomes, genes, or enzymes.

Chromatid Half of a mitotic prophase chromosome, which consists of duplicate “sister” chromatids that are attached to each other by the kinetochore.

Chromatin The complex of DNA and protein in which eukaryotic genes are contained.

Chromosome diminution The fragmentation of chromosomes just prior to cell division, resulting in cells in which only a portion of the original chromosome survives. Chromosome diminution occurs during cleavage in Parascaris aequorum in the cells that will generate the somatic cells while the future germ cells are protected from this phenomenon and maintain an intact genome.

Chromosomes Structures in a cell that contain genetic material in the form of deoxyribonucleic acid (DNA). In eukaryotes, they are contained within the nucleus and consist of DNA and proteins; they become condensed prior to cell division.

Ciliary body A vascular structure at the junction between the neural retina and the iris that secretes the aqueous humor.

Cis-regulatory elements Regulatory elements (promoters and enhancers) that reside on the same stretch of DNA as the gene they regulate.

Cleavage A series of rapid mitotic cell divisions following fertilization in many early embryos; cleavage divides the embryo without increasing its mass.

Cleavage furrow A groove formed in the cell membrane in a dividing cell due to tightening of the microfilamentous ring.

Cleft of Brachet In amphibian gastrulation, it is a region of extracellular matrix that separates the ectoderm from the involuting mesendoderm.

Cloaca Latin, “sewer.” An endodermally lined chamber at the caudal end of the embryo that will become the receptacle for waste from the intestine and the kidneys and products from the gonads. Amphibians, reptiles, and birds retain this organ and use it to void gametes and both liquid and solid wastes. In mammals, the cloaca becomes divided by a septum into the urogenital sinus and the rectum.

Cloacal membrane At the caudal end of the hindgut formed by closely apposed endoderm and ectoderm; future site of the anus.

Cloning See Somatic cell nuclear transfer.

Clonogenic neoblasts (cNeoblasts)  Pluripotent stem cells in flatworms that migrate to a wound site and regenerate the tissue; form the regeneration blastema of flatworms.

cNeoblasts See Clonogenic neoblasts.

Cochlea In amniotes, the portion of the inner ear involved in hearing. The mammalian cochlea is derived from the otic placode. It is spiral in shape and contains the organ of Corti, the sensory structure for hearing.

Cochleovestibular ganglion The ganglion adjacent to the otic vesicle. It forms the major neural connection between the brain and the inner ear structures.

Coelom Space between the somatic mesoderm and splanchnic mesoderm that becomes the body cavity. In mammals, the coelom becomes subdivided into the pleural, pericardial, and peritoneal cavities, enveloping the thorax, heart, and abdomen, respectively.

Coherence Scientific evidence that fits into a system of other findings and is therefore more readily accepted.

Cohesin proteins Protein rings that encircle the sister chromatids during meiosis, provide a scaffold for the assembly of the meiotic recombination complex, resist the pulling forces of the spindle microtubules, and thereby keep the sister chromatids attached during the first meiotic division and promote pairing of homologous chromosomes, allowing recombination.

Collective cell migration The movement of a sheet of cells, wherein the cells at the leading edge of the sheet in part provide the locomotory force, using pseudopodia to pull the rest of the cells forward. Cells behind the leading edge, being surrounded by other cells, are prevented from forming locomotory pseudopodia due to contact inhibition of cell movement. However, during chemoattractive responses the cells at the rear of the cluster can form actomyosin arrays that squeeze these cells forward.

Collective migration Migration of self-propelled cells exerting directionally coordinated forces upon one another, as opposed to individually migrating cells or the movement of a group of cells caused by tissue pushing due to proliferation or intercalation.

Colonial theory The theory, originally proposed by Ernst Haeckel in 1874, that multicellular organisms arose through the symbiosis of unicellular organisms of the same species.

Columns of Terni Groups of preganglionic autonomic motor neurons in the thoracic region that are among the motor neurons whose axons are migrating away from the spinal cord during vertebrate development.

Combinatorial association In developmental genetics, the principle that enhancers contain regions of DNA that bind transcription factors, and it is this combination of transcription factors that activates the gene.

Commensalism A symbiotic relationship that is beneficial to one partner and neither beneficial nor harmful to the other partner.

Commissureless (Comm) An endosomal protein in Drosophila, expressed in axons prior to their crossing the midline; functions to route Robo proteins to the lysosome instead of permitting their expression in the cell membrane.

Commitment Describes a state in which a cell’s developmental fate has become restricted even though it is not yet displaying overt changes in cellular biochemistry and function.

Committed stem cells Includes multipotent and unipotent stem cells that have the potential to become any of a relatively few cell types (multipotent) or only one cell type (unipotent).

Compaction A unique feature of mammalian cleavage, mediated by the cell adhesion molecule E-cadherin. The cells in the early (around eight-cell) embryo change their adhesive properties and become tightly attached to each other.

Comparative embryology Study of how anatomy changes during the development of different organisms.

Compensatory regeneration Form of regeneration in which the differentiated cells divide but maintain their differentiated functions (e.g., mammalian liver).

Competence The ability of cells or tissues to respond to a specific inductive signal.

Conditional specification The ability of cells to achieve their respective fates by interactions with other cells. What a cell becomes is in large measure specified by paracrine factors secreted by its neighbors.

Cones Color-sensitive photoreceptor cells in the neural retina. See Neural retina.

Congenital adrenal hyperplasia A condition causing female pseudo-hermaphroditism due to the presence of excess testosterone.

Congenital defect Any defect that an individual is born with. Congenital defects can be hereditary. or they can have an environmental cause (e.g., exposure to teratogenic plants, drugs, chemicals, radiation, etc.). They can also be idiopathic (i.e., cause is unknown).

Conjoined twins Monozygotic twins that share some part of their bodies; they may even share a vital organ, such as a heart or liver.

Consensus sequence When referring to an intron, these are located at the 5′ and 3′ ends of the introns that signal the “splice sites” of the intron.

Conserved dopamine neurotrophic factor (CDNF) A neurotrophin that enhances the survival of the midbrain dopaminergic neurons. See also Neurotrophin.

Contact inhibition of locomotion The mechanism whereby cells are prohibited from forming locomotory pseudopodia along contact surfaces with other cells. These interactions with the cell membranes of other cells prevent “backward” migration over other cells and result in “forward” migration of the leading edge of cells.

Context dependency The meaning or role of an individual component of a system (such as a transcription factor) is dependent on its context. For example, in the formation of tetrapod limb joints, the same BMPs can induce either cell death or cell differentiation, depending on the stage of the responding cell.

Conus arteriosus Cardiac outflow tract; along with the truncus arteriosus will become the base of the aorta and pulmonary arteries.

Convergent evolution The independent evolution of similar traits among organisms not closely related but adapting to a similar environment.

Convergent extension A phenomenon wherein cells intercalate to narrow the tissue and at the same time move it forward. Mechanism used for elongation of the archenteron in the sea urchin embryo, notochord of the tunicate embryo, and involuting mesoderm of the amphibian. This movement is reminiscent of traffic on a highway when several lanes must merge to form a single lane.

Coordinated gene expression The simultaneous expression of many different genes in a specific cell type. Its basis is often a single transcription factor (e.g., Pax6) that is crucial to several different enhancer sequences; the different enhancers are differentially “primed,” and the binding of the same factor to all of them activates all the genes at once.

Cornified layer (stratum corneum) The outer layer of the epidermis, consisting of keratinocytes that are now dead, flattened sacs of keratin protein with their nuclei pushed to one edge of the cell. These cells are continually shed throughout life and are replaced by new cells.

Corona radiata The innermost layer of cumulus cells around a mammalian egg, immediately adjacent to the zona pellucida.

Corpora allata Insect glands that secrete juvenile hormone (JH) during larval molts.

Correlative evidence Evidence based on the association of events. The “find it” of “find it, lose it, move it.” See also Gain-of-function evidence; Loss-of-function evidence.

Cortex An outer structure (in contrast with medulla, an inner structure).

Cortical cytoplasm A thin layer of gel-like cytoplasm lying immediately beneath the cell membrane of a cell. In an egg, the cortex contains high concentrations of globular actin molecules that will polymerize to form microfilaments and microvilli during fertilization.

Cortical granule reaction The basis of the slow block to polyspermy in many animal species, including sea urchins and most mammals. A mechanical block to polyspermy that in sea urchins becomes complete about a minute after successful sperm-egg fusion, in which enzymes from the egg’s cortical granules contribute to the formation of a fertilization envelope that blocks further sperm entry.

Cortical granules Membrane-bound, Golgi-derived structures located in the egg cortex; contain enzymes and other components. The exocytosis of these granules at fertilization is homologous to the exocytosis of the acrosome in sperm in the acrosome reaction.

Cortical plate The layer of cells in the developing cerebrum of mammals formed by neurons in the ventricular zone migrating outward along radial glial processes to a position near the outer surface of the brain, where they will set up the six layers of the neocortex.

Cotyledons The embryonic leaves contained within the seed of a plant, which provide nutrients that support embryogenesis and germination of the seedling. During germination, they emerge from the seed before true leaves are formed.

CpG islands Regions of DNA rich in the CpG sequence: a cytosine and a guanosine connected by a normal phosphate bond. Promoters often contain such islands, and transcription is often initiated nearby, possibly because they bind the basal transcription factors that recruit RNA polymerase II.

Cranial (cephalic) neural crest Neural crest cells in the future head region that migrate to produce the craniofacial mesenchyme, which differentiates into the cartilage, bone, cranial neurons, glia, and connective tissues of the face. These cells also enter the pharyngeal arches and pouches to give rise to thymic cells, the odontoblasts of the tooth primordia, and the bones of the middle ear and jaw.

Cranial sensory placodes Ectodermal thickenings that form in the cranial region of the vertebrate embryo; includes the olfactory (nasal), otic (ear), and lens (eye) placodes, and placodes that give rise to sensory neurons of various cranial nerves. Also called cranial ectodermal placodes.

Craniorachischisis The failure of the entire neural tube to close.

Cranium The vertebrate skull, composed of the neurocranium (skull vault and base) and the viscerocranium (jaws and other pharyngeal arch derivatives).

Cre-lox  A site-specific recombinase technology that allows control over the spatial and temporal pattern of a gene knockout or gene misexpression.

CRISPR Clustered Regularly Interspaced Short Palindromic Repeat. A stretch of DNA in prokaryotes that when transcribed into RNA serve as guides for recognizing segments of viral DNA. Used in association with Cas9 (CRISPR-associated enzyme 9) in a method for gene editing that is relatively fast and inexpensive.

Crossing over The exchange of genetic material during meiosis, whereby genes from one chromatid are exchanged with homologous genes from another.

Crown cells Cells neighboring the nodal cells, critical to setting up the left-right axis in the mammalian embryo. Crown cells each have a single immobile cilium that senses the left-to-right movement of fluids caused by the motile cilia on node cells. This sets up a cascade of events within the crown cells that serve to maintain Nodal expression on the left side, where it can activate Pitx1 genes, which determine the left and right-sidedness.

Crypt A deep tubular recess or pit. Example: intestinal crypts between the intestinal villi.

Crystallins Transparent, lens-specific proteins.

Cumulus  A layer of cells surrounding the mammalian egg, made up of ovarian follicular (granulosa) cells that nurture the egg until it is released from the ovary. The innermost layer of cumulus cells, the corona radiate, is released with the egg at ovulation.

Cutaneous appendages Species-specific epidermal modifications that include hairs, scales, scutes, feathers, hooves, claws, and horns.

CXCR4 The receptor for stromal-derived factor 1 (SDF1). See also Stromal-derived factor 1.

Cyclic adenosine 3′,5′-monophosphate (cAMP) An important component of several intracellular signaling cascades and the soluble chemotactic substance that directs the aggregation of the myxamoebae of Dictyostelium to form a grex.

Cyclin B The larger subunit of mitosis-promoting factor, shows the cyclical behavior that is key to mitotic regulation, accumulating during S and being degraded after the cells have reached M. Cyclin B regulates the small subunit of MPF, the cyclin-dependent kinase.

Cyclin-dependent kinase Small subunit of MPF, activates mitosis by phosphorylating several target proteins, including histones, the nuclear envelope lamin proteins, and the regulatory subunit of cytoplasmic myosin, resulting in chromatin condensation, nuclear envelope depolymerization, and the organization of the mitotic spindle. Requires cyclin B to function.

Cyclooxygenase-2 (COX2) An enzyme that generates prostaglandins from the fatty acid arachidonic acid.

Cyclopia Congenital defect characterized by a single eye, caused by mutations in genes that encode either Sonic hedgehog or the enzymes that synthesize cholesterol and can be induced by certain chemicals that interfere with the cholesterol biosynthetic enzymes.

Cystoblasts/cystocytes Derived from the asymmetric division of the germline stem cells of Drosophila, a cystoblast undergoes four mitotic divisions with incomplete cytokinesis to form a cluster of 16 cystocytes (one ovum and 15 nurse cells) interconnected by ring canals.

Cytokines Paracrine factors important in cell signaling and the immune response. During blood formation, they are collected and concentrated by the extracellular matrix of the stromal (mesenchymal) cells at the sites of hematopoiesis and are involved in blood cell and lymphocyte formation.

Cytokinesis The division of the cell cytoplasm into two daughter cells. The mechanical agent of cytokinesis is a contractile ring of microfilaments made of actin and the motor protein myosin. Each daughter cell receives one of the nuclei produced by nuclear division (karyokinesis).

Cytonemes Specialized filopodial projections that extend out from a cell (sometimes more than 100 µm) to make contact with another cell producing a paracrine factor. Paracrine factors may be delivered to target cells by attaching to receptors on the tips of cytonemes and traveling down the length of the cytonemes to the body of the target cells. A cytoneme can also extend from a cell producing a paracrine factor to make contact with a target cell.

Cytoplasmic bridges Continuity between adjacent cells that results from incomplete cytokinesis, e.g., during gametogenesis.

Cytoplasmic determinants Factors within the egg cytoplasm that determine cell fate; these are molecules, often transcription factors, that regulate gene expression. In autonomous specification, these are apportioned to different blastomeres of the early embryo. See Cytoplasmic determination factors.

Cytoplasmic determination factors Factors found in the cytoplasm of a cell that determine cell fate. Example: gradients of different cytoplasmic determination factors that dictate cell fate along the anterior-posterior axis are found in the syncytial blastoderm of the Drosophila embryo.

Cytoplasmic polyadenylation-element-binding-protein (CPEB) Protein that binds to mRNA in the 3′ UTR and helps to control translation. When phosphorylated, it allows for the elongation of the polyadenine (polyA) tail on the mRNA.

Cytotrophoblast Mammalian extraembryonic epithelium composed of the original trophoblast cells, it adheres to the endometrium through adhesion molecules and, in species with invasive placentation such as the mouse and human, secretes proteolytic enzymes that enable the cytotrophoblast to enter the uterine wall and remodel the uterine blood vessels so that the maternal blood bathes fetal blood vessels.

D

Dauer larva A metabolically dormant larval stage in C. elegans. See also Diapause.

De novo regeneration Regeneration of a structure anew (de novo) from cells that are reprogrammed to form the structure rather than from differentiated cells of that structure. For example, in certain plants de novo regeneration of whole organs is possible from single cells.

Decidua The maternal portion of the placenta, made from the endometrium of the uterus.

Decussate phyllotaxis In plants, the arrangement of lateral organs, such as leaves, in which successive opposite pairs of organs are offset by 180 degrees.

Deep cells A population of cells in the zebrafish blastula between the enveloping layer (EVL) and the yolk syncytial layer (YSL) that give rise to the embryo proper.

Deep homology Signal transduction pathways composed of homologous proteins arranged in a homologous manner that are used for the same function in both protostomes and deuterostomes.

Definitive endoderm The endoderm that enters the interior of the amniote embryo through the primitive streak during gastrulation, replacing the visceral endoderm, which is primarily forming the yolk sac and allantois along with the splanchnic lateral plate mesoderm.

Delamination The splitting of one cellular sheet into two more or less parallel sheets.

Delta protein Cell surface ligand for Notch; participates in juxtacrine interaction and activation of the Notch pathway.

Dendrites The fine, branching extensions (dendritic arbor) emanating from neurons; dendrites pick up electric impulses from other cells.

Dendritic arbor Extensive branching found in the dendrites of some neurons, such as Purkinje neurons.

Dental lamina A broad epidermal thickening in the jaw that later resolves into separate placodes, which together with the underlying mesenchyme form teeth.

Dermal bone Bone that forms in the dermis of the skin, such as most of the bones of the skull and face. They can be derived from head mesoderm or cranial neural crest-derived mesenchymal cells.

Dermal papilla A component of mesenchymal-epithelial induction during hair formation; a small node formed by dermal fibroblasts beneath the epidermal hair germ that stimulates proliferation of the overlying epidermal basal stem cells, which will give rise to the hair shaft.

Dermal tissue In animals, the tissue (the dermis) that underlies the epidermis; together they make up the skin. In plants, the tissue that makes up the outer layer (the epidermis) of the plant; epidermal cells and guard cells that surround stomata are examples of cell types found in dermal tissue.

Dermatome The central portion of the dermomyotome that produces the precursors of the dermis of the back and a population of muscle cells.

Dermomyotome Dorsolateral portion of the somite that contains skeletal muscle progenitor cells (including those that migrate into the limbs) and the cells that generate the dermis of the back.

Descent with modification Darwin’s theory to explain unity of type by descent from a common ancestor and to explain adaptations to the conditions of particular environments by natural selection.

Determination front Equivalent to the “wavefront” of the “clock-wavefront” model for somite formation; where boundaries of somites form, determined by a caudal^HIGH-to-rostral^LOW gradient of FGF in the presomitic mesoderm.

Determination The stage of commitment following specification; the determined stage, assumed irreversible, is when a cell or tissue is capable of differentiating autonomously even when placed into a non-neutral environment.

Determined Committed to a given fate. A cell is determined if it maintains its developmental maturation toward its fate even when placed in a new environment. See also Determination.

Deuterostomes In the deuterostome animal groups (including echinoderms, tunicates, cephalochordates, and vertebrates), during embryonic development the first opening (i.e., the blastopore) becomes the anus while the second opening becomes the mouth (hence, deutero stoma, “mouth second”). Compare with Protostomes.

Development The process of progressive and continuous change that generates a complex multicellular organism from a single cell. Development occurs throughout embryogenesis, maturation to the adult form, and continues into senescence.

Developmental biology The discipline that studies embryonic and other developmental processes, such as replacement of old cells by new, regeneration, metamorphosis, aging, and development of disease states such as cancer.

Developmental constraints In evolution, the limitation of the number and forms of possible phenotypes that can be created by the interactions that are possible among molecules and between modules in the developing organism.

Developmental plasticity The ability of an embryo or larva to react to an environmental input with a change in form, state, movement, or rate of activity (i.e., phenotypic change).

Dextral coiling  Right-coiling. In a snail, having its coils open to the right of its shell. See also Sinistral coiling.

Diacylglycerol (DAG) Second messenger generated in the IP₃ pathway from membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2), along with IP₃. DAG activates protein kinase C, which in turn activates a protein that exchanges sodium ions for hydrogen ions, raising the pH within the cell.

Diakinesis Greek, “moving apart.” In the first meiotic division, the stage that marks the end of prophase I, when the nuclear envelope breaks down and chromosomes migrate to the metaphase plate.

Diapause A metabolically dormant, nonfeeding stage of an organism during which development and aging are suspended; can occur at the embryonic, larval, pupal, or adult stage.

Dickkopf German, “thick head,” “stubborn.” A protein that interacts directly with the Wnt receptors, preventing Wnt signaling.

Dictyate resting stage The prolonged diplotene stage of the first meiotic division in mammalian primary oocytes. They remain in this stage until just prior to ovulation, when they complete meiosis I and are ovulated as secondary oocytes.

Diencephalon The caudal subdivision of the prosencephalon that will form the optic vesicles, retinas, pineal gland, and the thalamic and hypothalamic brain regions, which receive neural input from the retina.

Diethylstilbestrol (DES) A potent environmental estrogen. DES administration to pregnant women interferes with sexual and gonadal development in their female offspring resulting in infertility, subfertility, ectopic pregnancies, adenocarcinomas, and other effects.

Differential adhesion hypothesis A model explaining patterns of cell sorting based on thermodynamic principles. Cells interact so as to form an aggregate with the smallest interfacial free energy and therefore, the most thermodynamically stable pattern.

Differential gene expression A basic principle of developmental genetics: In spite of the fact that all the cells of an individual body contain the same genome, the specific proteins expressed by the different cell types are widely diverse. Differential gene expression, differential nRNA processing, differential mRNA translation, and differential protein modification all work to allow the extensive differentiation of cell types.

Differential RNA processing The splicing of mRNA precursors into messages that specify different proteins by using different combinations of potential exons.

Differentiation The process by which an unspecialized cell becomes specialized into one of the many cell types that make up the body.

Differentiation therapy Treatments for cancer that use transcription factors and other molecules to “normalize” cancers—that is, to cause cancerous cells to revert to differentiation rather than continued proliferation.

Digestive tube The primitive gut of the embryo, which extends the length of the body from the pharynx to the cloaca. Buds from the digestive tube form the thyroid, thymus, and parathyroid glands, lungs, liver, gallbladder, and pancreas.

5α-Dihydrotestosterone (DHT) A steroid hormone derived from testosterone by the action of the enzyme 5α-ketosteroid reductase 2. DHT is required for masculinization of the male urethra, prostate, penis, and scrotum.

Diploblasts “Two-layer” animals; they possess endoderm and ectoderm but most species lack true mesoderm. Includes the ctenophores (comb jellies) and cnidarians (jellyfish, corals, hydra, sea anemones). Compare with Bilaterians.

Diplotene Greek, “double threads.” In the first meiotic division, the fourth and last stage of prophase I, when the synaptonemal complex breaks down and the two homologous chromosomes start to separate but remain attached at points of chiasmata where crossing-over is occurring. Follows pachytene stage.

Direct development Embryogenesis characterized by the lack of a larval stage, where the embryo proceeds to construct a small adult.

Discoidal cleavage Meroblastic cleavage pattern for telolecithal eggs, in which the cell divisions occur only in the small blastodisc, as in birds, reptiles, and fish.

Discoidal meroblastic cleavage See Discoidal cleavage.

Disruption Abnormality or congenital defect caused by exogenous agents (teratogens) such as plants, chemicals, viruses, radiation, or hyperthermia.

Dissociation The ability of one module to develop differently from other modules.

Distal tip cell A single nondividing cell located at the end of each gonad in C. elegans that maintains the nearest germ cells in mitosis by inhibiting their going into meiosis.

Dizygotic twins “Two eggs.” Twins that result from two separate but approximately simultaneous fertilization events. Genetically such “fraternal” (Latin frater, “brother”) twins are full siblings. Compare with Monozygotic twins.

Dmrt1 Protein that in birds, frogs, and fish appears to activate Sox9, the central male-determining gene in vertebrates. Dmrt1 is also needed for maintaining testicular structures in mammals.

DNA methylation A method of controlling the level of gene transcription in vertebrates by the enzymatic methylation of the promoters of inactive genes. Certain cytosine residues that are followed by guanosine residues are methylated and the resulting methylcytosine stabilizes nucleosomes and prevents transcription factors from binding. Important in X chromosome inactivation and DNA imprinting.

DNA-binding domain Transcription factor domain that recognizes a particular DNA sequence.

Dormancy In seed plants, a prolonged period of quiescence that a seed can undergo prior to germination.

Dorsal blastopore lip Location of the involuting marginal zone cells of amphibian gastrulation. Migrating marginal cells sequentially become the dorsal lip of the blastopore, turn inward and travel along the inner surface of the outer animal cap cells (i.e., the blastocoel roof).

Dorsal closure A process that brings together the two sides of the epidermis of the Drosophila embryo at the dorsal surface.

Dorsal mesentery A derivative of the splanchnic mesoderm, this fibrous membrane connects the endoderm to the body wall. Involved in the looping of the developing intestines.

Dorsal root ganglia (DRG) Sensory spinal ganglia derived from the trunk neural crest that migrate along the ventral pathway and stay in the sclerotome. Sensory neurons of the DRG connect centrally with neurons in the dorsal horn of the spinal cord.

Dorsal-ventral (dorsoventral or DV) axis The plane defining the back (dorsum) versus the belly (ventrum). When referring to the limb, this axis refers to the knuckles (dorsal) and palms (ventral).

Dorsolateral hinge points (DLHPs) In the formation of the avian and mammalian neural tube, two hinge regions in the lateral sides of the neural plate that bend the two sides of the plate inward toward each other after the medial hinge point (MHP) has bent the plate along its midline.

Dorsolateral pathway Pathway taken by trunk neural crest cells traveling dorsolaterally beneath the ectoderm to become melanocytes.

Dosage compensation Equalization of expression of X chromosome-encoded gene products in male and female cells. Can be achieved by (1) doubling the transcription rate of the male X chromosomes (Drosophila), (2) partially repressing both X chromosomes (C. elegans), or (3) inactivating one X chromosome in each female cell (mammals).

Double fertilization In angiosperms, a process wherein one sperm nucleus combines with the egg nucleus to produce a zygote, while the other sperm combines with somatic cells to produce the triploid endosperm.

Double-negative gate A mechanism whereby a repressor locks the genes of specification, and these genes can be unlocked by the repressor of that repressor. (In other words, activation by the repression of a repressor.)

Doublesex (Dsx) A Drosophila gene active in both males and females, but whose RNA transcript is spliced in a sex-specific manner to produce sex-specific transcription factors: the female-specific transcription factor activates female-specific genes and inhibits male development; the male-specific transcription factor inhibits female traits and promotes male traits.

Down syndrome Syndrome caused by having an extra copy of chromosome 21 in humans; includes anomalies such as facial muscle changes, heart and gut abnormalities, and cognitive problems.

Ductus arteriosus A vessel that forms from left aortic arch VI, serves as a shunt between the embryonic/fetal pulmonary artery and the descending aorta in mammals. It normally closes at birth (if not, a pathological condition results called patent ductus arteriosus).

Duplication and divergence Tandem gene duplications resulting from replication errors. Once replicated, the gene copies can diverge by random mutations developing different expression patterns and new functions.

Dynein A motor protein that travels along microtubules. It is an ATPase, an enzyme that hydrolyzes ATP, converting the released chemical energy into mechanical energy. In cilia and flagella, dynein is attached to the axoneme microtubules that provides the force for propulsion by allowing the active sliding of the outer doublet microtubules, causing the flagellum or cilium to bend.

Dysgenesis Greek, “bad beginning.” Refers to defective development.

E

20E See 20-Hydroxyecdysone.

E-cadherin A type of cadherin expressed in epithelial tissues as well as all early mammalian embryonic cells (the E stands for epithelial). See Cadherins.

Early allocation and progenitor expansion model An alternative to the progress zone model of proximal-distal specification of the limb, wherein the cells of the entire early limb bud are already specified; subsequent cell divisions simply expand these cell populations.

Ecdysone Insect steroid hormone, secreted by the prothoracic glands, that is modified in peripheral tissues to become the active molting hormone 20-hydroxyecdysone. Crucial to insect metamorphosis.

Ecdysone receptor (EcR) Nuclear protein that binds to ecdysone in insects; when bound it forms an active complex with another protein that binds to DNA, inducing transcription of ecdysone-responsive genes. Evolutionarily related to, and almost identical in structure to, thyroid hormone receptors.

Ecdysozoans One of the two major protostome groups; characterized by exoskeletons that periodically molt. The arthropods (including insects and crustaceans) and the nematodes (roundworms, including the model organism C. elegans) are two prominent groups. See also Lophotrochozoans.

Ecological evolutionary developmental biology (eco-evo-devo) The science studying the ways by which developmental changes initiated by the environment can affect evolution. It deals primarily with the evolutionary aspects of developmental symbiosis, developmental plasticity, and niche construction.

Ecomorph See Morph.

Ectoderm Greek ektos, “outside.” The cells that remain on either the outside (amphibian) or dorsal (avian, mammalian) surface of the embryo following gastrulation. Of the three germ layers, the ectoderm forms the nervous system from the neural tube and neural crest; also generates the epidermis covering the embryo.

Ectodermal appendage placodes Thickenings of the epidermal ectoderm involved in forming non-sensory structures such as hair, teeth, feathers, mammary and sweat glands.

Ectodermal appendages Structures that form from specific regions of epidermal ectoderm and underlying mesenchyme through a series of interactive inductions; includes hairs, scales, scutes (such as the coverings of turtle shells), teeth, sweat glands, mammary glands, and feathers.

Ectodermal placodes Thickenings of the surface ectoderm in embryos that become the rudiment of numerous organs. Includes cranial placodes, ectodermal appendage placodes.

Ectodysplasin (EDA) cascade A gene cascade specific for cutaneous appendage formation. Vertebrates with dysfunctional EDA proteins exhibit a syndrome called anhidrotic ectodermal dysplasia characterized by absent or malformed cutaneous appendages (hair, teeth, and sweat glands).

Efferent Carried away from. Often used in reference to neurons that carry information away from the central nervous system (brain and spinal cord) to be acted on by the peripheral nervous system (muscles), or a vessel that carries fluid away from a structure. Compare with Afferent.

Efferent ducts Ducts that link the rete testis to the Wolffian duct, formed from remodeled tubules of the mesonephric kidney.

Efflux transport A process found whereby transporter proteins move a substance from the inside to the outside of a cell. Example: PIN proteins in plants use efflux transport to move auxin from inside to outside the cell.

Egg chamber An ovariole or egg tube (over a dozen per ovary) in which the Drosophila oocyte will develop, containing 15 interconnected nurse cells and a single oocyte.

Egg jelly A glycoprotein meshwork outside the vitelline envelope in many species, most commonly it is used to attract and/or to activate sperm.

Embryo A developing organism prior to birth or hatching. In humans, the term embryo generally refers to the early stages of development, starting with the fertilized egg until the end of organogenesis (first 8 weeks of gestation). After this, the developing human is called a fetus until its birth.

Embryo sac The female gametophyte of an angiosperm. Found inside the ovule, it consists of eight or fewer cells formed by the division of the haploid nucleus of the megaspore cell. See also Megaspores.

Embryogenesis The stages of development between fertilization and hatching (or birth).

Embryology The study of animal development from fertilization to hatching or birth.

Embryonic axis Any of the positional axes in an embryo; includes anterior-posterior (head-tail), dorsal-ventral (back-belly), and right-left.

Embryonic epiblast In mammals, the epiblast cells that contribute to the embryo proper that split off from the epiblast cells that line the amniotic cavity.

Embryonic germ cells (EGCs) Pluripotent embryonic cells with characteristics of the inner cell mass derived from PGCs that have been treated particular paracrine factors to maintain cell proliferation.

Embryonic period In human development, the first 8 weeks in utero prior to the fetal period; the time during which most organ systems form.

Embryonic shield A localized thickening on the future dorsal side of the fish embryo; functionally equivalent to the dorsal blastopore lip of amphibians.

Embryonic stem cells (ESCs) Pluripotent stem cells derived from cultures of the mammalian inner cell mass blastomeres that are capable of generating all the cell types of the body.

Embryophytes Land plants. These are named embryophytes because they all undergo embryogenesis.

Emergent properties See Level-specific properties and emergence.

EMT See Epithelial-mesenchymal transition.

Enamel knot The signaling center for tooth development, a group of cells induced in the epithelium by the neural crest-derived mesenchyme that secretes paracrine factors that pattern the cusp of the tooth.

Endfoot A swollen membrane extension at the basal end of the neuroepithelial or radial glial cell. Radial glial endfeet wrap around blood vessels in the brain to establish the blood-brain barrier.

Endoblast See Secondary hypoblast.

Endocardial cushions Tissue in the developing vertebrate heart derived from the endocardium. It forms the septa that divide the atrioventricular area of the originally tubular heart into left and right atria and ventricles in amniotes; in amphibians, it separates the two atria (the ventricle remains undivided; in fish, all chambers remain undivided). The endocardial cushions also form the atrioventricular valves.

Endocardium The internal lining of the heart chambers, derived from the heart fields.

Endochondral ossification Bone formation in which mesodermal mesenchyme becomes cartilage and the cartilage is replaced by bone. It characterizes the bones of the trunk and limbs.

Endocrine disruptors Hormonally active compounds in the environment (e.g., DES; BPS; aromatase) that can have major detrimental effects on development, particularly of the gonads. Many endocrine disruptors are also obesogens (cause increased production of fat cells and fat accumulation).

Endocrine factors Hormones that travel through the blood to their target cells and tissues to exert their effects.

Endoderm Greek endon, “within.” The innermost germ layer; forms the epithelial lining of the respiratory tract, the gastrointestinal tract, and the accessory organs (e.g., liver, pancreas) of the digestive tract. In the amphibian embryo, the yolk-containing cells of the vegetal hemisphere become endoderm. In amniote embryos, the endoderm is the most ventral of the three germ layers, and also forms the epithelium of the yolk sack and allantois.

Endomesoderm The combination of endodermal and mesodermal cells.

Endometrium The epithelial lining of the uterus.

Endosome A membrane-bound vesicle that is internalized by a cell through endocytosis. Internalizing ligand-receptor complexes in endosomes is a common mechanism in paracrine signaling.

Endosperm A triploid seed tissue found in angiosperms, providing nutrition for the developing embryo.

Endosteal osteoblasts Osteoblasts that line the bone marrow and are responsible for providing the niche that attracts hematopoietic stem cells (HSCs), prevents apoptosis, and keeps the HSCs in a state of plasticity.

Endosymbiosis Greek, “living within.” Describes the situation in which one cell lives inside another cell or one organism lives within another.

Endothelins Small peptides secreted by blood vessels that have a role in vasoconstriction and can direct the migration of certain neural crest cells as well as the extension of certain sympathetic axons that have endothelin receptors, e.g. targeting of neurons from the superior cervical ganglia to the carotid artery.

Endothelium The single-layer sheet of epithelial cells lining of the blood vessels.

Energids In Drosophila, the nuclei at the periphery of the syncytial blastoderm and their associated cytoplasmic islands of cytoskeletal proteins.

Enhancer A DNA sequence that controls the efficiency and rate of transcription from a specific promoter. Enhancers bind specific transcription factors that activate the gene by (1) recruiting enzymes (such as histone acetyltransferases) that break up the nucleosomes in the area or (2) stabilizing the transcription initiation complex.

Enhancer modularity The principle that having multiple enhancers allows a protein to be expressed in several different tissues while not being expressed at all in others, according to the combination of transcription factor proteins the enhancers bind.

Enteric ganglia See Parasympathetic ganglia.

Enterocoely The embryonic process of forming the coelom by extending mesodermal pouches from the gut. Typical of most deuterostomes. See also Schizocoely.

Enveloping layer (EVL) A cell population in the zebrafish embryo at the mid-blastula transition made up of the most superficial cells from the blastoderm, which form an epithelial sheet a single cell layer thick. The EVL is an extraembryonic protective covering that is sloughed off during later development.

Environmental integration Describes the influence of cues from the environment surrounding the embryo, fetus, or larva on their development.

Ependyma Epithelial lining of the spinal cord canal and the ventricles of the brain.

Ependymal cells Epithelial cells that line the ventricles of the brain and canal of the spinal cord; they secrete cerebrospinal fluid.

Eph receptors Receptor for ephrin ligands.

Ephrins Juxtacrine ligands. Binding between an ephrin ligand on one cell and an Eph receptor on an adjacent cell results in signals being sent to both cells. These signals are often those of either attraction or repulsion, and ephrins are often seen directing cell migration and defining where cell boundaries are to form. As well as directing neural crest cell migration, ephrins and Eph receptors function in the formation of blood vessels, neurons, and somites.

Epialleles Variants of chromatin structure that can be inherited between generations. In most known cases, epialleles are differences in DNA methylation patterning that are able to affect the germ line and thereby be transmitted to offspring.

Epiblast The outer layer of the thickened margin of the epibolizing blastoderm in the gastrulating fish embryo or the upper layer of the bilaminar gastrulating embryonic disc in amniotes (reptiles, birds and mammals. The epiblast contains ectoderm precursors in fish and all three germ layer precursors of the embryo proper (plus the amnion) in amniotes. It also forms the avian chorion and allantois.

Epiboly The movement of epithelial sheets (usually of ectodermal cells) that spread as a unit (rather than individually) to enclose the deeper layers of the embryo. Epiboly can occur by the cells dividing, by the cells changing their shape, or by several layers of cells intercalating into fewer layers. Often, all three mechanisms are used.

Epibranchial placodes A subgroup of cranial placodes that form in the pharyngeal region of the vertebrate embryo. Gives rise to the sensory neurons of three cranial nerves: facial (VII), glossopharyngeal (IX), and vagus (X).

Epicardium The outer surface of the heart that forms the coronary blood vessels that feed the heart, derived from the heart fields.

Epidermal placodes The thickenings of epidermal ectoderm associated with ectodermal appendages. See Ectodermal appendage placodes.

Epidermis Outer layer of the skin, derived from ectoderm.

Epididymis Derived from the Wolffian duct, the tube adjacent to the testis that links the efferent tubules to the ductus deferens.

Epigenesis The view supported by Aristotle and William Harvey that the organs of the embryo are formed de novo (“from scratch”) at each generation.

Epigenetics The study of mechanisms that act on the phenotype without changing the nucleotide sequence of the DNA. Specifically, these changes work “outside the gene” (i.e., epigenetically) by altering gene expression rather than by altering the gene sequence as mutation does. Epigenetic changes can sometimes be transmitted to future generations, a phenomenon referred to as epigenetic inheritance.

Epimorphic regeneration See Epimorphosis.

Epimorphin A multifunctional protein: in the membranes of mesenchymal cells, it directs epithelial morphogenesis; when expressed by sclerotome cells, it acts to attract further prechondrogenic sclerotome cells to the region of the notochord and neural tube, where the cells form vertebrae.

Epimorphosis Form of regeneration observed when adult structures undergo dedifferentiation to form a relatively undifferentiated mass of cells that then redifferentiates to form the new structure (e.g., amphibian limb regeneration).

Epiphyseal plates Cartilaginous growth zones at the proximal and distal ends of the long bones that allow continued bone growth.

Episomal vectors Vehicles for gene delivery usually derived from viruses that do not insert themselves into host DNA.

Epithelial cells Cells of an epithelium. See Epithelium

Epithelial-mesenchymal interactions Induction involving interactions of sheets of epithelial cells with adjacent mesenchymal cells. Properties of these interactions include regional specificity (when placed together, the same epithelium develops different structures according to the region from which the mesenchyme was taken), genetic specificity (the genome of the epithelium limits its ability to respond to signals from the mesenchyme, i.e., the response is species-specific).

Epithelial-mesenchymal transition (EMT) An orderly series of events whereby epithelial cells are transformed into mesenchymal cells. In this transition, a polarized stationary epithelial cell, which normally interacts with basement membrane through its basal surface, becomes a migratory mesenchymal cell that can invade tissues and form organs in new places. See also Mesenchymal-to-epithelial transition.

Epithelium Epithelial cells tightly linked together on a basement membrane to form a sheet or tube with little extracellular matrix. Plural, epithelia.

Equatorial region The junction between the inner acrosomal membrane and the sperm cell membrane in mammals. It is exposed by the acrosomal reaction and is where membrane fusion between sperm and egg begins.

Equivalence group In the development of C. elegans, the group of six vulval precursor cells, each of which is competent to become induced by the anchor cell.

Erythroblast Cell that matures from the proerythroblast and synthesizes enormous amounts of hemoglobin.

Erythrocyte The mature red blood cell that enters the circulation where it delivers oxygen to the tissues. It is incapable of division, RNA synthesis, or protein synthesis. Amphibians, fish, and birds retain the functionless nucleus; mammals extrude it from the cell.

Erythroid progenitor cell A committed stem cell that can form only red blood cells.

Erythropoietin A hormone that acts on erythroid progenitor cells to produce proerythroblasts, which will generate red blood cells.

ESCs See Embryonic stem cells.

Estrogen A group of steroid hormones (including estradiol) needed for complete postnatal development of the Müllerian ducts (in females) and the Wolffian ducts (in males). Necessary for fertility in both sexes.

Estrus Greek oistros, “frenzy.” The estrogen-dominated stage of the ovarian cycle in female non-human mammals that are spontaneous or periodic ovulators, characterized by the display of behaviors consistent with receptivity to mating. Also called “heat.”

Euchromatin The comparatively open state of chromatin that contains most of the organism’s genes, most of which are capable of being transcribed. Compare with Heterochromatin.

Eukaryotic initiation factor-4 (eIF4E) A protein that is important for the initiation of translation. Binds to the 5′ cap of mRNAs and contributes to the protein complex that mediates RNA unwinding; brings the 3′ end of the message next to the 5′ end, allowing the mRNA to bind to and be recognized by the ribosome. Interacts with eukaryotic initiation factor-4G (eIF4G), a scaffold protein that allows the mRNA to bind to the ribosome.

Eukaryotic organisms Organisms whose cells contain membrane-bound organelles, including a nucleus with chromosomes that undergo mitosis. Can be single-celled or multicellular.

Evolutionary developmental biology (“evo-devo”) A model of evolution that integrates developmental genetics and population genetics to explain and the origin of biodiversity.

Exine The outer coating of a pollen grain or spore. It is extremely resistant to decay.

Exon In a gene, the region or regions of DNA that encode the protein. Compare with Intron.

Exosomes A type of membrane-bound extracellular vesicles that are released from cells and which may contain proteins and RNAs that can influence the development of other cells that receive them.

Extant Still in existence, such as extant species.

Extended evolutionary synthesis A model of evolution emphasizing developmental plasticity, epigenetic inheritance, niche constriction, and the reciprocal interactions between the organism and its environment.

External granular layer A germinal zone of cerebellar neuroblasts that migrate from the germinal neuroepithelium to the outer surface of the developing cerebellum.

External YSL (eYSL) A region of the yolk syncytial layer (YSL) in fish embryos. The eYSL forms from yolk syncytial nuclei that move further vegetally, staying ahead of the blastoderm margin as the blastoderm expands to surround the yolk cell. See Yolk syncytial layer.

Extracellular matrix (ECM) Macromolecules secreted by cells into their immediate environment, forming a region of noncellular material in the interstices between the cells. Extracellular matrices are made up of collagen, proteoglycans, and a variety of specialized glycoprotein molecules such as fibronectin and laminin.

Extraembryonic endoderm Formed by delamination of the hypoblast cells from the avian epiblast or mammalian inner cell mass to line the yolk sac.

Extraembryonic vasculogenesis The formation of blood islands in the yolk sac (i.e., outside the embryo).

Eye field Region in the anterior portion of the neural tube that will develop into the neural and pigmented retinas.

F

Fasciculation In neural development, the process of one axon adhering to and using another axon for growth.

Fast block to polyspermy Mechanism by which additional sperm are prevented from fusing with a fertilized sea urchin egg by changing the electric potential to a more positive level. Has not been demonstrated in mammals.

Fate map Diagrams based on having followed cell lineages from specific regions of the embryo in order to “map” larval or adult structures onto the region of the embryo from which they arose. The superimposition of a map of “what is to be” onto a structure that has yet to develop into these organs.

Female pronucleus The haploid nucleus of the egg.

Fertilization cone An extension from the surface of the egg where the egg and sperm have fused during fertilization. Caused by polymerization of actin, it provides a connection that widens the cytoplasmic bridge between egg and sperm, allowing the sperm nucleus and proximal centriole to enter the egg.

Fertilization envelope Forms from the vitelline envelope of the sea urchin egg following cortical granule release. Glycosaminoglycans released by the cortical granules absorb water to expand the space between the cell membrane and fertilization envelope.

Fertilization Fusion of male and female gametes followed by fusion of the haploid gamete nuclei to restore the full complement of chromosomes characteristic of the species and initiation in the egg cytoplasm of those reactions that permit development to proceed.

Fetal alcohol syndrome (FAS) Condition of babies born to alcoholic mothers, characterized by small head size, specific facial features, and small brain that often shows defects in neuronal and glial migration. FAS is the most prevalent congenital mental retardation syndrome. Another term, fetal alcohol spectrum disorder (FASD) has been coined to encompass the less visible behavioral effects on children exposed prenatally to alcohol.

Fetal period In human development, the period following the embryonic period, from the end of 8 weeks to birth; the period after organ systems have mostly formed and generally growth and modeling is occurring.

α-Fetoprotein In mammals, a protein that binds and inactivates fetal estrogen, but not testosterone, in both male and female fetuses and shown in rodents to be critical for normal sexual differentiation of the brain.

Fetus The stage in mammalian development between the embryonic stage and birth, characterized by growth and modeling. In humans, from the ninth week of gestation to birth.

Fibroblast growth factor 9 (Fgf9) A growth factor involved in testes development in mammals, stimulating proliferation and differentiation in Sertoli cells and their maintenance of Sox9 expression. Suppresses Wnt4 signaling, which would otherwise direct ovarian development. Also involved in metanephric kidney development, promoting development of a population of stem cell for nephrons. See also Fibroblast growth factors.

Fibroblast growth factor receptors (FGFRs) A set of receptor tyrosine kinases that are activated by FGFs, resulting in activation of the dormant kinase and phosphorylation of certain proteins (including other FGF receptors) within the responding cell.

Fibroblast growth factors (FGFs)  A family of paracrine factors that regulate cell proliferation and differentiation.

Fibronectin A very large (460 kDa) glycoprotein dimer synthesized by numerous cell types and secreted into the extracellular matrix. Functions as a general adhesive molecule, linking cells to one another and to other substrates such as collagen and proteoglycans, and provides a substrate for cell migration.

Filopodia Long, thin processes containing microfilaments; cells can move by extending, attaching, and then contracting filopodia. Produced e.g. by migrating mesenchyme cells in sea urchin embryos, growth cones for nerve outgrowth, tip cells in blood vessel formation.

Fin bud Bud of tissue in fish embryos that gives rise to a fin; homologous to the limb bud of tetrapods.

First polar body The smaller cell produced when a primary oocyte goes through its first meiotic division, producing one large cell, the secondary oocyte, which retains most of the cytoplasm, and a tiny cell, the first polar body, which is ultimately lost. Both cells are haploid.

Flagellum A long, motile extension of a cell containing a central axoneme of microtubules in a 9+2 arrangement (9 outer doublets and 2 central singlets). Its whipping action (“flagellation”) functions for propulsion, as in the tail of a sperm.

Floor plate Ventral region of the neural tube important in establishing dorsal-ventral polarity. Induced to form by Sonic hedgehog secreted from the adjacent notochord. It becomes a secondary signaling center that also secretes Sonic hedgehog, establishing a gradient that is highest ventrally.

Floral MADS-box genes Genes of flowering plants that code for MADS-box transcription factors involved in floral development. The MADS-box is a conserved sequence that codes for a specific DNA-binding domain.

Floral meristem identity genes A set of genes in angiosperms whose expression starts flower development, activating the floral organ identity genes to switch meristem cells from a proliferative to a reproductive fate. See also Floral organ identity genes.

Floral organ identity genes Angiosperm genes (sets A, B, C, D, and E) that determine the locations and fates of floral meristem cells.

Fluorescent dye Compounds, such as fluorescein and green fluorescent protein (GFP), that emit bright light at a specific wavelength when excited with ultraviolet light.

Focal adhesions Where the cell membrane adheres to the extracellular matrix in migrating cells, mediated by connections between actin, integrin and the extracellular matrix.

Follicle A small group of cells around a cavity. E.g., mammalian ovarian follicle, composed of a single ovum surrounded by granulosa cells and thecal cells; hair follicle, feather follicle, where a hair or feather is produced.

Follicle-stimulating hormone (FSH)  A peptide hormone secreted by the mammalian pituitary that promotes ovarian follicle development and spermatogenesis.

Follicular stem cells Multipotent adult stem cells that reside in the bulge niche of the hair follicle. They give rise to the hair shaft and sheath.

Follistatin A paracrine factor with organizer activity, an inhibitor of both activin and BMPs, causes ectoderm to become neural tissue.

Foot activation gradient A gradient, highest at the basal disc, that appears to be present in Hydra that permits the basal disc to form only in one place.

Foramen ovale In the fetal mammalian heart, an opening in the septum separating the right and left atria.

Forkhead transcription factors Transcription factors (e.g., Fox proteins, HNF4α) that are especially important in the endoderm that will form liver, where they help activate the regulatory regions surrounding liver-specific genes.

Forward genetics Genetic technique of exposing an organism to an agent that causes random mutations and screening for particular phenotypes. Compare with Reverse genetics.

Frizzled Transmembrane receptor for Wnt family of paracrine factors.

Frontonasal process Cranial prominence formed by neural crest cells from the midbrain and rhombomeres 1 and 2 of the hindbrain that forms the forehead, the middle of the nose, and the primary palate.

Fruit In flowering plants, a ripened and mature seed-containing ovary or ovaries.

G

G protein A protein that binds GTP and is activated or inactivated by GTP modifying enzymes (such as GTPases). They play important roles in the RTK pathway and in cytoskeletal maintenance.

Gain-of-function evidence A strong type of evidence, wherein the initiation of the first event causes the second event to happen even in instances where or when neither event usually occurs. The “move it” of “Find it, lose it, move it.” See also Correlative evidence; Loss-of-function evidence.

Gamete A specialized reproductive cell through which sexually reproducing parents pass chromosomes to their offspring; an egg or a sperm.

Gametogenesis The production of gametes.

Gametophytic Referring to the gametophyte, the haploid stage of the alternating life cycle in plants and algae that produces gametes (eggs and sperm); the sexual phase. Compare with Sporophytic.

Ganglia Clusters of neuronal cell bodies whose axons form a nerve. Singular, ganglion.

Gap genes Drosophila zygotic genes expressed in broad (about three segments wide), partially overlapping domains. Gap mutants lacked large regions of the body (several contiguous segments).

Gastrula A stage of the embryo following gastrulation that contains the three germ layers that will interact to generate the organs of the body.

Gastrulation A process involving movement of the blastomeres of the embryo relative to one another resulting in the formation of the three germ layers of the embryo. GDNF See Glial-derived neurotrophic factor.

GEF See GTP exchange factor; RTK pathway.

Gene regulatory networks (GRNs) Patterns generated by the interactions among transcription factors and their enhancers that help define the course that development follows.

Generative cell In angiosperms, the cell of a pollen grain that divides to produce the two male gamete nuclei.

Genetic assimilation The process by which a phenotypic character initially produced only in response to some environmental influence becomes, through a process of selection, taken over by the genotype so that it is formed even in the absence of the environmental influence that had first been necessary.

Genetic heterogeneity The production of similar phenotypes by mutations in different genes.

Geniculate placodes A pair of epibranchial placodes in vertebrates; they give rise to the sensory components of the paired 7th cranial nerve (the facial nerve) and innervate tastebuds, tonsils and ear lobes.

Genital disc Region of the Drosophila larva that will generate male or female genitalia. Male and female genitalia are derived from separate cell populations of the genital disc, as induced by paracrine factors.

Genital ridge A thickening of the splanchnic mesoderm and of the underlying intermediate mesodermal mesenchyme on the medial edge of the mesonephros; it forms the testis or ovary. Also called the germinal ridge. See also Germinal epithelium.

Genital tubercle A structure cranial to the cloacal membrane during the indifferent stage of differentiation of the mammalian external genitalia. It will form either the clitoris in the female fetus or the penis in the male.

Genome The complete DNA sequence of an individual organism.

Genomic equivalence The theory that every cell of an organism has the same genome as every other cell.

Genomic imprinting A phenomenon in mammals whereby only the sperm-derived or only the egg-derived allele of the gene is expressed, sometimes due to inactivation of one allele by DNA methylation during spermatogenesis or oogenesis.

Germ band A collection of cells along the ventral midline of the Drosophila embryo that forms during gastrulation by convergence and extension that includes all the cells that will form the trunk of the embryo and the thorax and abdomen of the adult.

Germ cell lineage The cells that form the gametes, including the primordial germ cells, the developing sperm and eggs, and the mature gametes.

Germ cells A group of cells set aside for reproductive function; germ cells become the cells of the gonads (ovary and testis) that undergo meiotic cell divisions to generate the gametes. Compare with Somatic cells.

Germ layer One of the three layers of the embryo, ectoderm, mesoderm, and endoderm, in triploblastic organisms, or of the two layers, ectoderm and endoderm, in diploblastic organisms, generated by the process of gastrulation, that will form all of the tissues of the body except for the germ cells.

Germ line The line of cells that become germ cells, separate from the somatic cells, found in many animals, including insects, roundworms, and vertebrates. Specification of the germ line can occur autonomously from determinants found in cytoplasmic regions of the egg, or can occur later through induction by neighboring cells.

Germ plasm Cytoplasmic determinants (mRNA and proteins) in the eggs of some species, including frogs, nematodes, and flies, that autonomously specify the primordial germ cells.

Germ plasm theory The first testable model of cell specification, proposed by Weismann in 1888, in which each cell of the embryo would develop autonomously. Instead of dividing equally, the chromosomes were hypothesized to divide in such a way that different chromosomal determinants entered different cells. Only the nuclei in those cells destined to become germ cells (gametes) were postulated to contain all the different types of determinants. The nuclei of all other cells would have only a subset of the original determinants.

Germ ring A thickened ring of cells in the margin of the deep cells that appears in a fish embryo once the blastoderm has covered about half of the yolk cell. Composed of a superficial layer, the epiblast, and an inner layer, the hypoblast.

Germ stem cell (GSC) In female Drosophila, the stem cell that gives rise to the oocyte.

Germarium In female Drosophila, niche in the anterior region of an ovariole containing germ stem cells and several somatic cell types.

Germinal crescent A region in the anterior portion of the avian and reptilian blastoderm area pellucida containing the hypoblasts displaced by migrating endodermal cells. It contains the primordial germ cells (precursors of the germ cells), which later migrate through the blood vessels to the gonads.

Germinal epithelium Epithelium of the bipotential gonad, derived from splanchnic mesoderm, that will form the somatic (i.e., non-germ cell) component of the gonads.

Germinal neuroepithelium A layer of rapidly dividing neural stem cells one cell layer thick that constitute the original neural tube.

Germinal ridge See Genital ridge.

Germinal vesicle breakdown (GVBD) Disintegration of the primary oocyte nuclear membrane (germinal vesicle) upon resumption of meiosis during oogenesis.

Germline stem cells In Drosophila, pole cell (primordial germ cells) derivatives that divide asymmetrically to produce another stem cell and a differentiated daughter cell called a cystoblast, which in turn produces a single ovum and 15 nurse cells.

GFP See Green fluorescent protein.

Glia Supportive cells of the central nervous system, derived from the neural tube, and of the peripheral nervous system, derived from neural crest.

Glial guidance A mechanism important for positioning young neurons in the developing mammalian brain (e.g., the granule neuron precursors travel on the long processes of the Bergmann glia in the cerebellum).

Glial-derived neurotrophic factor (GDNF) A paracrine factor that binds to the Ret receptor tyrosine kinase. It is produced by the gut mesenchyme that attracts vagal and sacral neural crest cells, and it is produced by the metanephrogenic mesenchyme to induce the formation and branching of the ureteric buds.

Glochidium The larva of some freshwater bivalve molluscs, such as uniod clams; has a shell resembling a tiny bear trap, used to attach to the gills or fins of fish. It feeds on the fish’s body fluids until it drops off to metamorphose into an adult clam.

Glycogen synthase kinase 3 (GSK3)  Targets β-catenin for destruction.

Glycosaminoglycans (GAGs) Complex acidic polysaccharides consisting of unbranched chains assembled from many repeats of a two-sugar unit. The carbohydrate component of proteoglycans.

Gonadal sex determination See Primary sex determination.

Gonadotropin-releasing hormone (GRH; GnRH) Peptide hormone released from the hypothalamus that stimulates the pituitary to release the gonadotropins follicle-stimulating hormone and luteinizing hormone, which are required for mammalian gametogenesis and steroidogenesis.

Gonialblast In male Drosophila, a committed progenitor cell that divides to become the precursors of the sperm.

Gonocytes Mammalian primordial germ cells (PGCs) that have arrived at the genital ridge of a male embryo and have become incorporated into the sex cords.

Granule cells Derived from neuroblasts of the external granule layer of the developing cerebellum. Granule neurons migrate back toward the ventricular (ependymal) zone, where they produce a region called the internal granule layer.

Granulosa cells Cortical epithelial cells of the fetal ovary, granulosa cells surround individual germ cells that will become the ova and will form, with thecal cells, the follicles that envelop the germ cells and secrete steroid hormones. The number of granulosa cells increase and form concentric layers around the oocyte as the oocyte matures prior to ovulation.

Gray crescent A band of inner gray cytoplasm that appears following a rotation of the cortical cytoplasm with respect to the internal cytoplasm in the marginal region of the 1-cell amphibian embryo. Gastrulation starts in this location.

Gray matter Regions of the brain and spinal cord rich in neuronal cell bodies. Compare with White matter.

Green fluorescent protein (GFP) A protein that occurs naturally in certain jellyfish. It emits bright green fluorescence when exposed to ultraviolet light. The GFP gene is widely used as a transgenic label for cells in developmental and other research, since cells that express GFP are easily identified by a bright green glow.

GRNs See Gene regulatory networks.

Ground tissue In plants, all tissue that is not dermal or vascular; functions primarily in storage, support, and photosynthesis, and includes filler tissue called parenchyma and the more supportive collenchyma and sclerenchyma.

Growth and differentiation factors (GDFs) See Paracrine factors.

Growth cone The motile tip of a neuronal axon; leads nerve outgrowth.

Growth factor A secreted protein that binds to a receptor and initiates signals to promote cell division and growth.

Growth plate closure Causes the cessation of bone growth at the end of puberty. High levels of estrogen induce apoptosis in the hypertrophic chondrocytes and stimulate the invasion of bone-forming osteoblasts into the growth plate.

GTP exchange factor (GEF) In the RTK (receptor tyrosine kinase) pathway, this factor exchanges a phosphate that transforms a bound GDP on a G protein into a bound GTP, activating the G protein. See also RTK pathway.

GTPase-activating protein (GAP) The protein that enables the G protein Ras to quickly return to its inactive state. This is done by hydrolyzing Ras’s bound GTP back to GDP. Ras becomes activated through the RTK pathway.

Gurken A protein coded for by the gurken gene. The gurken message is synthesized in the nurse cells of the Drosophila ovary and transported into the oocyte, where it is translated into the protein along an anterior-posterior gradient. It signals follicle cells closest to the oocyte nucleus to posteriorize; part of the process that will set up the anterior-posterior axis of the egg and future embryo.

Gynandromorph Greek gynos, “female”; andros, “male.” An animal in which some body parts are male and others are female. Compare with Hermaphrodite.

Gyrencephalic Having numerous folds in the cerebral cortex, as in humans and cetaceans. Compare with Lissencephalic.

H

Hair cells Sensory receptors that transform the movement of fluid into electrical signals. In the inner ear, they are in the organ of Corti of the cochlea for hearing and the semicircular canals for balance. They are also in the lateral line organs of fish and amphibians for detecting movement and changes in pressure in the water.

Hair follicle stem cells See Follicular stem cells.

Halteres A pair of balancers on the third thoracic segment of two-winged flies, such as Drosophila.

Haptotaxis Directional migration of cells on a substrate, up a gradient of adhesiveness.

Hatched blastula Free-swimming sea urchin embryo, after the cells of the animal hemisphere synthesize and secrete a hatching enzyme that digests the fertilization envelope.

Head activation gradient A morphogenetic gradient in Hydra that is highest at the hypostome and permits the head to form.

Head mesoderm Mesoderm located anterior to the trunk mesoderm, consisting of the unsegmented paraxial mesoderm and prechordal mesoderm. This region provides the head mesenchyme that forms much of the connective tissues and musculature of the head.

Head process In avian embryos, the anterior portion of the chordamesoderm that passes through Hensen’s node and migrates anteriorly, ahead of the notochordal mesoderm, to come to lie underneath cells that will form forebrain and midbrain.

Heart fields (cardiogenic mesoderm)  In vertebrates, two regions of splanchnic mesoderm, one on each side of the body, that become specified for heart development. In amniotes, the cardiac cells of the heart field migrate through the primitive streak during gastrulation such that the medial-lateral arrangement of these early cells will become the anterior-posterior (rostral-caudal) axis of the developing heart tube.

Heart tube Linear (anterior-to-posterior) structure formed at the midline of the heart fields; will become the atria, ventricles, and the base of the aorta and pulmonary arteries.

Heat shock proteins Intercellular proteins induced by stress, they help other proteins to fold correctly and maintain their functions.

Hedgehog A family of paracrine factors used by the embryo to induce particular cell types and to create boundaries between tissues. Hedgehog proteins must become complexed with a molecule of cholesterol in order to function. Vertebrates have at least three homologues of the Drosophila hedgehog gene: sonic hedgehog (shh), desert hedgehog (dhh), and indian hedgehog (ihh).

Hedgehog pathway Proteins activated by the binding of a Hedgehog protein to the Patched receptor. When Hedgehog binds to Patched, the Patched protein’s shape is altered such that it no longer inhibits Smoothened. Smoothened acts to release the Ci protein from the microtubules and to prevent its being cleaved. The intact Ci protein can now enter the nucleus, where it acts as a transcriptional activator of the same genes it once repressed.

Hemangioblasts  Rapidly dividing cells, usually stem cells, that form blood vessels and blood cells.

Hematopoiesis The generation of blood cells.

Hematopoietic inductive microenvironments (HIMs) Cell regions that induce different sets of transcription factors in multipotent hematopoietic stem cells; these transcription factors specify the developmental path taken by descendants of those cells.

Hematopoietic stem cell (HSC) A pluripotent stem cell type that generates a series of intermediate progenitor cells whose potency is restricted to certain blood cell lineages. These lineages are then capable of producing all the blood cells and lymphocytes of the body.

Hemimetabolous A form of insect metamorphosis that includes pronymph, nymph, and imago (adult) stages.

Hemogenic endothelial cell Primary endothelial cells of the dorsal aorta, in the ventral area, derived from the lateral plate. They give rise to the hematopoietic stem cells (HSCs) that migrate to the liver and bone marrow and become the adult hematopoietic stem cells.

Hensen’s node  In avian embryos, a regional thickening of cells at the anterior end of the primitive streak. The center of Hensen’s node contains a funnel-shaped depression (sometimes called the primitive pit) through which cells can enter the embryo to form the notochord and prechordal plate. Hensen’s node is the functional equivalent of the dorsal lip of the amphibian blastopore (i.e., the organizer) and the fish embryonic shield. Also known as the primitive knot.

Heparan sulfate proteoglycans (HSPGs)  One of the most widespread proteoglycans in the extracellular matrix, it can bind many members of different paracrine families and present them in high concentrations to their receptors.

Hepatectomy Surgical removal of part of the liver.

Hepatic diverticulum The liver precursor, a bud of endoderm that extends out from the foregut into the surrounding mesenchyme.

Hepatocyte growth factor (HGF) Paracrine factor secreted by the stellate cells of the liver that allows the hepatocytes to re-enter the cell cycle during compensatory regeneration. Also called scatter factor.

Hermaphrodite An individual in which both ovarian and testicular tissues exists, having either ovotestes (gonads containing both ovarian and testicular tissue) or an ovary on one side and a testis on the other. Compare with Gynandromorph.

Heterochromatin Chromatin that remains condensed throughout most of the cell cycle and replicates later than most of the other chromatin. Usually transcriptionally inactive. Compare with Euchromatin.

Heterochronic parabiosis Surgically joining the circulatory systems of two animals of different ages; has been used to study the effects of aging on stem cells in mice.

Heterochrony Greek, “different time.” A shift in the relative timing of two developmental processes as a mechanism to generate phenotypic variation available for natural selection. One module changes its time of expression or growth rate relative to the other modules of the embryo.

Heterometry Greek, “different measure.” A change in the amount of a gene product as a mechanism to generate phenotypic variation available for natural selection.

Heterophilic binding Binding between different molecules, as when a receptor in the membrane of one cell binds to a different type of receptor in the membrane of another cell.

Heterotopy Greek, “different place.” The spatial alteration of gene expression (e.g., transcription factors or paracrine factors) as a mechanism to generate phenotypic variation available for natural selection.

Heterotypy Greek, “different kind.” The alteration of the actual coding region of the gene, changing the functional properties of the protein being synthesized, as a mechanism to generate phenotypic variation available for natural selection.

High CpG-content promoters (HCPs)  Promoters with many CpG islands; these promoters often regulate developmental genes required for the construction of the organism; their default state is “on.” See also CpG islands.

Histoblast nests Clusters of imaginal cells that will form the adult abdomen in holometabolous insects.

Histoblasts Imaginal cells that will form the adult abdomen of a holometabolous insect; they are carried around in the larval stages, growing in number by cell division, until the pupal stage when they begin their differentiation. See Histoblast nests.

Histone acetylation The addition of negatively charged acetyl groups to histones, which neutralizes the basic charge of lysine and loosens the histones, and thus activates transcription.

Histone acetyltransferases Enzymes that place acetyl groups on histones (especially on lysines in histones H3 and H4). Acetyltransferases destabilize the nucleosomes so that they come apart easily, thus facilitating transcription.

Histone deacetylases Enzymes that remove acetyl groups from histones, stabilizing the nucleosomes and preventing transcription.

Histone methylation The addition of methyl groups to histones. Can either activate or further repress transcription, depending on the amino acid that is methylated and the presence of other methyl or acetyl groups in the vicinity.

Histone methyltransferases Enzymes that add methyl groups to histones and either activate or repress transcription.

Histone Positively charged proteins that are the major protein component of chromatin. See also Nucleosome.

Holobiont Term for the composite organism of a host and its persistent symbionts.

Holoblastic cleavage Greek holos, “complete.” Refers to a cell division (cleavage) pattern in the embryo in which the entire egg is divided into smaller cells, as it is in echinoderms, amphibians and mammals.

Holometabolous The type of insect metamorphosis found in flies, beetles, moths, and butterflies. There is no pronymph stage. The insect hatches as a larva (a caterpillar, grub, or maggot) and progresses through instar stages as it gets bigger between larval molts, a metamorphic molt to become a pupa, an imaginal molt and finally the emergence (eclose) of the adult (imago).

Homeobox A 180-base pair DNA sequence that characterizes genes that code for homeodomain proteins, including Hox genes.

Homeorhesis How the organism stabilizes its different cell lineages while it is still constructing itself.

Homeostasis Maintenance of a stable physiological state by means of feedback responses.

Homeotic complex (Hom-C) The region of Drosophila chromosome 3 containing both the Antennapedia complex and the bithorax complex.

Homeotic mutants Result from mutations of homeotic selector genes, in which one structure is replaced by another (as where an antenna is replaced by a leg).

Homeotic selector genes A class of Drosophila genes regulated by the protein products of the gap, pair-rule, and segment polarity genes whose transcription determines the developmental fate of each segment.

Homeotic transformations The replacement of one structure by another during development due to a homeotic mutation. See Homeotic mutants.

Homing The ability of a cell to migrate and find its tissue specific destination.

Homodimer Two identical protein molecules bound together.

Homologous Structures and/or their respective components whose similarity arises from their being derived from a common ancestral structure. For example, the wing of a bird and the forelimb of a human. Compare with Analogous.

Homologue (1) One of a pair (or larger set) of chromosomes with the same overall genetic composition. For example, diploid organisms have two copies (homologues) of each chromosome, one inherited from each parent. (2) Evolutionary features in different species that are similar by reason of descent from a common ancestor.

Homophilic binding Binding between like molecules, as when a receptor in the membrane of one cell binds to the same type of receptor in the cell membrane of another cell.

Horizontal neurons Neurons in the neural retina that transmit electrical impulses in the plane of the retina; help to integrate sensory signals coming from many photoreceptor cells.

Horizontal transmission When a host that is born free of symbionts but subsequently becomes infected, either by its environment or by other members of the species. Can also refer to the transfer of genes from one organism to another without involving reproduction, as can occur in bacteria. Compare with Vertical transmission.

Host The larger organism in a symbiotic relationship in which one of the organisms involved is much larger than the other, and the smaller organism may live on the surface or inside the body of the larger. Also refers to the organism receiving a graft from a donor in a tissue transplant.

Hox genes Large family of related genes that dictate (at least in part) regional identity in the embryo, particularly along the anterior-posterior axis. Hox genes encode transcription factors that regulate the expression of other genes. All known mammalian genomes contain four copies of the Hox complex per haploid set, located on four different chromosomes (Hoxa through Hoxd in the mouse, HOXA through HOXD in humans). The mammalian Hox/HOX genes are numbered from 1 to 13, starting from that end of each complex that is expressed most anteriorly.

Hu proteins RNA binding proteins that stabilize mRNAs involved in neuronal development, preventing them from being quickly degraded. Examples: HuA, HuB, HuC, and HuD.

Hub A regulatory microenvironment in Drosophila testes where the stem cells for sperm reside.

Hyaline layer A coating around the sea urchin egg formed by the cortical granule protein hyalin. The hyaline layer provides support for the blastomeres during cleavage.

Hydatidiform mole A human tumor which resembles placental tissue, arise when a haploid sperm fertilizes an egg in which the female pronucleus is absent and the entire genome is derived from the sperm, which precludes normal development and is cited as evidence for genomic imprinting.

20-Hydroxyecdysone (20E) An insect hormone, the active form of ecdysone, that initiates and coordinates each molt, regulates the changes in gene expression that occur during metamorphosis, and signals imaginal disc differentiation.

Hyperactivation The increased and more forceful motility displayed by capacitated sperm of some mammalian species. Hyperactivation has been proposed to help detach capacitated sperm from the oviductal epithelium, allow sperm to travel more effectively through viscous oviductal fluids, and facilitate penetration of the extracellular matrix of the cumulus cells.

Hypermorphosis The extension of development beyond its ancestral state; it is an evolutionary mechanism whereby the total developmental time is extended without altering the rate of development. Example: In humans, the extension of the fetal rate of brain growth beyond birth.

Hypertrophic chondrocytes Formed during the fourth phase of endochondral ossification, when the chondrocytes, under the influence of the transcription factor Runx2, stop dividing and increase their volume dramatically.

Hypoblast islands (primary hypoblast)  Derived from area pellucida cells of the avian blastoderm that migrate individually into the subgerminal cavity to form individual disconnected clusters containing 5–20 cells each. Does not contribute to the embryo proper.

Hypoblast The inner layer of the thickened margin of the epibolizing blastoderm in the gastrulating fish embryo or the lower layer of the bilaminar embryonic blastoderm in birds and mammals. The hypoblast in fish (but not in birds and mammals) contains the precursors of both the endoderm and mesoderm. In birds and mammals, it contains precursors to the extraembryonic endoderm of the yolk sac.

Hypomorphic mutations Mutations that reduce gene function, as opposed to a “null” mutation that results in the loss of a protein’s function.

Hypostome A conical region of the “head” of a hydra that contains the mouth.

I

Imaginal cells Cells carried around in the larva of the holometabolous insect that will form the structures of the adult. During the larval stages, these cells increase in number, but do not differentiate until the pupal stage; include imaginal discs, histoblasts, and clusters of imaginal cells within each larval organ.

Imaginal discs Clusters of relatively undifferentiated cells set aside to produce adult structures. Imaginal discs will form the cuticular structures of the adult, including the wings, legs, antennae, halters, eyes, head, thorax, and genitalia in holometabolous insects.

Imaginal molt Final molt in a holometabolous insect when the adult (imago) cuticle forms beneath the pupal cuticle, and the adult later emerges from the pupal case at adult eclosion.

Imaginal rudiment Develops from the left coelomic sac of the pluteus larva and will form many of the structures of the adult sea urchin.

Imago A winged and sexually mature adult insect.

In situ Latin, “on site.” In its natural position or environment.

In situ probe Complementary DNA or RNA used to localize a specific DNA or RNA sequence in a tissue.

Indel An insertion or deletion of DNA bases.

Indeterminate growth Growth that is not halted, as opposed to determinate growth, which stops once a structure reaches a genetically predetermined size. Unlike animals, plants can have indeterminate growth.

Indifferent gonad See Bipotential gonad.

Indirect developers Animals for which embryonic development includes a larval stage with characteristics very different from those of the adult organism, which emerges only after a period of metamorphosis.

Indole-3-acetic acid (IAA)  The most common type of auxin. See Auxin.

Induced pluripotent stem (iPS) cells Adult cells that have been converted to cells with the pluripotency of embryonic stem cells. Usually accomplished by the activation of certain transcription factors.

Inducer Tissue that produces a signal (or signals) that induces a cellular behavior in some other tissue.

Induction The process by which one cell population influences the development of neighboring cells via interactions at close range.

Inductive signals Signals produced by inducers; often these signals are secreted proteins called paracrine factors. See Inducer and Paracrine factor.

Inflorescence meristem The meristem that develops from the shoot apical meristem when the plant begins flowering; the inflorescence meristem produces the floral meristems, which form the carpels, stamens, petals and sepals of each flower. See Meristem.

Ingression Migration of individual cells from the surface layer into the interior of the embryo. The cells become mesenchymal (i.e., they separate from one another) and migrate independently.

Initial cells Totipotent stem cells generated by the early plant embryo; there are two clusters of these: the shoot apical meristem and the root apical meristem.

Inner cell mass (ICM) A small group of internal cells within a mammalian blastocyst that will eventually develop into the embryo proper and its associated yolk sac, allantois, and amnion.

Inositol 1,4,5-trisphosphate (IP₃) A second messenger generated by the phospholipase C enzyme that releases intracellular Ca²⁺ stores. Important in the initiation of both cortical granule release and sea urchin development.

Inside-out gradient of development The developmental process in the neocortex and the rest of the brain in which the neurons with the earliest birthdays form the layer closest to the ventricle and subsequent neurons travel greater distances to form the more superficial layers.

Instar The stages between larval molts in holometabolous insects. During these stages, the larva (caterpillar, grub, or maggot) feeds and grows larger between each molt, until the end of the final instar stage, when the larva is transformed into a pupa.

Instructive interaction A mode of inductive interaction in which a signal from the inducing cell is necessary for initiating new gene expression in the responding cell.

Insulator DNA sequence that limits the range within which an enhancer can activate a given gene’s expression (thereby “insulating” a promoter from being activated by another gene’s enhancers).

Insulin signaling pathway Pathway involving a receptor for insulin and insulin-like proteins; may be an important component of genetically limited life spans, wherein downregulation of the pathway can correspond to an increased lifespan.

Insulin-like growth factors (IGFs)  Growth factors that initiate an FGF-like signal transduction cascade that interferes with the signal transduction pathways of both BMPs and Wnts. IGFs are required for the formation of the anterior neural tube, including the brain and sensory placodes of amphibians.

Integration A principle of the theoretical systems approach: How the parts are put together, and how they interact to form the whole.

Integrins A family of receptor proteins, named for the fact that they integrate extracellular and intracellular scaffolds, allowing them to work together. On the extracellular side, integrins bind to sequences found in several adhesive proteins in extracellular matrix, including fibronectin, vitronectin (in the basal lamina of the eye), and laminin. On the cytoplasmic side, integrins bind to talin and α-actinin, two proteins that connect to actin microfilaments. This dual binding enables the cell to move by using myosin to contract the actin microfilaments against the fixed extracellular matrix.

Integuments An outer protective layer such as the skin. In plants, the seed coat comes from the integuments of the ovule.

Interdigital necrotic zone A zone of programmed cell death in the developing tetrapod limb that separates the digits from one another; when the cells in this zone do not die, webbing between the digits remains, as in the duck foot.

Interior necrotic zone A zone of programmed cell death in the developing tetrapod limb that separates the radius from the ulna.

Interkinesis The brief period between the end of meiosis I and the beginning of meiosis II.

Interkinetic nuclear migration The movement of nuclei within certain cells as they go through the cell cycle; seen in the germinal neuroepithelium in which nuclei translocate from the basal end to the apical end of the cells near the ventricular surface, where they undergo mitosis, after which they slowly migrate basally again.

Intermediate mesoderm Mesoderm immediately lateral to the paraxial mesoderm. It forms the outer (cortical) portion of the adrenal gland and the urogenital system, consisting of the kidneys, gonads, and their associated ducts.

Intermediate progenitor cells (IP cells)  Neuron precursor cells of the subventricular zone; derived from radial glial cells.

Intermediate spermatogonia The first committed stem cell type of the mammalian testis, they are committed to becoming spermatozoa.

Intermediate zone See Mantle zone.

Internal granular layer A layer in the cerebellum that is formed by the migration of granule cells from the external granular layer back toward the ventricular zone.

Internal YSL (iYSL) A region of the yolk syncytial layer (YSL) in fish embryos. The iYSL forms from yolk syncytial nuclei that move under the blastoderm as it expands to surround the yolk cell. See Yolk syncytial layer.

Intersex A condition in which male and female traits are observed in the same individual.

Interstitial stem cell A type of stem cell found within the ectodermal layer of Hydra that generates neurons, secretory cells, nematocytes, and gametes.

Intine The inner wall of a pollen grain, composed mostly of cellulose.

Intraembryonic vasculogenesis The formation of blood vessels during embryonic organogenesis. Compare with Extraembryonic vasculogenesis.

Intramembranous bone Bone formed by intramembranous ossification.

Intramembranous ossification Formation of bone directly in mesenchyme without a cartilaginous precursor. There are three main types of intramembranous bone: sesamoid bone and periosteal bone, which come from mesoderm, and dermal bone which originate from cranial neural crest-derived mesenchymal cells.

Introns Non-protein-coding regions of DNA within a gene. Compare with Exon.

Invagination The infolding of a region of cells, much like the indenting of a soft rubber ball when it is poked.

Invariant cell lineage When each cell of an embryo gives rise to the same number and type of cells in every embryo of that species, as seen in the embryos of the roundworm Caenorhabditis elegans.

Involuting marginal zone (IMZ) Cells that involute during Xenopus gastrulation, includes precursors of the pharyngeal endoderm, head mesoderm, notochord, somites, and heart, kidney, and ventral mesoderm.

Involution Inturning or inward movement of an expanding outer layer so that it spreads over the internal surface of the remaining external cells.

Ionophore A compound that allows the diffusion of ions such as Ca²⁺ across lipid membranes, permitting them to traverse otherwise impermeable barriers.

Ipsilateral An anatomical term meaning on the same side of the body.

Iris A pigmented ring of muscular tissue in the eye that controls the size of the pupil and determines eye color.

Isolecithal Greek, “equal yolk.” Describes eggs with sparse, equally distributed yolk particles, as in sea urchins, mammals, and snails.

Isthmus The narrow segment of the mammalian oviduct adjacent to the uterus.

Izumo A protein found on the equatorial region of mature mammalian sperm that binds to Juno, on the cell membrane of the oocyte. These proteins help stabilize sperm-egg binding.

J

Jagged protein Ligand for Notch, participates in juxtacrine interaction and activation of the Notch pathway.

JAK Janus kinase proteins. Linked to FGF receptors in the JAK-STAT cascade.

JAK-STAT cascade A pathway activated by paracrine factors binding to receptors that span the cell membrane and are linked on the cytoplasmic side to JAK (Janus kinase) proteins. The binding of ligand to the receptor phosphorylates the STAT (signal transducers and activators of transcription) family of transcription factors.

Junctional neurulation Formation of the neural tube in the transition zone between the primary neural tube (which lies anterior to the hindlimbs) and the secondary neural tube (which extends posteriorly from the sacral region in mammals or is just in the tail region in fish and amphibians).

Juno A protein found anchored to the mammalian oocyte cell membrane that is critical in binding to Izumo, a protein on mammalian sperm.

Juvenile hormone (JH) A lipid hormone in insects that prevents the ecdysone-induced changes in gene expression that are necessary for metamorphosis. Thus, its presence during a molt ensures that the result of that molt is another larval instar, not a pupa or an adult.

Juxtacrine interactions When cell membrane proteins on one cell surface interact with receptor proteins on adjacent (juxtaposed) cell surfaces.

Juxtacrine signaling Signaling between cells that are juxtaposed, i.e., in direct contact with one another.

K

Kairomones Chemicals that are released by a predator and can induce defenses in its prey.

Karyokinesis The mitotic division of the cell’s nucleus. The mechanical agent of karyokinesis is the mitotic spindle.

Keratinocytes Differentiated epidermal cells that are bound tightly together and produce a water-impermeable seal of lipid and protein.

Koller’s sickle See Primitive streak.

Kupffer’s vesicle Transient fluid-filled organ housing the cilia that control left-right asymmetry in zebrafish.

L

Labioscrotal folds Folds surrounding the cloacal membrane in the indifferent stage of differentiation of mammalian external genitalia. They will form the labia majora in the female and the scrotum in the male. Also called urethral folds or genital swellings.

lacZ gene The E. coli gene for β-galactosidase; commonly used as a reporter gene.

Lamellipodia Broad locomotory pseudopods containing actin networks; found on migrating cells, also found on growth cones of neurons.

Laminae Layers. In the brain, neurons are organized into laminae and clusters (nuclei).

Laminin A large glycoprotein and major component of the basal lamina, plays a role in assembling the extracellular matrix, promoting cell adhesion and growth, changing cell shape, and permitting cell migration.

Lampbrush chromosomes Chromosomes in an amphibian primary oocyte during the diplotene stage of the first meiotic prophase that stretch out large loops of DNA, representing sites of upregulated RNA synthesis.

Lanugo The first hairs of human embryos, usually shed before birth.

Large micromeres A tier of cells produced by the fifth cleavage in the sea urchin embryo when the micromeres divide. Become the primary mesenchyme cells, which form the skeletal spicules of the larva.

Larva The sexually immature stage of an organism, often of significantly different appearance than the adult and frequently the stage that lives the longest and is used for feeding or dispersal.

Larval settlement Ability of marine larvae to suspend development until they experience a particular environmental cue for settlement.

Laryngotracheal groove An outpouching of endodermal epithelium in the center of the pharyngeal floor, between the fourth pair of pharyngeal pouches, that extends ventrally. The laryngotracheal groove then bifurcates into the branches that form the paired bronchi and lungs.

Last eukaryotic common ancestor (LECA) The hypothetical ancestor to all plants, animals and fungi, thought to have been a unicellular protist that had flagella and mitochondria.

Last universal common ancestor (LUCA) The ancient common ancestor to all life on Earth.

Lateral inhibition The inhibition of a cell by the activity of a neighboring cell.

Lateral line placodes Paired ectodermal placodes that form as posterior cranial placodes in amphibians and fish. They generate neuromasts, which contain mechanosensing hair cells and their innervating neurons; function to detect the flow of water, weak bioelectric fields, and changes in pressure. See Hair cells.

Lateral plate mesoderm Mesodermal sheet lateral to the intermediate mesoderm. Gives rise to appendicular bones, connective tissues of the limb buds, circulatory system (heart, blood vessels, and blood cells), muscles and connective tissues of the digestive and respiratory tracts, and lining of coelom and its derivatives. It also helps form a series of extraembryonic membranes that are important for transporting nutrients to the embryo.

Lateral somitic frontier The boundary between the primaxial and abaxial muscles and between the somite-derived and lateral plate-derived dermis.

Leader sequence See 5′ Untranslated region.

Leghemoglobin An oxygen-carrying protein, similar to hemoglobin, found in the nitrogen-fixing root nodules of legumes. It is a plant protein whose genes are induced by symbiotic bacteria. This protein protects the nitrogenase enzyme from being inactivated by oxygen.

Lens placode Paired epidermal thickenings induced by the underlying optic cups to invaginate to form the lens vesicles, which differentiate into the adult transparent eye lenses that allow light to impinge on the retinas.

Lens vesicle The vesicle that forms from the lens placode. It differentiates into the lens. It also induces the overlying ectoderm to become the cornea, and induces the inner side of the optic cup to differentiate into the neural retina.

Leptotene Greek, “thin thread.” In the first meiotic division, the first stage of prophase I, when the chromatin is stretched out thinly such that one cannot identify individual chromosomes. DNA replication has already occurred, and each chromosome consists of two parallel chromatids.

Level-specific properties and emergence A principle of the theoretical systems approach: The properties of a system at any given level of organization cannot be totally explained by those of levels “below” it.

Leydig cells Testis cells derived from the interstitial mesenchyme cells surrounding the testis cords that make the testosterone required for secondary sex determination and, in the adult, required to support spermatogenesis.

Life expectancy The length of time an average individual of a given species can expect to live; it is characteristic of populations, not of species.

Ligand A molecule secreted by a cell that elicits a response in another cell by binding to a receptor on that cell.

Lim genes Genes coding for transcription factors that are structurally related to proteins encoded by Hox genes.

Limb bud A circular bulge that will form the future limb. The limb bud is formed by the proliferation of mesenchyme cells from the somatic layer of the limb field lateral plate mesoderm (the limb skeletal precursor cells) and from the somites (the limb muscle precursor cells).

Limb field An area of the embryo containing all of the cells capable of forming a limb.

Lineage tracing Tracking the development of cell maturation over time. Embryonic cells can be labeled and tracked to see what they become in the larva or adult organism; this allows the development of a fate map. See Fate map.

Lineage-restricted stem cells Stem cells derived from multipotent stem cells, and which can now generate only a particular cell type or set of cell types.

Lissencephalic Having a cerebral cortex that lacks folds, as in mice. Compare with Gyrencephalic.

Long noncoding RNAs (lncRNAs) Transcriptional regulators that inactivate genes on one of the two chromosomes of a diploid organism. For example, Xist is a lncRNA involved in the inactivation of genes on the second X chromosome of females. Some lncRNAs appear to be specific for either the maternal or paternal copy of a gene.

Lophotrochozoans One of two major protostome groups, many of which are characterized spiral cleavage and by the larval form known as the trochophore. A diverse group that includes the annelids (segmented worms such as earthworms), molluscs (e.g., snails), and flatworms (e.g., Planaria). See also Ecdysozoans.

Loss-of-function evidence The absence of the postulated cause is associated with the absence of the postulated effect. The “lose it” of “find it, lose it, move it.” See also Correlative evidence; Gain-of-function evidence.

Low CpG-content promoters (LCPs) These promoters are usually found in the genes whose products characterize mature, fully differentiated cells. The CpG sites are usually methylated and their default state is “off,” although they can be activated by specific transcription factors. See also CpG islands.

Lumen The hollow space within any tubular or globular structure or organ.

Luteinizing hormone (LH) A hormone secreted by the mammalian pituitary that stimulates the production of steroid hormones, such as estrogen from the ovarian follicle cells and testosterone from the testicular Leydig cells. A surge in LH levels causes the primary oocyte to complete meiosis I and prepares the follicle for ovulation.

Lymphatic vasculature The vessels of the circulatory system that transport lymph (as opposed to the blood vessels of the circulatory system).

M

Macromeres Larger cells generated by asymmetrical cleavage, e.g., the four large cells generated by the fourth cleavage when the vegetal tier of the sea urchin embryo undergoes an unequal equatorial cleavage.

MADS-box transcription factors A family of proteins that all share a conserved motif in their DNA-binding domains; they are found in diverse groups of eukaryotes.

Male pronucleus The haploid nucleus of the sperm.

Malformation Abnormalities caused by genetic events such as gene mutations, chromosomal aneuploidies, and translocations.

Mammalian gut-associated lymphoid tissue (GALT) Lymphoid tissue that mediates mucosal immunity and oral immune tolerance, allowing mammals to eat food without creating an immune response to it. Intestinal microbes are critical for the maturation of GALT.

Mantle zone (intermediate zone) Second layer of the developing spinal cord and medulla that forms around the original neural tube. Because it contains neuronal cell bodies and has a grayish appearance grossly, it will form the gray matter.

Marginal zone (1) The third and outer zone of the developing spinal cord and medulla composed of a cell-poor region composed of axons extending from neurons residing in the mantle zone. Will form the white matter as glial cells cover the axons with myelin sheaths, which have a whitish appearance. (2) In amphibian gastrula, where gastrulation begins, the region surrounding the equator of the blastula, where the animal and vegetal hemispheres meet. (3) In bird and reptile gastrulae (= marginal belt), a thin layer of cells between the area pellucida and the area opaca, important in determining cell fate during early development. Maskin Protein in amphibian oocytes that creates a repressive loop structure in messenger RNA, preventing its translation. It creates the loop by binding to two other proteins, cytoplasmic polyadenylation-element-binding protein (CPEB) and eIF4E factor, which are bound to opposite ends of the mRNA.

Master regulator Transcription factors that can control cell differentiation by (1) being expressed when the specification of a cell type begins, (2) regulating the expression of genes specific to that cell type, and (3) being able to redirect a cell’s fate to this cell type.

Maternal contributions The stored mRNAs and proteins within the cytoplasm of the egg, produced from the maternal genome during the primary oocyte stage. See also Maternal message.

Maternal effect An effect occurring during embryonic development that is controlled by gene products that were stored in the egg while it was in the ovary; these gene products were made using the maternal genome through gene transcription within the egg itself, prior to its undergoing meiosis, or within nurse cells that transport gene products into the egg. See Maternal message.

Maternal effect genes Genes belonging to the maternal genome that are used to make messenger RNAs or proteins that are localized to different regions of an egg and affect embryonic development, as seen in the Drosophila egg. See Maternal effect.

Maternal message Messenger RNA that is either made in the egg and stored in the egg’s cytoplasm while the egg is a primary oocyte or is made in nurse cells within the ovary and transported to the egg’s cytoplasm. At the primary oocyte stage, the egg within the ovary is still diploid, as are any surrounding nurse cells. The mRNA, therefore, is being made from the maternal genome.

Maternal-to-zygote transition The embryonic stage when maternally provided mRNAs are degraded and control of development is handed over to the zygote’s own genome; often occurs in the mid-blastula stage. Seen in many different animal groups.

Maximum lifespan Maximum number of years an individual of a given species has been known to survive and is characteristic of that species.

Mechanical anisotropy Having a difference in a mechanical property, such as stretchability, along different axes.

Medial hinge point (MHP) In birds and mammals, formed by the cells at the midline of the neural plate. MHP cells become anchored to the notochord beneath them and form a hinge, which forms a furrow at the dorsal midline and helps bend the neural plate as it forms a neural tube.

Mediator A large, multimeric complex of nearly 30 protein subunits that in many genes is the link that connects RNA polymerase II (bound to the promoter) to an enhancer sequence, thus forming a pre-initiation complex at the promoter.

Medullary cord Forms by condensation of mesenchyme cells and then mesenchymal-to-epithelial transition in the caudal region of the avian embryo during the process of secondary neurulation. It will then cavitate to form the caudal section of the neural tube.

Megasporangium The structure in which megaspores form.

Megaspores Haploid cells derived from the diploid megaspore mother cell. At least of one these four cells produces the female gametophyte that produces the egg cell.

Meiosis A unique division process that in animals occurs only in germ cells, to reduce the number of chromosomes to a haploid complement. All other cells divide by mitosis. Meiosis differs from mitosis in that (1) meiotic cells undergo two cell divisions without an intervening period of DNA replication, and (2) homologous chromosomes (each consisting of two sister chromatids joined at a kinetochore) pair together and recombine genetic material.

Melanoblasts Pigment progenitor cells.

Melanocyte stem cells Adult stem cells derived from trunk neural crest cells that form melanoblasts and come to reside in the bulge niche of the hair or feather follicle and which give rise to the pigment of the skin, hair, and feathers.

Melanocytes Cells containing the pigment melanin. Derived from neural crest cells that undergo extensive migration to all regions of the epidermis.

Meltrins Set of metalloproteinases involved in cell fusion events, such as the fusion of myoblasts to form a myofiber and of macrophages to form osteoclasts. See also Metalloproteinases.

Meridional When pertaining to cell division, a cleavage that is transverse through the equatorial plane.

Meristem Tissue in plants containing undifferentiated and actively dividing cells. This is where production of new plant tissue occurs. Different types of meristems give rise to different structures of the plant. The two main meristems are the shoot and root apical meristems.

Meroblastic cleavage Greek meros, “part.” Refers to the cell division (cleavage) pattern in zygotes containing large amounts of yolk, wherein only a portion of the cytoplasm is cleaved. The cleavage furrow does not penetrate the yolky portion of the cytoplasm because the yolk platelets impede membrane formation there. Only part of the egg is destined to become the embryo, while the other portion—the yolk—serves as nutrition for the embryo, as in insects, fish, reptiles, and birds.

Meroistic oogenesis Type of oogenesis found in certain insects (including Drosophila and moths), in which cytoplasmic connections remain between the cells produced by the oogonium.

Mesencephalon The midbrain, the middle vesicle of the developing vertebrate brain; major derivatives include optic tectum and tegmentum. Its lumen becomes the cerebral aqueduct.

Mesenchymal cells Unconnected or loosely connected cells that can act as independent migratory units. These are in contrast to epithelial cells.

Mesenchymal stem cells (MSCs) Also called bone marrow-derived stem cells, or BMDCs. Multipotent stem cells that originate in the bone marrow, MSCs are able to give rise to numerous bone, cartilage, muscle, and fat lineages.

Mesenchymal-to-epithelial transition (MET) Transformation of mesenchymal cells into epithelial cells. Occurs, for example, during somite formation, when somites form from presomitic mesoderm. See also Epithelial-mesenchymal transition.

Mesenchyme cap cells A population of multipotent stem cells, derived from metanephric kidney mesenchyme, that cover the tips of the ureteric bud branches and can form all the cell types of the nephron.

Mesenchyme Loosely organized embryonic connective tissue consisting of scattered fibroblast-like and sometimes migratory mesenchymal cells separated by large amounts of extracellular matrix.

Mesendodermal Pertaining to mesendoderm, which develops into mesoderm and endoderm. Synonym for endomesodermal.

Mesentoblast In snail embryos, the 4d blastomere whose progeny give rise to most of the mesodermal (heart, kidney and muscles) and endodermal (gut tube) structures.

Mesoderm Greek mesos, “between.” The middle of the three embryonic germ layers, lying between the ectoderm and the endoderm. The mesoderm gives rise to muscles and skeleton, connective tissue, the urogenital system (kidneys, gonads, and ducts), blood and blood vessels, and most of the heart.

Mesodermal mantle The cells that involute through the ventral and lateral blastopore lips during amphibian gastrulation and will form the heart, kidneys, bones, and parts of several other organs.

Mesomeres The eight cells generated in the sea urchin embryo by the fourth cleavage when the four cells of the animal tier divide meridionally into eight blastomeres, each with the same volume.

Mesonephric duct See Wolffian duct.

Mesonephros The second kidney of the amniote embryo, induced in the adjacent mesenchyme by the middle portion of the nephric (Wolffian) duct. It functions briefly in urine filtration in some mammalian species and mesonephric tubules form the tubes that transport the sperm from the testes to the urethra (the epididymis and vas deferens). Forms the adult kidney of anamniotes (fish and amphibians).

Mesp1 A gene for a transcription factor that is critical in the regulatory network that specifies heart cells. These networks are conserved across vertebrates. See also Nkx2-5.

Messenger RNA (mRNA) RNA that codes for a protein and leaves the nucleus after being processed from nuclear RNA in a manner that excises non-coding domains and protects the ends of the strand.

MET See Mesenchymal-to-epithelial transition.

Metalloproteinases Matrix metalloproteinases (MMP). Enzymes that digest extracellular matrices and are important in many types of tissue remodeling in disease and development, including metastasis, branching morphogenesis of epithelial organs, placental detachment at birth, and arthritis.

Metamorphic climax When the major metamorphic changes, such as tail and gill resorption, and intestinal remodeling, occur in the amphibian. The concentration of T₄ rises dramatically and TRβ levels peak.

Metamorphic molt Pupal molt; in holometabolous insects, the molt at the end of the final instar stage, when the larva becomes a pupa.

Metamorphosis Changing from one form to another, such as the transformation of an insect larva to a sexually mature adult or a tadpole to a frog.

Metanephric mesenchyme An area of mesenchyme, derived from posterior regions of the intermediate mesoderm, involved in mesenchymal-epithelial interactions that generate the metanephric kidney and will form the secretory nephrons. Also called metanephrogenic mesenchyme.

Metanephros/metanephric kidney The third kidney of the amniote embryo and the permanent kidney of amniotes.

Metaphase plate A structure present during mitosis or meiosis in which the chromosomes are attached via their kinetochores to the microtubule spindle and are lined up between the two poles of the cell. If the metaphase plate forms midway between the two poles the division will be symmetrical; if it is closer to one pole, it will be asymmetrical, producing one larger cell and one smaller.

Metastasis The invasion of cancerous cells into other tissues.

Metazoa Animals.

Metencephalon The anterior subdivision of the rhombencephalon; gives rise to the cerebellum (coordinates movements, posture, and balance) and pons (fiber tracts for communication between brain regions).

Methylation See Histone methylation.

5-Methylcytosine A “fifth” base in DNA, made enzymatically after DNA is replicated by converting cytosine to 5-methycytosine—only cytosines followed by a guanosine can be converted. In mammals, about 5% of cytosines in DNA are converted to 5-methylcytosine.

Microfilaments Long cables of polymerized actin and a major component of the cytoskeleton. In combination with myosin, forms contractile forces necessary for cytokinesis; formed during fertilization in the egg’s cortex to extend microvilli; attached indirectly by other molecules to transmembrane adhesion molecules, such as cadherins and integrins.

Microglia Small glial cells of the central nervous system that carry out an immune function by engulfing dying and dysfunctional neurons and glia.

Micromeres Small cells created by asymmetrical cleavage, e.g., four small cells generated by the fourth cleavage at the vegetal pole when the vegetal tier of the sea urchin embryo undergoes an unequal equatorial cleavage.

Micropyle The only place where Drosophila sperm can enter the egg, at the future dorsal anterior region of the embryo, a tunnel in the chorion (eggshell) that allows sperm to pass through it one at a time.

MicroRNA (miRNA) Small (about 22 nucleotide) RNAs complementary to a portion of a particular mRNA that regulates translation of a specific message. MicroRNAs usually bind to the 3′ UTR of mRNAs and inhibit their translation.

Microspikes Essential for neuronal pathfinding, microfilament-containing pointed filopodia of the growth cone that elongate and contract to allow axonal migration. Microspikes also sample the microenvironment and send signals back to the soma.

Microsporangia The places within the anther where the microspores are produced.

Microspores In plants, the haploid cell that develops into the pollen tube, the male gametophyte.

Microtubule organizing centers (MTOCs) Eukaryotic cell structure that polymerizes tubulin into microtubules. These are critical in making cilia, flagella, and the spindles of the meiotic and mitotic spindle apparatus.

Microvilli Small microfilament-containing projections that extend from the surface of cells; e.g., on the egg surface during fertilization where they may aid sperm entry into the cell.

Mid-blastula transition (MBT) The transition from the early rapid biphasic (only M and S phases) mitoses of the embryo to a stage characterized by (1) mitoses that include the “gap” stages (G1 and G2) of the cell cycle, (2) loss of synchronicity of cell division, and (3) transcription of new (zygotic) mRNAs needed for gastrulation and cell specification.

Midpiece Section of sperm flagellum near the head that contains rings of mitochondria that provide the ATP needed to fuel the dynein ATPases and support sperm motility.

miRNA See MicroRNA.

MITF Microphthalmia-associated transcription factor. A transcription factor necessary for melanoblast specification and pigment production. Its name comes from the fact that a mutation in the gene for this transcription factor causes small eyes (microphthalmia) in mice.

Mitosis-promoting factor (MPF) Consists of cyclin B and a cyclin-dependent kinase (CDK), required to initiate entry into the mitotic (M) phase of the cell cycle in both meiosis and mitosis.

Model systems Species that are easily studied in the laboratory and have special properties that allow their mechanisms of development to be readily observed (e.g., sea urchins, Drosophila, C. elegans, zebrafish, and mouse).

Modularity A principle of the theoretical systems approach. The organism develops as a system of discrete and interacting modules.

Module A discrete unit of growth, characterized by more internal than external integration.

Molecular parsimony The principle that development in all lineages uses the same types of molecules (the “small toolkit”). The “toolkit” includes transcription factors, paracrine factors, adhesion molecules, and signal transduction cascades that are remarkably similar from one phylum to another.

Monospermy Only one sperm enters the egg, and a haploid sperm nucleus and a haploid egg nucleus combine to form the diploid nucleus of the fertilized egg (zygote), thus restoring the chromosome number appropriate for the species.

Monozygotic twins Greek, “one-egg.” Genetically “identical” twins; form when the cells of a single early-cleavage embryo become dissociated from one another, either by the separation of early blastomeres or by the separation of the inner cell mass into two regions within the same blastocyst. Compare with Dizygotic twins.

Morph One of several different potential phenotypes that result from environmental conditions. Also called an ecomorph.

Morphallactic regeneration See Morphallaxis.

Morphallaxis Type of regeneration that occurs through the repatterning of existing tissues with little new growth (e.g., Hydra).

Morphogenesis The organization of the cells of the body into functional structures via coordinated cell growth, cell migration, and cell death.

Morphogenetic determinants Transcription factors or their mRNAs that will influence the cell’s development.

Morphogens Greek, “form-givers.” Diffusible biochemical molecules that can determine the fate of a cell by their concentrations, in that cells exposed to high levels of a morphogen will activate different genes than those exposed to lower levels.

Morpholino An antisense oligonucleotide against an mRNA; used to experimentally inhibit protein expression.

Morula Latin, “mulberry.” Vertebrate embryo of 16–64 cells; precedes the blastula or blastocyst stage. Mammalian morula occurs at the 16-cell stage, consists of a small group of internal cells (that will form the inner cell mass) surrounded by a larger group of external cells (that will form the trophoblast).

Mosaic embryos Embryos in which most of the cells are determined by autonomous specification, with each cell receiving its instructions independently and without cell-cell interaction.

Mosaic pleiotropy A gene is independently expressed in several tissues. Each tissue needs the gene product and develops abnormally in its absence.

mRNA cytoplasmic localization The spatial regulation of mRNA translation, mediated by (1) diffusion and local anchoring, (2) localized protection, and (3) active transport along the cytoskeleton.

Müller glial cells Cells of the neural retina that support and maintain the neurons therein.

Müllerian duct (paramesonephric duct)  Duct running lateral to the mesonephric (Wolffian) duct in both male and female mammalian embryos. These ducts regress in the male fetus, but form the oviducts, uterus, cervix, and upper part of the vagina in the female fetus. Compare with Wolffian duct.

Müllerian-inhibiting factor (MIF) See Anti-Müllerian hormone.

Multicellular eukaryotic organism A eukaryotic organism with multiple cells that remain together as a functional whole; subsequent generations form the same coherent individuals composed of multiple cells. (Includes plants, fungi, and animals.)

Multicellularity Consisting of multiple cells.

Multipotent Refers to the ability of a stem cell to generate different cell types with restricted specificity for the tissue in which they reside. Example: Most adult stem cells in organs of animals are multipotent.

Multipotent cardiac progenitor cells Progenitor cells of the heart field that form cardiomyocytes, endocardium, epicardium, and the Purkinje fibers of the heart.

Multipotent stem cells Adult stem cells whose commitment is limited to a relatively small subset of all the possible cells of the body.

Mutualism A form of symbiosis in which the relationship benefits both partners.

Mycorrhizae Fungi that form symbiotic relationships with plants to extend their roots. While the plant supplies the fungus with sugars, the fungus absorbs water and mineral nutrients from the soil.

Myelencephalon The posterior subdivision of the rhombencephalon; becomes the medulla oblongata.

Myelin sheath Modified oligodendrocyte (in CNS) or Schwann cell (in peripheral NS) plasma membrane that surrounds nerve cell axons, providing insulation that confines and speeds electrical impulses transmitted along axons.

Myoblast Muscle precursor cell.

Myocardium Heart muscle.

Myoepithelia Epithelia whose cells possess characteristics of both epithelial and muscle cells, e.g., the two epithelial layers of Hydra.

Myofiber Muscle cell that is multinucleate and forms from the fusion of myoblasts; skeletal muscle cell.

Myogenic regulatory factors (MRFs)  Basic helix-loop-helix transcription factors (such as MyoD, Myf5 and myogenin) that are critical regulators of muscle development.

Myogenin A myogenic regulatory factor that regulates several genes involved in the differentiation and repair of skeletal muscle cells. See also Myogenic regulatory factors.

Myostatin Greek, “muscle stopper.” A member of the TGF-β family, it negatively regulates muscle development. Genetic defects in the gene or its negative regulatory miRNA cause huge muscles to develop in some mammals, including humans.

Myotome Portion of the somite that gives rise to all skeletal muscles of the vertebrate body except for those in the head. The myotome has two components: the primaxial component, closest to the neural tube, which forms the musculature of the back and rib cage, and the abaxial component, away from the neural tube, which forms the muscles of the limbs and ventral body wall.

N

N-cadherin A type of cadherin that is highly expressed on cells of the developing central nervous system (the N stands for Neural). May play roles in mediating neural signals. See also Cadherins.

NAD⁺ kinase Activated during the early response of the sea urchin egg to the sperm, converts NAD⁺ to NADP⁺, which can be used as a coenzyme for lipid biosynthesis and may be important in the construction of the many new cell membranes required during cleavage. NADP⁺ is also used to make NAADP.

Naïve Unaffected, lacking experience.

Naïve ESC An embryonic stem cell (ESC) that is the most immature, undifferentiated ESC with the greatest potential for pluripotency. Compare with Primed ESC. Also see Embryonic stem cells.

Naïve pluripotent state The most immature, undifferentiated state of embryonic stem cells with the greatest potential for pluripotency.

Nanos Protein critical for the establishment of anterior-posterior polarity of the Drosophila embryo. Nanos mRNA is tethered to the posterior end of the oocyte and is translated after ovulation and fertilization. Nanos protein diffuses from the posterior end, while Bicoid diffuses from the anterior end, setting up two opposing gradients that establish the anterior-posterior polarity of the embryo.

Necrosis Pathologic cell death caused by factors such as inflammation of toxic injury. Compare with Apoptosis.

Necrotic zones Regions of the tetrapod limb “sculpted” by apoptotic (programmed) cell death; the term “necrotic” zone is a holdover from a time when no distinction was made between necrosis and apoptosis. The four necrotic regions are interdigital, anterior, posterior, and interior.

Negative feedback loop A process in which the product of the process inhibits an earlier step in the process.

Neocortex A layer of gray matter in the cerebrum that is a distinguishing feature of the mammalian brain; it stratifies into six layers of neuronal cell bodies, each with different functional properties.

Neoteny Retention of the juvenile body form throughout life while the germ cells and reproductive system mature (e.g., the Mexican axolotl). See also Progenesis.

Nephric duct See Wolffian duct.

Nephron Functional unit of the kidney.

Nerve growth factor (NGF) Neurotrophin involved primarily in the growth of nerve cells. Released from potential target tissues, it works at short ranges as either a chemotactic factor or chemorepulsive factor for axonal guidance. Also important in the selective survival of different subsets of neurons.

Netrins Paracrine factors found in a gradient that guide axonal growth cones. They are important in commissural axon migration and retinal axon migration. Netrin-1 is secreted by the floor plate; netrin-2 is secreted by the lower region of the spinal cord.

Neural crest A transient band of cells, arising from the lateral edges of the neural plate, that joins the neural tube to the epidermis. It gives rise to a cell population—the neural crest cells—that detach during formation of the neural tube and migrate to form a variety of cell types and structures, including sensory neurons, enteric neurons, glia, pigment cells, and (in the head) bone and cartilage. Neural crest cells See Neural crest.

Neural crest effectors Transcription factors (e.g., MITF and Rho GTPase) activated by neural crest specifiers that give the neural crest cells their migratory properties and some of their differentiated properties.

Neural crest specifiers A set of transcription factors (e.g., FoxD3, Sox9, Id, Twist, and Snail) induced by the neural plate border-specifying transcription factors, that specify the cells that are to become the neural crest.

Neural folds Thickened edges of the neural plate that move upward during neurulation and migrate toward the midline and eventually fuse to form the neural tube.

Neural groove U-shaped groove that forms in the center of the neural plate during primary neurulation.

Neural keel A band of neural precursor cells that are brought into the dorsal midline during convergence and extension movements in the epiblast of the fish embryo. It extends over the axial and paraxial mesoderm and eventually forms a rod of tissue that separates from the epidermal ectoderm and develops a slit-like lumen to become the neural tube.

Neural plate border specifiers A set of transcription factors (e.g., Distalless-5, Pax3, and Pax7), induced by the neural plate inductive signals, that collectively confer upon the border region the ability to form neural crest and dorsal neural tube cell types. Induce expression of neural crest specifiers.

Neural plate border The border between the neural plate and the epidermis.

Neural plate inductive signals Paracrine factors (e.g., BMPs, Wnts, FGFs and Notch) that interact to specify the boundaries between neural and non-neural ectoderm during gastrulation. In amphibians, inductive signals secreted by the notochord are sufficient to specify neural plate; in chick, signals secreted by the ventral ectoderm and paraxial mesoderm specify the boundaries.

Neural plate The region of the dorsal ectoderm that is specified to be neural ectoderm. It later folds upward to become the neural tube.

Neural restrictive silencer element (NRSE) A regulatory DNA sequence found in several mouse genes that prevents a promoter’s activation in any tissue except neurons, limiting the expression of these genes to the nervous system.

Neural restrictive silencer factor (NRSF) A zinc finger transcription factor that binds the NRSE and is expressed in every cell that is not a mature neuron.

Neural retina Derived from the inner layer of the optic cup, composed of a layered array of cells that include the light and color-sensitive photoreceptor cells (rods and cones), the cell bodies of the ganglion cells, bipolar interneurons that transmit electric stimuli from the rods and cones to the ganglion cells, Müller glial cells that maintain its integrity, amacrine neurons (which lack large axons), and horizontal neurons that transmit electric impulses in the plane of the retina.

Neural stem cells (NSCs) Stem cells of the central nervous system capable of neurogenesis throughout life. In vertebrates, NSCs retain much of the characteristics of their embryonic progenitor cell, the radial glial cell.

Neural tube The embryonic precursor to the central nervous system (brain and spinal cord).

Neuroblast An immature dividing precursor cell that can differentiate into the cells of the nervous system.

Neurocranium The vault and base of the skull.

Neuromesodermal progenitors (NMPs) In vertebrate embryos, a population of multipotent progenitor cells with the potential to contribute to both the neural tube and paraxial (somitic) mesoderm, found in the posteriormost region (caudal end) of the embryo.

Neuromesodermal Giving rise to both neural and somitic cell types. See Neuromesodermal progenitors (NMPs).

Neurons Nerve cells; cells specialized for the conduction and transmission of information via electrical and chemical signals.

Neuropore The two open ends (anterior neuropore and posterior neuropore) of the neural tube that later close.

Neurotransmitters Molecules (e.g., acetylcholine, GABA, serotonin) secreted at the ends of axons. These molecules cross the synaptic cleft and are received by the adjacent neuron, thus relaying the neural signal. See also Synapse.

Neurotrophin/neurotropin Neurotrophic (Greek, “nourishing”) refers to a factor’s ability to keep the neuron alive, usually by supplying growth factors. Neurotropic (Latin, “turning”) refers to a substance that attracts or repulses neurons. Because many factors have both properties, both terms are used; in the recent literature, neurotrophin appears to be preferred. See also Nerve growth factor; Brain-derived neurotrophic factor; Conserved dopamine neurotrophic factor (CDNF); Neurotrophins 3 and 4/5.

Neurotrophins 3 and 4/5 (NT3, NT4/5) Neurotrophin 3 attracts sensory neurons from the dorsal root ganglia; NT4/5 attracts facial motor neurons and cerebellar granule cells.

Neurula Refers to an embryo during neurulation (i.e., while the neural tube is forming).

Neurulation Process of folding of the neural plate and closing of the cranial and caudal neuropores to form the neural tube.

Newt anterior gradient protein (nAG) Factor released by neurons in the blastema of a regenerating salamander limb that is thought to be the nerve-derived factor necessary for proliferation of the blastema cells.

Nieuwkoop center The dorsalmost vegetal blastomeres of the amphibian blastula, formed as a consequence of the cortical rotation initiated by the sperm entry; an important signaling center on the dorsal side of the embryo. One of its main functions is to induce the Organizer.

Nkx2-5 A gene that codes for a transcription factor that is critical in the regulatory network that specifies the heart cells. These networks are conserved across vertebrates. See also Mesp1.

NMPs See Neuromesoderm progenitors.

Nodal A paracrine factor and member of the TGF-β family involved in establishing left-right asymmetry in vertebrates and invertebrates.

Node The mammalian homologue of Hensen’s node.

Nodose placodes A pair of epibranchial placodes in vertebrates; they give rise to the sensory components of the paired 10th cranial nerve (the vagus nerve) that innervates many organs of the body, such as the heart, lungs, and gastrointestinal tract.

Noggin A BMP antagonist (i.e., blocks BMP signaling).

Non-skeletogenic mesenchyme Formed from the veg2 layer of the 60-cell sea urchin embryo, it generates pigment cells, immunocytes, and muscle cells. Also called secondary mesenchyme.

Noninvoluting marginal zone (NIMZ) Region of cells on the exterior of the gastrulating amphibian embryo that do not involute. They expand by epiboly along with the animal cap cells to cover the entire embryo, eventually forming the surface ectoderm.

Notch protein Transmembrane protein that is a receptor for Delta, Jagged, or Serrate, participants in juxtacrine interactions. Ligand binding causes Notch to undergo a conformational change that enables a part of its cytoplasmic domain to be cut off by the presenilin-1 protease. The cleaved portion enters the nucleus and binds to a dormant transcription factor of the CSL family. When bound to the Notch protein, the CSL transcription factors activate their target genes.

Notochord A transient mesodermal rod in the most dorsal portion of the embryo that plays an important role in inducing and patterning the nervous system. Characteristic feature of chordates. Nuclear RNA (nRNA) The original transcription product. Sometimes called heterogeneous nuclear RNA (hnRNA) or pre-messenger RNA (pre-mRNA); contains the cap sequence, the 5′ UTR, exons, introns, and the 3′ UTR.

Nuclear RNA selection Means of controlling gene expression by processing specific subsets of the nRNA population into mRNA in different types of cells.

Nuclei pulposi A gel-like mass in the center of the intervertebral discs derived from notochordal cells.

Nucleosome The basic unit of chromatin structure, composed of an octamer of histone proteins (two molecules each of histones H2A, H2B, H3, and H4) wrapped with two loops containing approximately 147 base pairs of DNA.

Nucleus (1) The membrane-enclosed organelle housing the eukaryotic chromosomes. (2) An organized cluster of the cell bodies of neurons in the brain with specific functions and connections.

Nurse cells Cells that provides nourishment to a developing egg. In Drosophila ovarioles, fifteen interconnected nurse cells generate mRNAs and proteins that are transported to a single developing oocyte.

Nymph Insect larval stage that resembles an immature adult of the species. Becomes progressively more mature through a series of molts.

O

Obesogens Substances that increase the production and accumulation of fat and adipose (fat) cells in the body. Several endocrine disruptors, including DES and BPA, have been shown to be obesogens.

Obligate mutualism Symbiosis in which the species involved are interdependent with one another to such an extent that neither partner could survive without the other.

Olfactory placodes Paired epidermal thickenings that form the nasal epithelium (smell receptors) as well as the ganglia for the olfactory nerves.

Oligodendrocytes  A type of glial cell within the central nervous system that wrap themselves around axons to produce a myelin sheath. Also called oligodendroglia.

Omphalomesenteric (umbilical) veins The veins that form from yolk sac blood islands. These veins bring nutrients to the mammalian embryo and transport gases to and from sites of respiratory exchange with the mother.

Oncogenes Regulatory genes that promote cell division, reduce cell adhesion, and prevent cell death. Can promote tumor formation and metastasis. Proto-oncogenes are the normal version of these genes, which, when overexpressed or misexpressed through mutations or inappropriate methylations, are called oncogenes and can result in cancer.

Oocyte A developing egg. A primary oocyte is in a stage of growth, has not gone through meiosis, and has a diploid nucleus. A secondary oocyte has completed its first meiotic division but not the second, and is haploid.

Oogenesis The development of the egg (ovum), including meiotic divisions and maturation.

Oogonia In animals, the female germ line cells that divide mitotically to become oocytes. Singular, oogonium.

Optic chiasm In vertebrates, the part of the lower side of the brain where the two optic nerves cross the midline, forming an x-shaped structure that then extends and innervates target cells on the contralateral side of the brain. (Chiasm comes from Chi, Greek for the letter X.)

Optic cups Double-walled chambers formed by the invagination of the optic vesicles.

Optic nerve Cranial nerve (CN II) that forms from axons of the neural retina that grow back to the brain by traveling down the optic stalk.

Optic vesicle Extend from the diencephalon and activate the head ectoderm’s latent lens-forming ability.

Oral plate A region where the ectoderm of the stomodeum meets the endoderm of the primitive gut. It later breaks open to form the oral opening.

Organ of Corti The receptor organ in the cochlea of the inner ear. It contains hair cells that reside in a fluid-filled chamber. Pressure waves from the movement of fluid in this chamber are transformed by the hair cells into action potentials that are sent to the brain by the auditory nerve and interpreted as sound.

Organization/activation hypothesis The theory that sex hormones act during the fetal or neonatal stage of a mammal’s life to organize the nervous system in a sex-specific manner, and that during adult life, the same hormones may have transitory motivational (or “activational”) effects.

Organizer In amphibians, the dorsal lip cells of the blastopore and their derivatives (notochord and head endomesoderm). Functionally equivalent to Hensen’s node in chick, the node in mammals, and the shield in fish. Organizer action establishes the basic body plan of the early embryo. Also known as the Spemann Organizer or (more correctly) the Spemann-Mangold organizer.

Organogenesis Interactions between, and rearrangement of, cells of the three germ layers to produce tissues and organs.

Organoids Rudimentary organs, usually the size of a pea, grown in culture from pluripotent stem cells.

Orthologues Genes from different species that are similar in DNA sequence because those genes were inherited from a common ancestor. Compare with Paralogues.

Oskar A protein involved in setting up the anterior-posterior axis of the Drosophila egg and future embryo by binding nanos mRNA in the posterior region of the egg, which will establish the posterior end of the future embryo.

Ossification See Osteogenesis.

Osteoblast A committed bone precursor cell.

Osteoclasts Multinucleated cells derived from a blood cell lineage that enter the bone through the blood vessels and destroy bone tissue during remodeling.

Osteocytes Bone cells. Derived from osteoblasts that become embedded in the calcified osteoid matrix.

Osteogenesis Bone formation; the transformation of mesenchyme into bone tissue through a progression from osteoclast to osteoblast to osteocyte. See Endochondral ossification; Intramembranous ossification.

Osteoid matrix A collagen-proteoglycan secreted by osteoblasts that is able to bind calcium.

Otic cup The structure formed during the morphogenesis of the inner ear when the otic placode invaginates to the point of forming the shape of a cup. This stage of inner ear development comes after the otic pit stage. Once the edges of the otic cup come together and fuse, the structure is called the otic vesicle (otocyst).

Otic pit The structure formed during the morphogenesis of the inner ear when the otic placode starts to invaginate, creating an indentation.

Otic placodes Paired epidermal thickenings that invaginate to form the inner ear labyrinth, whose neurons form the acoustic ganglia that enable us to hear.

Outer radial glia (oRG) Progenitor cells that reside in the subventricular zone of the cerebrum and give rise to intermediate progenitor (IP) cells.

Outflow tract In the developing heart, made up of the conus arteriosus and truncus arteriosus; becomes the base of the aorta and the pulmonary arteries.

Oval cells A population of progenitor cells in the liver that divide and form new hepatocytes and bile duct cells when hepatocytes themselves are unable to regenerate the liver sufficiently.

Ovariole The Drosophila egg chamber.

Ovary The structure that produces an ovum, the female gamete. In mammals, there is a pair of ovaries in the abdomen, which propel eggs into the oviducts. In angiosperms, the ovary is part of the carpel that contains the ovule(s).

Ovastacin A protease released by the cortical granules of mammalian eggs after fertilization to digest ZP2 and thereby prevent further sperm from entering the egg.

Oviparity Young hatch from eggs ejected by the mother, as in birds, amphibians, and most invertebrates.

Ovoviviparity Young hatch from eggs held within the mother’s body where they continue to develop for a period of time, as in certain reptiles and sharks. Compare with Viviparity.

Ovulation Release of the egg from the ovary.

Ovules In angiosperms, the structure comprising the megasporangium and the integument, which, after fertilization, develops into a seed.

Ovum The mature egg (at the stage of meiosis at which it is fertilized). Plural, ova.

P

P-cadherin  A type of cadherin found predominantly on the placenta, where it helps the placenta stick to the uterus (the P stands for placenta). See also Cadherins.

P-granules The germ plasm in C. elegans. Isolated to a single germline precursor cell (P4 blastomere) early in cleavage.

p53 A transcription factor that can stop the cell cycle, cause cellular senescence in rapidly dividing cells, instruct the initiation of apoptosis, and activate DNA repair enzymes. One of the most important regulators of cell division.

Pachytene Greek, “thick thread.” In the first meiotic division, the third stage of prophase I during which the chromatids thicken and shorten and can be seen by light microscopy as individual chromatids. Crossing over occurs during this stage.

Pair-rule genes Drosophila zygotic genes, regulated by gap gene proteins. Pair-rule genes are each expressed in seven stripes that divide the embryo into transverse bands perpendicular to the anterior-posterior axis. Pair-rule mutants lack portions of every other segment.

PAL-1  A maternally expressed transcription factor in the oocyte of the nematode C. elegans that is required for the differentiation of the P1 lineage of cells. P1 is one of the cells of the two-cell embryo.

PAR proteins Found in the cytoplasm of oocytes of the nematode C. elegans; involved in determining the anterior-posterior axis of the embryo following fertilization.

Paracrine factor A secreted, diffusible protein that provides a signal that interacts with and changes the cellular behavior of neighboring cells and tissues.

Paracrine interaction An interaction whereby proteins synthesized by one cell diffuse over a distance to induce changes in neighboring cells.

Paracrine signaling Signaling between cells that occurs across long distances through the secretion of paracrine factors into the extracellular matrix.

Paralogues Genes that are similar in sequence because they are the result of gene duplication events in an ancestral species. Compare with Orthologues.

Parasegment A “transegmental” unit in Drosophila that includes the posterior compartment of one segment and the anterior compartment of the immediately posterior segment; appears to be the fundamental unit of embryonic gene expression.

Parasitism Type of symbiosis in which one partner benefits at the expense of the other.

Parasympathetic (enteric) ganglia Ganglia of the parasympathetic (“rest and digest”) nervous system derived from vagal and sacral neural crest cells.

Paraxial (somitic) mesoderm Thick bands of embryonic mesoderm immediately adjacent to the neural tube and notochord. In the trunk, paraxial mesoderm gives rise to somites, in the head it (along with the neural crest) gives rise to the skeleton, connective tissues and musculature of the face and skull.

Paraxial protocadherin Adhesion protein expressed specifically in the paraxial (somite-forming) mesoderm during amphibian gastrulation; essential for convergent extension.

Parietal endoderm Cells of the primitive endoderm that contact the trophoblast of the mammalian embryo. See Primitive endoderm.

Parietal mesoderm See Somatic mesoderm.

Parthenogenesis Greek, “virgin birth.” When an ovum is activated in the absence of sperm. Normal development can proceed in many invertebrates and some vertebrates.

Pathway selection The first step in the specification of axonal connection, wherein the axons travel along a route that leads them to a particular region of the embryo.

Pattern formation The set of processes by which embryonic cells form ordered spatial arrangements of differentiated tissues.

Peri-implantation In placental mammals, the embryonic period from when the blastocyst is free in the uterus through its first interactions with the uterine endometrium.

Pericardial cavity The division of the coelom that surrounds the heart. Compare with Peritoneal cavity; Pleural cavity.

Perichondrium Connective tissue that surrounds most cartilage, except at joints.

Periclinal divisions In plants, cell divisions in which the new cell walls are laid down parallel to the surface of the plant. Compare with Anticlinal divisions.

Pericycle A layer of cells in the roots of plants, located between the endodermis and vascular tissue. It contains adult stem cells that can form new root apical meristems to grow lateral roots.

Pericytes Smooth-musclelike cells recruited to cover endothelial cells during vasculogenesis.

Periderm A temporary epidermis-like covering in the embryo that is shed once the inner layer differentiates to form a true epidermis.

Periosteal bone Bone that adds thickness to long bones and is derived from mesoderm via intramembranous ossification.

Periosteum A fibrous sheath containing connective tissue, capillaries, and bone progenitor cells and that covers the developing and adult bone.

Peripheral nervous system All the nerves and neurons lying outside the CNS (central nervous system; brain and spinal cord).

Peritoneal cavity The division of the coelom that encloses the abdominal organs. Compare with Pericardial cavity; Pleural cavity.

Permissive interaction Inductive interaction in which the responding tissue has already been specified, and needs only an environment that allows the expression of these traits.

Petals In an angiosperm flower, a non-sexual, non-photosynthetic, modified leaf. These are frequently brightly colored and can attract pollinating insects to the flower.

Petrosal placodes A pair of epibranchial placodes in vertebrates; they give rise to the sensory components of the paired 9th cranial nerve (the glossopharyngeal nerve) that innervates the tongue, carotid sinus, and carotid body, among other structures.

Pharyngeal arches Paired bars of mesenchymal tissue (derived from paraxial mesoderm, lateral plate mesoderm, and neural crest cells), covered by endoderm internally and ectoderm externally. Found near the pharynx of the vertebrate embryo, the arches form gill supports in fish, and many skeletal and connective tissue structures in the face, jaw, mouth, and larynx in other vertebrates. Also called branchial arches.

Pharyngeal clefts Clefts (invaginations) of external ectoderm that separate the pharyngeal arches. In amniotes, there are four pharyngeal clefts in the early embryo, but only the first becomes a structure (the external auditory meatus).

Pharyngeal pouches Inside the pharynx, these are where the pharyngeal epithelium (endoderm) pushes out laterally to form pairs of pouches between the pharyngeal arches. These give rise to the auditory tube, wall of the tonsil, thymus gland, parathyroids and thyroid.

Pharyngula Term often applied to the late neurula stage of vertebrate embryos.

Pharynx The region of the digestive tube anterior to the point at which the respiratory tube branches off.

Phenotypic heterogeneity Refers to the same mutation producing different phenotypes in different individuals.

Phenotypic plasticity The ability of an organism to react to an environmental input with a change in form, state, movement, or rate of activity.

Pheromones Vaporized chemicals emitted by an individual that results in communication with another individual. Pheromones are recognized by the vomeronasal organ of many mammalian species and play a major role in sexual behavior.

Phloem In vascular plants, the conduits that carry sugars produced by photosynthesis, along with other metabolites, from sources to sinks—primarily from the leaves to the nonphotosynthetic parts of the plant.

Phosphatidylinositol 4,5-bisphosphate (PIP₂) A membrane phospholipid that during the IP₃ pathway is split by the enzyme phospholipase C (PLC) to yield two active compounds: IP₃ and diacylglycerol (DAG). The IP₃ pathway is activated during fertilization, launching the slow block to polyspermy and activating the egg to start developing.

Phospholipase C (PLC) Enzyme in the IP₃ pathway that splits membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PIP₂) to yield IP₃ and diacylglycerol (DAG).

Phragmoplast A structure found in plants during cytokinesis that forms between the two daughter nuclei. Made up of cellulose-filled fusing vesicles, microtubules, microfilaments, and endoplasmic reticulum, it builds the cell wall between the two daughter cells.

Phyllotaxis The arrangement of leaves along a plant stem.

Phylotypic stage The stage that typifies a phylum, such as the late neurula or pharyngula of vertebrates, and which appears to be relatively invariant and to constrain its evolution.

Phytohormone A hormone, such as auxin, found in plants.

Pial surface The outer surface of the brain; “pial” refers to its being next to the pia mater, one of the meninges of the brain.

PIE-1 A maternally expressed transcription factor in the oocyte of the nematode C. elegans that is necessary for germline cell fate.

Pigmented epithelium Another term for pigmented retina. See Pigmented retina.

Pigmented retina The melanin-containing layer of the vertebrate eye that lies behind the neural retina. It forms from the outer layer of the optic cup. The black melanin pigment absorbs light coming through the neural retina, preventing it from bouncing back through the neural retina, which would distort the image perceived. Also referred to as pigmented epithelium.

Pioneer nerve fibers Axons that go ahead of other axons and serve as guides for them.

Pioneer transcription factors Transcription factors (e.g., Fox A1 and Pax7) that can penetrate repressed chromatin and bind to their enhancer DNA sequences, a step critical to establishing certain cell lineages.

Pistil See Carpel.

Piwi One of the proteins, along with Tudor, Vasa, and Nanos, expressed in germ cells to suppress gene expression.

Placenta The organ in placental mammals that serves as the interface between fetal and maternal circulations and has endocrine, immune, nutritive and respiratory functions. It consists of a maternal portion (the uterine endometrium, or decidua, which is modified during pregnancy) and a fetal component (the chorion).

Placodes An area of ectodermal thickening. These include the cranial placodes (e.g., the olfactory, lens, and otic placodes); and the epidermal placodes of cutaneous appendages such as hair and feathers, which are formed via inductive interactions between the dermal mesenchyme and the ectodermal epithelium.

Plasmodesmata (singular, Plasmo-desma) Cytoplasmic channels that form between adjacent plant cells, allowing for direct transport of substances between the cells.

Plastids Organelles found in plant cells that perform many functions, including photosynthesis. Example: Chloroplasts.

PLC See Phospholipase C.

PLCζ (Phospholipase C zeta) A soluble form of phospholipase C found in the head of mammalian sperm that is released during gamete fusion in fertilization. It sets off the IP₃ pathway in the egg that results in Ca²⁺ release and activation of the egg.

Pleiotropy The production of several effects by one gene or pair of genes.

Pleural cavity The division of the coelom that surrounds the lungs. Compare with Pericardial cavity; Peritoneal cavity.

Pluripotent hematopoietic stem cell See Hematopoietic stem cell (HSC).

Pluripotent Latin, “capable of many things.” A single pluripotent stem cell has the ability to give rise to different types of cells that develop from the three germ layers (mesoderm, endoderm, ectoderm) from which all the cells of the body arise. The cells of the mammalian inner cell mass (ICM) are pluripotent, as are embryonic stem cells. Each of these cells can generate any cell type in the body, but because the distinction between ICM and trophoblast has been established, it is thought that ICM cells are not able to form the trophoblast. Germ cells and germ cell tumors (such as teratocarcinomas) can also form pluripotent stem cells. Compare with Totipotent.

Pluteus larva Type of larva found in sea urchins and brittle stars; a planktonic larva that is bilaterally symmetrical, ciliated, and has long arms supported by skeletal spicules.

Polar body The smaller cell, containing hardly any cytoplasm, generated during the asymmetrical meiotic division of the oocyte. The first polar body is haploid and results from the first meiotic division and the secondary polar body is also haploid and results from the second meiotic division.

Polar granule component (PGC) A protein important for germ line specification and localized to Drosophila polar granules. PGC inhibits transcription of somatic cell-determining genes by preventing the phosphorylation of RNA polymerase II.

Polar granules Particles containing factors important for germ line specification that are localized to the pole plasm and pole cells of Drosophila.

Polar lobe An anucleate bulb of cytoplasm extruded immediately before first cleavage, and sometimes before the second cleavage, in certain spirally cleaving embryos (mostly in the mollusc and annelid phyla). It contains the determinants for the proper cleavage rhythm and the cleavage orientation of the D blastomere.

Polarization The first stage of cell migration, wherein a cell defines its front and its back ends, directed by diffusing signals (such as a chemotactic protein) or by signals from the extracellular matrix. These signals will reorganize the cytoskeleton such that the front part of the cell will form lamellipodia (or filopodia) with newly polymerized actin.

Pole cells About five nuclei in the Drosophila embryo that reach the surface of the posterior pole during the ninth division cycle and become enclosed by cell membranes. The pole cells give rise to the gametes of the adult.

Pole plasm Cytoplasm at the posterior pole of the Drosophila oocyte that contains the determinants for producing the abdomen and the germ cells.

Pollination The process by which pollen grains are transferred from the male anther of the flower to the female stigma of that flower or another flower.

PolyA tail A series of adenine (A) residues that are added by enzymes to the 3′ terminus of the mRNA transcript in the nucleus. The polyA tail confers stability on the mRNA, allows the mRNA to exit the nucleus, and permits the mRNA to be translated into protein.

Polyadenylation The insertion of a “tail” of some 200–300 adenylate residues on the RNA transcript, about 20 bases downstream of the AAUAAA sequence. This polyA tail (1) confers stability on the mRNA, (2) allows the mRNA to exit the nucleus, and (3) permits the mRNA to be translated into protein.

Polycomb proteins Family of proteins that bind to condensed nucleosomes, keeping the genes in an inactive state.

Polydactyly The presence of extra (supernumerary) digits, such as the dew claw on Great Pyrenees dogs.

Polyphenism A type of phenotypic plasticity, refers to discontinuous (“either/or”) phenotypes elicited by the environment. Compare with Reaction norm.

Polyspermy The entrance of more than one sperm during fertilization resulting in aneuploidy (abnormal chromosome number) and either death or abnormal development. An exception, called physiological polyspermy, occurs in some organisms such as Drosophila and birds, where multiple sperm enter the egg but only one sperm pronucleus fuses with the egg pronucleus.

Polytene chromosomes Chromosomes in the larval cells of Drosophila (but not the imaginal cells that give rise to the adult) in which the DNA undergoes many rounds of replication without separation, forming large “puffs” that are easily visible and indicate active gene transcription.

Population asymmetry Mode of maintaining homeostasis in a population of stem cells in which some of the cells are more prone to producing differentiated progeny, while others divide to maintain the stem cell pool.

Posterior marginal zone (PMZ) The end of the chick blastoderm where primitive streak formation begins and acts as the equivalent of the amphibian Nieuwkoop center. The cells of the PMZ initiate gastrulation and prevent other regions of the margin from forming their own primitive streaks.

Posterior necrotic zone  A zone of programmed cell death on the posterior side of the developing tetrapod limb that helps shape the limb.

Posterior neuropore  See Neuropore.

Posterior progenitor zone A region in the tailbud of vertebrate embryos that is made up of multipotent neuromesoderm progenitor cells. Also referred to as Caudal progenitor zone.

Postsynaptic cell  The target cell that receives chemical neurotransmitters from a presynaptic neuron, causing depolarization or hyperpolarization of the target cell’s membrane.

Posttranslational regulation Modifications that determine whether the translated protein will be active. These modifications can include cleaving an inhibitory peptide sequence; sequestration and targeting to specific cell regions; assembly with other proteins to form a functional unit; binding an ion (such as Ca²⁺); or modification by the covalent addition of a phosphate or acetate group.

Potency In referring to stem cells, the power to produce different types of differentiated cells.

Pre-granulosa cells The cells of the primordial follicle in the ovary that develop most closely to the germ cells. These become the granulosa cells of the follicle.

Pre-initiation complex The complex of RNA polymerase II at the promoter with transcription factors on the enhancer, as brought together by the Mediator molecules. See also Mediator.

Pre-metamorphosis The first stage in amphibian metamorphosis; the thyroid gland has begun to mature and is secreting low levels of T₄ and very low levels of T₃. The TRα receptor is present, but the TRβ receptor is not.

Prechordal plate See Prechordal plate mesoderm.

Prechordal plate mesoderm Precursor of the head mesoderm. The mesoderm cells that move inward during gastrulation ahead of the chordamesoderm.

Precursor cells (precursors) Widely used term to denote any ancestral cell type (stem or progenitor cells) of a particular lineage (e.g., neuronal precursors; blood cell precursors).

Predator-induced polyphenism The ability to modulate development in the presence of predators in order to express a more defensive phenotype.

Preeclampsia Medical condition of pregnant women characterized by hypertension, poor renal filtration, and fetal distress. A leading cause of premature birth and both fetal and maternal deaths. Pluripotent hematopoietic stem cell See Hematopoietic stem cell (HSC).

Preformationism The view, supported by the early microscopist Marcello Malpighi, that the organs of the embryo are already present, in miniature form, within the egg (or sperm). A corollary, embôitment (encapsulation), stated that the next generation already existed in a prefigured state within the germ cells of the first prefigured generation, thus ensuring that the species would remain constant.

Preimplantation genetics Testing for genetic diseases using blastomeres from embryos produced by in vitro fertilization before implanting the embryo in the uterus.

Prenatal diagnosis The use of chorionic villus sampling or amniocentesis to diagnose many genetic diseases before a baby is born.

Presomitic mesoderm (PSM) The mesoderm that will form the somites. Also known as the segmental plate.

Presynaptic neuron Neuron that transmits chemical neurotransmitters to a target cell, causing the depolarization or hyperpolarization of the target cell’s membrane.

Primary capillary plexus A network of capillaries formed by endothelial cells during vasculogenesis.

Primary cilium A single, non-motile cilium found on most cells; lacks a central pair of microtubules and is involved in part of the hedgehog signaling pathway by transporting signaling molecules on its microtubules using motor proteins.

Primary embryonic induction The process whereby the dorsal axis and central nervous system forms through interactions with the underlying mesoderm, derived from the dorsal lip of the blastopore in amphibian embryos.

Primary hypoblast During gastrulation in the chick embryo, a cellular layer that forms from cells that first delaminate from the anterior epiblast to form islands of disconnected cells and then migrate to form the primary hypoblast layer below the anterior epiblast.

Primary larvae Larvae that represent dramatically different body plans than the adult form and that are morphologically distinct from the adult; the plutei of sea urchins are such larvae. Compare with Secondary larvae.

Primary mesenchyme See Skeletogenic mesenchyme.

Primary neurulation The process that forms the anterior portion of the neural tube. The cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow tube.

Primary oocytes A developing egg that has passed through the oogonial stage and is in a stage of growth prior to any meiotic division. Contains a large nucleus called a germinal vesicle. At this stage, mRNA (maternal mRNA) is being made and stored in the egg. In mammals, a primary oocyte is arrested in first meiotic prophase until just prior to ovulation, when the first meiotic division is completed and the egg becomes a secondary oocyte. The second meiotic division is then arrested and is not completed until after fertilization.

Primary sex determination (or gonadal sex determination) The determination of the gonads to form either the egg-forming ovaries or sperm-forming testes. Primary sex determination is chromosomal and is not usually influenced by the environment in mammals, but can be affected by the environment in other vertebrates.

Primary spermatocytes Derived from mitotic division of the type B spermatogonia, these are the cells that first go through a period of growth and then enter meiosis.

Primaxial muscles The intercostal musculature between the ribs and the deep muscles of the back, formed from those myoblasts in the myotome closest to the neural tube.

Primed Prepared; in the context of embryonic stem cells, ready for differentiation.

Primed ESC An embryonic stem cell (ESC) that was cultured from an inner cell mass cell that already had some maturation toward the epiblast lineage. Compare with Naïve ESC. Also see Embryonic stem cells.

Primed pluripotent state The state of an embryonic stem cell that has undergone some maturation toward the epiblast lineage.

Primitive endoderm The layer of endoderm cells created during early mammalian development when the inner cell mass splits into two layers. The lower layer, in contact with the blastocoel, is the primitive endoderm, and is homologous to the hypoblast of the avian embryo. It will form the inner lining of the yolk sac and will be used for positioning the site of gastrulation, regulating the movements of cells in the epiblast, and promoting the maturation of blood cells. It is an extraembryonic layer that does not provide cells to the body of the embryo.

Primitive groove A depression that forms within the primitive streak that serves as an opening through which migrating cells pass into the deep layers of the embryo.

Primitive knot/pit See Hensen’s node.

Primitive pit During chick gastrulation, a funnel-shaped depression at the center of Hensen’s node through which cells migrate to form the notochord and prechordal plate. See Hensen’s node.

Primitive streak The first morphological sign of gastrulation in amniotes, it first arises from a local thickening of the epiblast at the posterior edge of the area pellucida, called Koller’s sickle. Homologous to the amphibian blastopore.

Primordial germ cells (PGCs) Gamete progenitor cells, which typically arise elsewhere and migrate into the developing gonads.

Proacrosin The inactive form of a mammalian sperm proteinase that is stored in the acrosome and released during the acrosomal reaction and helps the sperm move through the zona pellucida of the egg.

Procambium In plants, a layer of stem cells that produces the vascular tissue; it can also give rise to the pericycle in the roots.

Proembryo During development in seed plants, the stage created by the asymmetrical first cleavage of the zygote. At this two-cell stage, the smaller apical cell will give rise to all parts of the plant proper, except the tip of the root; the larger basal cell will generate the root apex and the suspensor, which connects that embryo to the nutrients in the seed.

Proerythroblast A red blood cell precursor.

Progamic phase The events of pollen development from pollination to fertilization; the period of pollen tube growth through the female pistil.

Progenesis Condition in which the gonads and germ cells develop at a faster rate than the rest of the body, becoming sexually mature while the rest of the body is still in a juvenile phase. Compare with Neoteny.

Progenitor An ancestor in the direct lineage; a predecessor or precursor.

Progenitor cells Relatively undifferentiated cells that have the capacity to divide a few times before differentiating and, unlike stem cells, are not capable of unlimited self-renewal. They are sometimes called transit amplifying cells because they divide while migrating.

Progerias Premature aging syndromes; in humans and mice, appear to be caused by mutations that prevent the functioning of DNA repair enzymes.

Progesterone A steroid hormone important in the maintenance of pregnancy in mammals. Progesterone secreted from the cumulus cells may act as a chemotactic factor for sperm.

Programmed cell death See Apoptosis.

Progress zone (PZ) Highly proliferative limb bud mesenchyme directly beneath the apical ectodermal ridge (AER). The proximal-distal growth and differentiation of the limb bud are made possible by a series of interactions between the AER and the progress zone. Also called the undifferentiated zone.

Progress zone model Model for specification of proximal-distal specification of the limb that postulates that each mesoderm cell is specified by the amount of time it spends dividing in the progress zone. The longer a cell spends in the progress zone, the more mitoses it achieves and the more distal its specification becomes.

Prometamorphosis The second stage in amphibian metamorphosis, during which the thyroid matures and secretes more thyroid hormones.

Promoter Region of a gene containing the DNA sequence to which RNA polymerase II binds to initiate transcription. See also CpG islands; Enhancer.

Pronephric duct Arises in the intermediate mesoderm, migrates caudally, and induces the adjacent mesenchyme to form the pronephros, or tubules of the initial kidney of the embryo. The pronephric tubules form functioning kidneys in fish and in amphibian larvae but are not believed to be active in amniotes. As the duct continues growing downward it induces the mesonephric mesenchyme to form tubules, at which point it is called the mesonephric duct. Also called Wolffian duct and nephric duct.

Pronephros The first region of kidney mesenchyme to form kidney tubules in vertebrates. The pronephros is a functioning kidney in fish and amphibian larvae, but is not believed to be active in amniotes, and degenerates after other regions of the kidney develop.

Pronuclei The male and female haploid nuclei within a fertilized egg that fuse to form the diploid nucleus of the zygote.

Pronymph The stage immediately after hatching in ametabolous insects, when the organism bears the structures that enabled it to get out of the egg; after this stage, the insect looks like a small adult.

Prosencephalon The forebrain; the most anterior vesicle of the developing vertebrate brain. Will form two secondary brain vesicles: the telencephalon and the diencephalon.

Protamines Basic proteins, tightly compacted through disulfide bonds, that package the DNA of the sperm nucleus.

Protein-protein interaction domain A domain of a transcription factor that enables it to interact with other proteins on the enhancer or promoter.

Proteoglycans Large extracellular matrix molecules consisting of core proteins (such as syndecan) with covalently attached glycosaminoglycan polysaccharide side chains. Two of the most widespread are heparan sulfate proteoglycan and chondroitin sulfate proteoglycan.

Proteome The number and type of proteins encoded by the genome.

Prothoracic gland In insects, a gland that secretes ecdysone, a molting hormone; production of ecdysone is stimulated by the prothoracicotropic hormone.

Prothoracicotropic hormone (PTTH) A peptide hormone that initiates the molting process in insects when it is released by neurosecretory cells in the brain in response to neural, hormonal, or environmental signals. PTTH stimulates the production of ecdysone by the prothoracic gland.

Protocadherins A class of cadherins that lack the attachment to the actin skeleton through catenins. They are an important means of keeping migrating epithelia together, and they are important in separating the notochord from surrounding mesoderm during its formation.

Protostomes Greek, “mouth first.” Animals that form their mouth regions from the blastopore, such as molluscs. Compare with Deuterostomes.

Proximal-distal axis The close-far axis, e.g., shoulder-finger or hip-toe (in relation to the body’s center).

Pseudohermaphroditism Intersex conditions in which the secondary sex characteristics differ from what would be expected from the gonadal sex. Male pseudohermaphroditism (e.g., androgen insensitivity syndrome) describes conditions wherein the gonadal sex is male and the secondary sex characteristics are female, while female pseudohermaphroditism describes the reverse situation (e.g., congenital adrenal hyperplasia).

Pupa A non-feeding stage of a holometabolous insect following the last instar when the organism is going through metamorphosis, being transformed from a larva into an adult (imago).

Purkinje fibers Modified heart muscle cells in the inner walls of the ventricles, specialized for rapid conduction of the contractile signal. Essential for synchronizing the contractions of the ventricles in amniotes.

Purkinje neurons Large, multibranched neurons that are the major cell type of the cerebellum.

Q

Quiescence A period of inactivity or dormancy; usually affiliated with a period of stem cell behavior.

R

R-cadherin  A type of cadherin critical in forming the retina (the R stands for retina). See Cadherins.

R-spondin1 (Rspo1) Small, soluble protein that upregulates the Wnt pathway and is critical for ovary formation in mammals.

RA See Retinoic acid.

Radial glial cells (radial glia) Neural progenitor cells found in the ventricular zone (VZ) of the developing brain. At each division, they generate another VZ cell and a more committed cell type that leaves the VZ to differentiate.

Radial holoblastic cleavage Cleavage pattern in echinoderms. The cleavage planes, which divide the egg completely into separate cells (holoblastic), are parallel or perpendicular to the animal-vegetal axis of the egg.

Radial intercalation In fish embryos, the movement of deep epiblast cells into the more superficial epiblast layer, helping to power epiboly during gastrulation.

Random epigenetic drift The hypothesis that the chance accumulation of inappropriate epigenetic methylation due to errors made by the DNA methylating and demethylating enzymes could be the critical factor in aging and cancers.

Ras A G-protein in the RTK pathway. Mutations in the RAS gene account for a large proportion of cancerous human tumors.

Rathke’s pouch An outpocketing of the ectoderm in the roof of the oral region that forms the glandular portion of the pituitary gland in vertebrates. It meets the infundibulum, an outpocketing of the floor of the diencephalon, which forms the neural portion of the pituitary gland.

Reaction norm A type of phenotypic plasticity in which the genome encodes the potential for a continuous range of potential phenotypes; the environment the individual encounters determines which of the potential phenotypes develops. Compare with Polyphenism.

Reaction-diffusion mechanism Model for developmental patterning, especially that of the limb, wherein two homogeneously distributed substances (an activator, substance A, that activates itself as well as forming its own, faster-diffusing inhibitor, substance I) interact to produce stable complex patterns during morphogenesis. According to this model, set forth in the early 1950s by mathematician Alan Turing, the patterns generated by this reaction-diffusion mechanism represent regional differences in the concentrations of the two substances.

Reactive oxygen species (ROS) Metabolic by-products that can damage cell membranes and proteins and destroy DNA. ROS are generated by mitochondria due to insufficient reduction of oxygen atoms and include superoxide ions, hydroxyl (“free”) radicals, and hydrogen peroxide.

Receptor A protein that functions to bind a ligand. See also Ligand.

Receptor tyrosine kinase (RTK) A receptor that spans the cell membrane and has an extracellular region, a transmembrane region, and a cytoplasmic region. Ligand (paracrine factor) binding to the extracellular domain causes a conformational change in the receptor’s cytoplasmic domains, activating kinase activity that uses ATP to phosphorylate specific tyrosine residues of particular proteins.

Reciprocal inductions A common sequential feature of induction: One tissue induces another, and that tissue then acts back on the original inducing tissue and induces it, thus the inducer becomes the induced.

Reelin An extracellular matrix protein found in the developing cerebellum and cerebrum. In the cerebellum it permits neurons to bind to glial cells as neurons migrate and form layers; in the cerebrum it directs migration of neurons toward the pial surface.

Regeneration blastema A collection of relatively undifferentiated cells that are organized into new structures by paracrine factors located at the cut surface. The collection of cells may be derived from differentiated tissue near the site of amputation that dedifferentiate, go through a period of mitosis, and then redifferentiate into the lost structures, as in the regenerating salamander limb, or may be from pluripotent stem cells that migrate to the cut surface, as in flatworm regeneration.

Regeneration The ability to reform body structure or organ that has been damaged or destroyed by trauma or disease.

Regenerative medicine The therapeutic use of stem cells to correct genetic pathologies (e.g., sickle-cell anemia) or repair damaged organs.

Regulation The ability to respecify cells so that the removal of cells destined to become a particular structure can be compensated for by other cells producing that structure. This is seen when an entire embryo is produced by cells that would have contributed only certain parts to the original embryo. It is also seen in the ability of two or more early embryos to form one chimeric individual rather than twins, triplets, or a multiheaded individual.

Relational pleiotropy The action of a gene in one part of the embryo that affects other parts, not by being expressed in these other parts but by having initiated a cascade of events that affect these other parts.

Reporter gene A gene with a product that is readily identifiable and not usually made in the cells of interest. Can be fused to regulatory elements from a gene of interest, inserted into embryos, and then monitored for reporter gene expression. If the sequence contains an enhancer, the reporter gene should become active at particular times and places. The genes for green fluorescent protein (GFP) and β-galactosidase (lacZ) are common examples.

Repressor A DNA or RNA-binding regulatory element that actively represses the transcription of a particular gene.

Resact A 14-amino-acid peptide that has been isolated from the egg jelly of the sea urchin Arbacia punctulata that acts as a chemotactic factor and sperm-activating peptide for sperm of the same species, i.e., it is species-specific and is thereby a mechanism to ensure that fertilization is also species-specific. See also Sperm-activating peptide.

Resegmentation Occurs during formation of the vertebrae from sclerotomes; the rostral segment of each sclerotome recombines with the caudal segment of the next anterior sclerotome to form the vertebral rudiment and this enables the muscles of the vertebral column derived from the myotomes to coordinate the movement of the skeleton, permitting the body to move laterally.

Respiratory tube The future respiratory tract, which forms as an epithelial outpocketing of the pharynx, and eventually bifurcates into the two lungs.

Responder During induction, the tissue being induced. Cells of the responding tissue must have receptors for the inducing molecules and be competent to respond to the inducer.

Resting membrane potential The membrane potential (membrane voltage) normally maintained by a cell, determined by the concentration of ions on either side of the membrane. Generally this is –70mV, where the inside of the cell is negatively charged with respect to the exterior.

Rete testis A network of thin canals that convey sperm from the seminiferous tubules to the efferent ducts.

Reticulocyte Cell derived from the mammalian erythroblast that has expelled its nucleus. Although reticulocytes, lacking a nucleus, can no longer synthesize globin mRNA, they can translate existing messages into globins. A reticulocyte differentiates into a mature red blood cell (erythrocyte), in which even translation of mRNA doesn’t take place.

Retina See Neural retina.

Retinal ganglion cells (RGCs) Neurons in the retina of the eye whose axons are guided to the optic tectum of the brain. Guidance cues come from netrin, slit, semaphorin, and ephrin families of molecules.

Retinal homeobox (Rx) A transcription factor coded for by the Rx gene. Produced in the eye field and helps specify the retina.

Retinoic acid (RA) A derivative of vitamin A and morphogen involved in anterior-posterior axis formation. Cells receiving high levels of RA express posterior genes.

Retinoic acid-4-hydroxylase An enzyme that degrades retinoic acid.

Retinotectal projection The map of retinal connections to the optic tectum. Point-for-point correspondence between the cells of the retina and the cells of the tectum that enables the animal to see an unbroken image.

Reverse development The transformation of a mature stage of an organism to a more juvenile stage of its life cycle. Seen in certain hydrozoan species where the sexually mature adult-stage medusa is able to revert to the polyp stage.

Reverse genetics Genetic technique of knocking out or knocking down the expression of a gene in an organism and then studying the phenotype that results. Compare with Forward genetics.

Rheotaxis A form of movement where a cell or animal turns to face a current of gas or liquid. Sperm traveling through the female reproductive tract are thought to have positive rheotaxis.

Rho GTPases A family of molecules including RhoA, Rac1, and Cdc42 that convert soluble actin into fibrous actin cables that anchor at the cadherins. These help mediate cell migration by lamellipodia and filopodia and the cadherin-dependent remodeling of the cytoskeleton.

Rhombencephalon The hindbrain, the most caudal vesicle of the developing vertebrate brain; will form two secondary brain vesicles, the metencephalon and myelencephalon.

Rhombomeres Periodic swellings that divide the rhombencephalon into smaller compartments, each with a different fate and different associated nerve ganglia.

Right-left axis Specification of the two lateral sides of the body.

Ring canals The cytoplasmic interconnections between the cystocytes that become the ovum and nurse cells in an ovariole of Drosophila.

RNA interference (RNAi) Process by which miRNAs inhibit expression of specific genes by degrading their mRNAs.

RNA polymerase II An enzyme that binds to a promoter on DNA and, when activated, catalyzes the transcription of an RNA template from the DNA.

RNA-induced silencing complex (RISC) A complex containing several proteins and a microRNA, which can then bind to the 3′ UTR of messages and inhibit their translation.

RNA-Seq (RNA sequencing) Using next-generation sequencing technology to sequence and quantify the RNA present in a biological sample.

Robo proteins See Roundabout proteins.

Robustness (canalization) The ability of an organism to develop the same phenotype despite perturbations from the environment or from mutations. It is a function of interactions within and between developmental modules.

Rods Photoreceptors in the neural retina of the vertebrate eye that are more sensitive to low light than cones. They contain only one light-sensitive pigment and therefore do not transmit information about color.

Roof plate Dorsal region of the neural tube important in the establishment of dorsal-ventral polarity. The adjacent epidermis induces expression of BMP4 in the roof plate cells, which in turn induces a cascade of TGF-β proteins in adjacent cells of the neural tube.

Root apical meristem (RAM) In plants, the meristem at the tip of a growing root. See Meristem.

Rosettes Pinwheel-like structures, such as the structures made up of small clusters of neural stem cells surrounded by ciliated ependymal cells found in the V-SVZ of the mammalian cerebrum.

Rostral-caudal Latin, “beak-tail.” An anterior-posterior positional axis; often used when referring to vertebrate embryos or brains.

Rotational cleavage The cleavage pattern for mammalian and nematode embryos. In mammals, the first cleavage is a normal meridional division while in the second cleavage, one of the two blastomeres divides meridionally and the other divides equatorially. In C. elegans, each asymmetrical division produces one founder cell that produces differentiated descendants; and one stem cell. The stem cell lineage always undergoes meridional division to produce (1) an anterior founder cell and (2) a posterior cell that will continue the stem cell lineage.

Roundabout proteins (Robo) Proteins that are receptors for slit proteins, involved in controlling the crossing of the midline of commissural axons.

Royalactin Protein that induces a honeybee larva to become a queen. Fed to the larva by worker bees, the protein binds to EGF receptors in the larva fat body and stimulates the production of juvenile hormone, which elevates the levels of yolk proteins necessary for egg production.

RTK pathway The receptor tyrosine kinase (RTK) is dimerized by ligand, which causes autophosphorylation of the receptor. An adaptor protein recognizes the phosphorylated tyrosines on the RTK and activates an intermediate protein, GEF, which activates the Ras G protein by allowing the phosphorylation of the GDP-bound Ras. At the same time, the GAP protein stimulates the hydrolysis of this phosphate bond, returning Ras to its inactive state. The active Ras activates the Raf protein kinase C (PKC), which in turn phosphorylates a series of kinases. Eventually, an activated kinase alters gene expression in the nucleus of the responding cell by phosphorylating certain transcription factors (which can then enter the nucleus to change the types of genes transcribed) and certain translation factors (which alter the level of protein synthesis). In many cases, this pathway is reinforced by the release of Ca²⁺.

S

Sacral neural crest Neural crest cells that lie posterior to the trunk neural crest and along with the vagal neural crest generate the parasympathetic (enteric) ganglia of the gut that are required for peristaltic movement in the bowels.

Sarcopterygian fishes Lobe-finned fish, including coelacanths and lungfish. Tetrapods evolved from sarcopterygian ancestors.

Satellite cells Populations of muscle stem cells and progenitor cells that reside alongside adult muscle fibers and can respond to injury or exercise by proliferating into myogenic cells that fuse and form new muscle fibers.

Scatter factor See Hepatocyte growth factor.

Schizocoely The embryonic process of forming the coelom by hollowing out a previously solid cord of mesodermal cells. Typical of protostomes. See also Enterocoely.

Schwann cell Type of glial cell of the peripheral nervous system that generates a myelin sheath, allowing rapid transmission of electrical signals along an axon.

Sclerotomes Blocks of mesodermal cells in the ventromedial half of each somite that will differentiate into the vertebrae, intervertebral discs (except for the nuclei pulposi) and ribs, in addition to the meninges of the spinal cord and the blood vessels that serve the spinal cord. They are also critical in patterning the neural crest and motor neurons.

Sebaceous gland Glands that are associated with hair follicles and produce an oily substance, sebum, that serves to lubricate the hair and skin.

Secondary hypoblast Underlies the epiblast in the bilaminar avian blastoderm. A sheet of cells derived from deep yolky cells at the posterior margin of the blastoderm that migrates anteriorly, displacing the hypoblast islands (primary hypoblast). Hypoblast cells do not contribute to the avian embryo proper, but instead form portions of the external membranes, especially the yolk sac, and provide chemical signals that specify the migration of epiblast cells. Also called endoblast.

Secondary larvae Larvae that possess the same basic body plan as the adult; caterpillars and tadpoles are examples. Compare with Primary larvae.

Secondary mesenchyme See Non-skeletal mesenchyme.

Secondary neurulation The process that forms the posterior portion of the neural tube by the coalescence of mesenchyme cells into a solid cord that subsequently forms cavities that coalesce to create a hollow tube.

Secondary oocyte The haploid oocyte following the first meiotic division (this division also generates the first polar body).

Secondary sex determination Developmental events, directed by hormones produced by the gonads that affect the phenotype outside the gonads. This includes the male or female duct systems and external genitalia, and, in many species, sex-specific body size, vocal cartilage, and musculature.

Secondary spermatocytes A pair of haploid cells derived from the first meiotic division of a primary spermatocyte, which then complete the second division of meiosis to generate the four haploid spermatids.

Seed The embryonic plant, a ripened ovule, enclosed by a protective coat.

Seed coat The outer protective jacket of the seed. The seed coat forms from the two integumental layers of the ovule.

Segment polarity genes Drosophila zygotic genes, activated by the proteins encoded by the pair-rule genes, whose mRNA and protein products divide the embryo into segment-sized units, establishing the periodicity of the embryo. Segment polarity mutants showed defects (deletions, duplications, polarity reversals) in every segment.

Segmental plate A synonym for presomitic mesoderm, the mesoderm that will form the somites.

Segmentation genes Genes whose products divide the early Drosophila embryo into a repeating series of segmental primordia along the anterior-posterior axis. Include gap genes, pair-rule genes, and segment polarity genes.

Selective affinity Principle that explains why disaggregated cells reaggregate to reflect their embryonic positions. Specifically, the inner surface of the ectoderm has a positive affinity for mesodermal cells and a negative affinity for the endoderm, while the mesoderm has positive affinities for both ectodermal and endodermal cells.

Self-renewal The ability of a cell to divide and produce a replica of itself.

Semaphorins Extracellular matrix proteins that repel migrating neural crest cells and axonal growth cones.

Seminiferous tubules In male mammals, form in the gonad from the testis cords. They contain Sertoli cells (nurse cells) and spermatogonia (sperm stem cells).

Senescence The physiological deterioration that characterizes old age.

Sensory placodes In vertebrates, the ectodermal placodes that contribute to the sense organs, forming the olfactory epithelium, inner ear, lens of the eye, and cranial sensory ganglia, as well as lateral line organs in amphibians and fish.

Sepals Outer structures of the flower, usually protective and photosynthetic, that surround the inner, fertile, portions of the flower.

Septum A partition that divides a chamber, such as the atrial septa that split the developing atrium into left and right atria. Plural, septa.

Sertoli cells Large secretory support cells in the seminiferous tubules of the testes involved in spermatogenesis in the adult through their role in nourishing and maintaining the developing sperm cells. They secrete AMH in the fetus and provide a niche for the incoming germ cells. They are derived from somatic cells, which are in turn derived from the genital ridge epithelium.

Sesamoid bone Small bones at joints that form as a result of mechanical stress (such as the patella). They are derived from mesoderm via intramembranous ossification.

Sex-lethal (Sxl) An autosomal gene in Drosophila involved in sex determination. It codes for a splicing factor that initiates a cascade of RNA processing events, which eventually lead to male-specific and female-specific transcription factors, the Doublesex proteins. See Doublesex.

Shh See Sonic hedgehog.

Shield See Embryonic shield.

Shoot apical meristem (SAM) In plants, the meristem at the tip of a growing shoot that is the source of stem cells for all plant organs above ground, such as leaves and flowers. See Meristem.

Signal transduction cascades Pathways of response whereby paracrine factors bind to a receptor that initiates a series of enzymatic reactions within the cell that in turn have often several responses as their end point, such as the regulation of transcription factors (such that different genes are expressed in the cells reacting to these paracrine factors) and/or the regulation of the cytoskeleton (such that the cells responding to the paracrine factors alter their shape or are permitted to migrate).

Silencer A DNA regulatory element that binds transcription factors that actively repress the transcription of a particular gene.

Single stem cell asymmetry A mode of stem cell division in which two types of cells are produced at each division, a stem cell and a developmentally committed cell.

Sinistral coiling Left-coiling. In a snail, having its coils open to the left of its shells. See also Dextral coiling.

Sinus venosus The posterior region of the developing heart, where the two major vitelline veins bringing blood to the heart fuse. Inflow tract to the atrial area of the heart.

Sinusoidal endothelial cells Cells that line the large blood channels (sinusoids) of the liver and critical to liver function. Also provides paracrine factors needed for division of hepatoblast stem cells during liver regeneration. Long considered mesodermal in origin, they now are known to be derived at least in part by specialized endodermal cells.

Sirtuin genes Encode histone deacetylation (chromatin-silencing) enzymes that guard the genome, preventing genes from being expressed at the wrong times and places, and may help repair chromosomal breaks. They may be important defenses against premature aging.

Sister chromatids Each of a pair of newly replicated chromatids. They have the same DNA sequence and are joined by a centromere.

Skeletogenic mesenchyme Also called primary mesenchyme, formed from the first tier of micromeres (the large micromeres) of the 60-cell sea urchin embryo. They ingress, moving into the blastocoel, and form the larval skeleton.

SKN-1 A maternally expressed transcription factor in the oocyte of the nematode C. elegans that controls the fate of the EMS cell, one of the cells of the 4-cell stage that marks the ventral region of the developing embryo.

Slit proteins  Proteins of the extracellular matrix that are chemorepulsive; involved in inhibiting migration of neural crest cells and in controlling growth of commissural axons.

Slow block to polyspermy See Cortical granule reaction.

Smad family Transcription factors activated by members of the TGF-β superfamily that function in the SMAD pathway. See also SMAD pathway.

SMAD pathway The pathway activated by members of the TGF-β superfamily. The TGF-β ligand binds to a type II TGF-β receptor, which allows that receptor to bind to a type I TGF-β receptor. Once the two receptors are in close contact, the type II receptor phosphorylates a serine or threonine on the type I receptor, thereby activating it. The activated type I receptor can now phosphorylate the Smad proteins. Smads 1 and 5 are activated by the BMP family of TGF-β factors, while the receptors binding activin, Nodal, and the TGF-β family phosphorylate Smads 2 and 3. These phosphorylated Smads bind to Smad4 and form the transcription factor complex that will enter the nucleus.

Small micromeres A cluster of cells produced by the fifth cleavage at the vegetal pole in the sea urchin embryo when the micromeres divide.

Solenoids Structures, created from tightly wound nucleosomes stabilized by histone H1, that inhibit transcription of genes by preventing transcription factors and RNA polymerases from gaining access to the genes.

Soma Greek, “body.” Can refer to the cell body (particularly of neurons) or to the cells that form an organism’s body (as distinct from the germ cells).

Somatic (parietal) mesoderm Derived from lateral mesoderm closest to the ectoderm (dorsal) and separated from other components of lateral mesoderm (splanchnic, near endoderm, ventral) by the intraembryonic coelom. Together with the overlying ectoderm, the somatic mesoderm comprises the somatopleure, which will form the body wall. The somatic mesoderm also forms part of the lining of the coelom. Not to be confused with somitic (paraxial) mesoderm.

Somatic cell nuclear transfer (SCNT) Less accurately known as “cloning,” the procedure by which a cell nucleus is transferred into an activated enucleated egg and directs the development of a complete organism with the same genome as the donor cell.

Somatic cells Cells that make up the body—i.e., all cells in the organism that are not germ cells. Compare with Germ cells.

Somatic mutation theory (SMT) A hypothesis for cancer initiation, positing that carcinogenesis is a cellular phenomenon, caused by mutations in otherwise normal cells, which instruct the cell to proliferate.

Somatopleure Made up of somatic lateral plate mesoderm and overlying ectoderm.

Somites Segmental blocks of mesoderm formed from paraxial mesoderm adjacent to the notochord (the axial mesoderm). Each contain major compartments: the sclerotome, which forms the axial skeleton (vertebrae and ribs), and the dermomyotome, which goes on to form dermatome and myotome. The dermatome forms the dermis of the back; the myotome forms musculature of the back, rib cage, and ventral body. Additional muscle progenitors detach from the lateral edge of the dermomyotome and migrate into the limbs to form the muscles of the fore and hindlimbs.

Somitic mesoderm See Paraxial mesoderm. Not to be confused with somatic mesoderm.

Somitogenesis The process of segmentation of the paraxial mesoderm to form somites, beginning cranially and extending caudally. Its components are (1) periodicity, (2) fissure formation (to separate the somites), (3) epithelialization, (4) specification, and (5) differentiation.

Somitomeres Early pre-somites, consisting of paraxial mesoderm cells organized into whorls of cells.

Sonic hedgehog (Shh) The major hedgehog family paracrine factor. Shh has distinct functions in different tissues of the embryo. For example, it is secreted by the notochord inducing the ventral region of the neural tube to form the floor plate. It is also involved in the establishment of left-right asymmetry, primitive gut tube differentiation, proper feather formation in birds, differentiation of the sclerotome, and patterning the anterior-posterior axis of limb buds.

Sox9 An autosomal gene involved in several developmental processes, most notably bone formation. In the genital ridge of mammals, it induces testis formation, and XX humans with an extra copy of SOX9 develop as males.

Specification The first stage of commitment of cell or tissue fate during which the cell or tissue is capable of differentiating autonomously (i.e., by itself) when placed in an environment that is neutral with respect to the developmental pathway. At the stage of specification, cell commitment is still capable of being reversed.

Specified The stage during development when a cell is capable of differentiating autonomously when placed in a neutral environment, such as a petri dish. A specified cell’s commitment to cell identity is still labile, however, and can be altered if the cell is transplanted to a population of differently specified cells. The specified stage precedes determination. Compare with Determination.

Spemann’s Organizer See Organizer.

Sperm head Consists of the nucleus, acrosome, and minimal cytoplasm.

Sperm-activating peptides (SAPs) Small chemotactic peptides found in the jelly of echinoderm eggs. They diffuse away from the egg jelly in seawater and are species specific, only attracting sperm of the same species. Resact, found in the sea urchin Arbacia punctulata, is an example.

Spermatids Haploid sperm cells, the stage following the second meiotic division. In mammals, spermatids are still connected to one another by cytoplasmic bridges, allowing for diffusion of gene products across the cytoplasmic bridges.

Spermatogenesis The production of sperm.

Spermatogonia Sperm stem cells. When a spermatogonium stops undergoing mitosis, it becomes a primary spermatocyte and increases in size prior to meiosis.

Spermatogonial stem cell population In mammals, the group of stem cells that will form the germ cell lineage leading up to the sperm. They divide mitotically, but not completely, forming clusters of spermatogonia.

Spermatozoa The male gamete or mature sperm cell.

Spermiogenesis The differentiation of the mature spermatozoa from the haploid round spermatid.

Spina bifida A congenital defect resulting from incomplete closure of the spine around the spinal cord, usually in the lower back. There are differing degrees of severity, the most severe being when the neural folds also fail to close.

Spiral phyllotaxis In plants, the arrangement of lateral organs, such as leaves and flowers in the inflorescence, in which successive organs emerge sequentially around the apex in accordance with Fibonacci’s “golden angle” of 137.5 degrees between each organ.

Spiral holoblastic cleavage Characteristic of several animal groups, including annelid worms, some flatworms, and most molluscs. Cleavage is at oblique angles to the animal-vegetal axis, forming a “spiral” arrangement of daughter blastomeres. The cells touch one another at more places than do those of radially cleaving embryos, assuming the most thermodynamically stable packing orientation.

Splanchnic (visceral) mesoderm Also called the visceral mesoderm and splanchnic lateral plate mesoderm; derived from lateral mesoderm closest to the endoderm (ventral) and separated from other component of lateral mesoderm (somatic, near ectoderm, dorsal) by the intraembryonic coelom. Together with the underlying endoderm, it forms the splanchnopleure. The splanchnic mesoderm will form the heart, capillaries, gonads, the visceral peritoneum and serous membranes that cover the organs, the mesenteries, and blood cells.

Splanchnopleure Made up of splanchnic lateral plate mesoderm and underlying endoderm. See Splanchnic mesoderm.

Spliceosome A complex made up of small nuclear RNAs (snRNAs) and splicing factors, that binds to splice sites and mediates the splicing of nRNA.

Splicing The cutting, rearranging, and ligating back together of the mRNA precursor into separate messages that specify different proteins by using different combinations of potential exons. See Differential RNA processing.

Splicing enhancer A cis-acting sequence on nRNA that promotes the assembly of spliceosomes at RNA cleavage sites.

Splicing factors Proteins that bind to splice sites or to the areas adjacent to them.

Splicing isoforms Different proteins encoded by the same gene and generated by alternative splicing.

Splicing silencer A cis-acting sequence on nRNA that acts to exclude exons from an mRNA sequence.

Sporophytic Referring to the sporophyte, the diploid growth stage in the alternating life cycle of plants and algae. Compare with Gametophytic.

Src family kinases (SFK) Family of enzymes that phosphorylate tyrosine residues; involved in many signaling events, including the responses of growth cones to chemoattractants.

Sry Sex-determining region of the Y chromosome. The Sry gene encodes the mammalian testis-determining factor. It is probably active for only a few hours in the genital ridge, during which time it synthesizes the Sry transcription factor, whose primary role is to activate the Sox9 gene required for testis formation.

Stamen The male organ of a flower. It usually comprises a stalk (filament) and a pollen-producing anther.

STAT Signal transducers and activators of transcription. A family of transcription factors, part of the JAK-STAT pathway. Important in the regulation of human fetal bone growth.

Stem cell A relatively undifferentiated cell from the embryo, fetus, or adult that, that divides and when it does so, produces (1) one cell that retains its undifferentiated character and remains in the stem cell niche; and (2) a second cell that leaves the niche and can undergo one or more paths of differentiation. See also Adult stem cell; Embryonic stem cell.

Stem cell factor (SCF) Paracrine factor important for maintaining certain stem cells, including hematopoietic, sperm, and pigment stem cells. Binds to the Kit receptor protein.

Stem cell mediated regeneration Process by which stem cells allow an organism to regrow certain organs or tissues (e.g., hair, blood cells) that have been lost.

Stem cell niche An environment (regulatory microenvironment) that provides a milieu of extracellular matrices and paracrine factors that allows cells residing within it to remain relatively undifferentiated. Regulates stem cell proliferation and differentiation.

Stereoblastulae Blastulae that have no blastocoel, e.g., blastulae produced by spiral cleavage.

Steroidogenic factor 1 (Sf1) A transcription factor that in mammals is necessary for creating the bipotential gonad. It declines in the developing ovary but remains at high levels in the developing testis, masculinizing both Leydig and Sertoli cells.

Stigma The surface of a carpel, usually at the peak of the style, that receives pollen.

Stochastic Pertaining to a random process that provides a set of random variables that can be analyzed statistically, but not necessarily predicted.

Stomata (singular, stoma) In plants, the pores in the epidermis of leaves and other organs that allow for gas exchange. Each pore is bordered by two guard cells that control the size of the pore, opening and closing the stoma in response to environmental conditions.

Stomodeum An ectoderm-lined invagination in the oral region of the embryo that meets the endoderm of the closed gut tube to form the oral plate.

Stratum corneum The outermost layer of the epidermis in the skin of tetrapods (amphibians, reptiles including birds, and mammals). It is a protective layer consisting of cornified cells, which are dead cells filled with keratin protein that are shed and replaced throughout the life of the organism.

Stratum germinativum See Basal layer.

Stromal derived factor 1 (SDF1) A chemoattractant. SDF1 is secreted, for example, by ectodermal placodes, thereby attracting cranial neural crest cells toward the placode.

Style A stalk, often elongated, between the stigma that receives pollen and the ovary, where the ovule is located.

Stylopod The proximal bones of a vertebrate limb, adjacent to the body wall; either the humerus (forelimb) or the femur (hindlimb).

Subgerminal cavity A space between the blastoderm and the yolk of avian eggs which is created when the blastoderm cells absorb water from the albumen (“egg white”) and secrete fluid between themselves and the yolk.

Subgranular zone (SGZ) A region of the hippocampus in the cerebrum that contains neural stem cells, allowing for adult neurogenesis in this region.

Subventricular zone A region in the vertebrate cerebrum that is formed as progenitor cells migrate away from the ventricular zone.

Sulcus limitans A longitudinal groove that divides the developing spinal cord and medulla into dorsal (receives sensory input) and ventral (initiates motor functions) halves.

Superficial cleavage The divisions of the cytoplasm of centrolecithal zygotes that occur only in the rim of cytoplasm around the periphery of the cell due to the presence of a large amount of centrally-located yolk, as in insects.

Surfactant A secretion of specific proteins and phospholipids such as sphingomyelin and lecithin produced by the type II alveolar cells of the lungs very late in gestation. The surfactant enables the alveolar cells to touch one another without sticking together.

Suspensor A plant structure within the germinating seed that connects the plant embryo to the nutrients within the seed. It develops from the basal cell of the proembryo. See Proembryo.

Symbiogenesis A hypothesis for the origin of eukaryotic cells, wherein the first eukaryotic cells emerged from the fusion of prokaryotic organisms, one forming the nucleus, the other forming the mitochondrion.

Symbiont The smaller organism in a symbiotic relationship in which the other organism is much larger and serves as the host, while the smaller organism may live on the surface or inside the body of the larger.

Symbiosis Greek, “living together.” Refers to any close association between organisms of different species.

Sympoiesis The phenomena of development through the interactions of multiple species, wherein symbionts provide developmental signals needed by the host, and the host often reciprocates in facilitating symbiont reproduction.

Synapse Junction at which a neuron contacts its target cell (which can be another neuron or another type of cell) and information in the form of neurotransmitter molecules (e.g., acetylcholine, GABA, serotonin) is exchanged across the synaptic cleft between the two cells.

Synapsis The highly specific parallel alignment (pairing) of homologous chromosomes during the first meiotic division.

Synaptic cleft The small cleft that separates the axon of a signaling neuron from the dendrite or soma of its target cell.

Synaptonemal complex The proteinaceous ribbon that forms during synapsis between homologous chromosomes, holding them together. A ladderlike structure with a central element and two lateral bars that are associated with the homologous chromosomes. See Synapsis.

Syncytial blastoderm Describes the Drosophila embryo during cleavage when nuclei have divided, but no cell membranes have yet formed to separate the nuclei into individual cells.

Syncytial specification The interactions of nuclei and transcription factors, which eventually result in cell specification, that take place in a common cytoplasm, as in the early Drosophila embryo.

Syncytiotrophoblast A population of cells from the mammalian trophoblast that undergoes mitosis without cytokinesis resulting in multinucleate cells. The syncytiotrophoblast tissue is thought to further the progression of the embryo into the uterine wall by digesting uterine tissue.

Syncytium Many nuclei residing in a common cytoplasm, results either from karyokinesis without cytokinesis or from cell fusion.

Syndetome Greek syn, “connected.” Derived from the most dorsal sclerotome cells, which express the scleraxis gene and generate the tendons.

Syndrome Greek, “happening together.” Several malformations or pathologies that occur concurrently. Genetically based syndromes are caused either by (1) a chromosomal event (such as trisomy 21, or Down syndrome) where several genes are deleted or added, or (2) by one gene having many effects.

Systems theory In development, refers to an approach that views the organism as coming together through the interactions of its component processes. Although the emphasis applied to each varies, the theoretical systems approach can be characterized by six principles: (1) context-dependent properties; (2) level-specific properties and emergence; (3) heterogeneous causation; (4) integration; (5) modularity and robustness; and (6) homeorhesis (stability while undergoing change).

T

T-box (Tbx) A specific DNA-binding domain found in certain transcription factors, including the T (Brachyury) gene, Tbx4 and Tbx5. Tbx4 and Tbx5 help specify hindlimbs and forelimbs, respectively.

Target selection The second step in the specification of axonal connection, wherein the axons, once they reach the correct area, recognize and bind to a set of cells with which they may form stable connections.

Telencephalon The anterior subdivision of the prosencephalon; will eventually form the cerebral hemispheres.

Telogen The resting phase of the hair follicle regeneration cycle.

Telolecithal Describes the eggs of birds and fish which have only one small area at the animal pole of the egg that is free of yolk.

Telomerase Enzyme complex that can extend the telomeres to their full length and maintains telomere integrity.

Telomeres Repeated DNA sequences at the ends of chromosomes that provide a protective cap to the chromosomes.

Telson A tail-like structure; the posterior most segment of certain arthropods. Seen in insect larvae such as Drosophila.

Temporal colinearity The mechanism that controls the timing of Hox gene activation, which occurs anteriorly first and progressively more posteriorly; sets up spatial colinearity of Hox gene expression relative to their 3′-to-5′ genomic organization.

Teratocarcinoma A tumor derived from malignant primordial germ cells and containing an undifferentiated stem cell population (embryonal carcinoma, or EC cells) that has biochemical and developmental properties similar to those of the inner cell mass. EC cells can differentiate into a wide variety of tissues, including gut and respiratory epithelia, muscle, nerve, cartilage, and bone.

Teratogens Greek, “monster-formers.” Exogenous agents that cause disruptions in development resulting in teratogenesis, the formation of congenital defects. Teratology is the study of birth defects and of how environmental agents disrupt normal development.

Terminal end bulbs  The ends of the extensive branches of ducts in the mammary glands of mammals. Under the influence of estrogens at puberty, the ducts grow by the elongation of these buds.

Testis cords Loops in the medullary (central) region of the developing testis formed by the developing Sertoli cells and the incoming germ cells. Will become the seminiferous tubules and site of spermatogenesis.

Testis-determining factor A protein encoded by the Sry gene on the mammalian Y chromosome that organizes the gonad into a testis rather than an ovary.

Testosterone A steroid hormone that is androgenic. In mammals, it is secreted by the fetal testes and masculinizes the fetus, stimulating the formation of the penis, male duct system, scrotum, and other portions of the male anatomy, as well as inhibiting development of the breast primordia.

Tetrad See Bivalent.

Tetrapods Latin, “four feet.” Includes the vertebrates amphibians, reptiles, birds, and mammals. Evolved from lobe-finned fish (sarcopterygian) ancestors.

TGF-β family Transforming growth factor-β. A family of growth factors within the TGF-β superfamily.

TGF-β superfamily  More than 30 structurally related members of a group of paracrine factors. The proteins encoded by TGF-β superfamily genes are processed such that the carboxy-terminal region contains the mature peptide. These peptides are dimerized into homodimers (with themselves) or heterodimers (with other TGF-β peptides) and are secreted from the cell. The TGF-β superfamily includes the TGF-β family, activin family, bone morphogenetic proteins (BMPs), Vg1 family, and other proteins, including glial-derived neurotrophic factor (GDNF; necessary for kidney and enteric neuron differentiation) and anti-Müllerian hormone (AMH; involved in mammalian sex determination).

Thecal cells Steroid hormone-secreting cells of the mammalian ovary that, together with the granulosa cells, form the follicles surrounding the germ cells. They differentiate from mesenchyme cells of the ovary.

Thermotaxis Migration that is directed by a gradient of temperature, either up or down the gradient.

Threshold model A model of development wherein biological events are triggered when a specific concentration of a morphogen or hormone is reached.

Thyroid hormone receptors (TRs)  Nuclear receptors that bind the thyroid hormones tri-iodothyronine (T₃), as well as thyroxine (T₄). Once bound to the hormone, the TR becomes a transcriptional activator of gene expression. There are several different TR types, including TRα and TRβ.

Thyroxine (T₄)  Thyroid hormone containing four iodine molecules; is converted to the more active T₃ form through removal of one iodine molecule. Increases basal metabolic rate in cells. Initiates metamorphosis in amphibians.

Tip cells Certain endothelial cells that can respond to vascular endothelial growth factor (VEGF) and begin “sprouting” to form a new vessel during angiogenesis. See also Ureteric bud tip cells.

Tissue engineering A regenerative medicine approach whereby a scaffold is generated from material that resembles extracellular matrix or decellularized extracellular matrix from a donor, is seeded with stem cells, and is used to replace an organ or part of an organ.

Tissue organization field theory (TOFT) A hypothesis for cancer initiation, positing that carcinogenesis is a tissue-based phenomenon and is caused by agents that interfere with the cell-cell communication that prevents cells from proliferating.

Torpedo The receptor protein for Gurken. When expressed in terminal follicle cells in a Drosophila egg chamber, it binds to Gurken produced by the egg, which signals these follicle cells to differentiate into posterior follicle cells and synthesize a molecule that activates protein kinase A in the egg; part of the process that sets up the anterior-posterior axis of the egg and future embryo.

Totipotent Latin, “capable of all.” Describes the potency of certain stem cells to form all structures of an organism, such as the earliest mammalian blastomeres (up to the 8-cell stage), which can form both trophoblast cells and the embryo precursor cells. Compare with Pluripotent.

Tracheal-esophageal fistula An abnormal connection between the gut tube (esophagus) and respiratory tube (trachea) that can occur in babies when the separation of these two tubes by the laryngotracheal groove during embryonic development is not complete. It is a condition that must be surgically repaired so the baby can breathe and swallow properly. See Laryngotracheal groove.

Trans-activating domain The transcription factor domain that activates or suppresses the transcription of the gene whose promoter or enhancer it has bound, usually by enabling the transcription factor to interact with the proteins involved in binding RNA polymerase or with enzymes that modify histones.

trans-regulatory elements Soluble molecules whose genes are located elsewhere in the genome and which bind to the cis-regulatory elements. They are usually transcription factors or microRNAs.

Transcription elongation complex (TEC) A complex of several transcription factors that breaks the connection between RNA polymerase II and the Mediator complex, allowing transcription (which has been initiated) to proceed.

Transcription elongation suppressor A repressive transcription factor that functions to prevent the transcription elongation complex from associating with RNA polymerase II, pausing transcription.

Transcription factor A protein that binds to DNA with precise sequence recognition for specific promoters, enhancers, or silencers.

Transcription factor domains The three major domains are a DNA-binding domain, a trans-activating domain and a protein-protein interaction domain.

Transcription initiation site DNA sequence of a gene that codes for the addition of a modified nucleotide “cap” at the 5′ end of the RNA soon after it is transcribed. Also called the cap sequence.

Transcription termination sequence DNA sequence of a gene where transcription is terminated. Transcription continues for about 1000 nucleotides beyond the AATAAA site of the 3′ untranslated region of the gene before being terminated.

Transcription The process of copying DNA into RNA.

Transcription-associated factors (TAFs) Proteins that stabilize RNA polymerase on the promoter of a gene and enable it to initiate transcription.

Transcriptional co-regulators Proteins, recruited by transcription factors, that make modifications in chromatin structure, which either enhance or repress transcription of specific genes.

Transcriptome Total messenger RNAs (mRNAs) expressed by genes in an organism or a specific type of tissue or cell.

Transdifferentiation The transformation of one cell type into another.

Transforming growth factor See TGF-β superfamily.

Transgene Exogenous DNA or gene introduced through experimental manipulation into a cell’s genome.

Transit amplifying cells See Progenitor cells.

Transition zone In neural tube development in vertebrates, the zone between the region that undergoes primary neurulation and the region that undergoes secondary neurulation. The size of this zone varies among different species. See also Primary neurulation and Secondary neurulation.

Translation initiation site The ATG codon (becomes AUG in mRNA), which signals the beginning of the first exon (protein-coding region) of a gene.

Translation termination codon Sequence in a gene, TAA, TAG, or TGA, which is transcribed as a codon in the mRNA—when a ribosome encounters this codon, the ribosome dissociates and the protein is released.

Translation The process in which the codons of a messenger RNA are translated into the amino acid sequence of a polypeptide chain.

Trefoil stage A stage in certain spirally cleaving embryos, wherein a particularly large polar lobe is extruded at first cleavage, giving the appearance of a third cell forming before the polar lobe is reabsorbed back into the CD blastomere.

Tri-iodothyronine (T₃)  The more active form of thyroid hormone, produced through the removal of an iodine molecular from thyroxine (T₄). See Thyroxine (T₄).

Trigeminal placode In vertebrates, a pair of intermediate cranial placodes that are subdivided into the ophthalmic and maxomandibular placodes and that generate the distal neurons of the paired trigeminal ganglions, the sensory ganglions of the paired 5th cranial nerve (the trigeminal nerve).

Triploblasts See Bilaterians.

Trisomy 21 Condition (in humans) of having three copies of chromosome 2 (an example of aneuploidy). Causes Down syndrome.

Trithorax Family of proteins that are recruited to retain the memory of the transcriptional state of regions of DNA as the cell goes through mitosis; keeps active genes active.

Trophectoderm cells In the mammalian embryo, the outer layer of cells of the blastocyst that surround the inner cell mass and blastocoel; develop into the embryonic side of the placenta.

Trophoblast The external cells of the early mammalian embryo (i.e., the morula and the blastocyst) that will bind to the uterus. Trophoblast cells form the chorion (the embryonic portion of the placenta). Also called trophectoderm.

Truncus arteriosus Cardiac outflow tract precursor that along with the conus arteriosus will form the base of the aorta and pulmonary artery.

Trunk neural crest Neural crest cells migrating from this region become the dorsal root ganglia containing the sensory neurons, sympathetic ganglia, adrenal medulla, the nerve clusters surrounding the aorta, and Schwann cells if they migrate along a ventral pathway, and they generate melanocytes of the dorsum and belly if they migrate along a dorsolateral pathway.

Tube cell Also called the vegetative cell, it is one of two cells produced by the division of the microspore nucleus in angiosperm pollen grains. It engulfs the generative cell, to give rise to the pollen tube.

Tubulin A dimeric protein that polymerizes to form microtubules. Microtubules are a major component of the cytoskeleton; they are found in centrioles and basal bodies; they also form the mitotic spindle and axoneme of cilia and flagella.

Tudor  One of the proteins, along with Piwi, Vasa, and Nanos, expressed in germ cells to suppress gene expression. Also involved in anterior-posterior polarity in the Drosophila embryo by localizing Nanos, a posterior morphogen.

Tumor angiogenesis factors Factors secreted by microtumors; these factors (including VEGFs, Fgf2, placenta-like growth factor, and others) stimulate mitosis in endothelial cells and direct the cell differentiation into blood vessels in the direction of the tumor.

Tumor suppressor genes Regulatory genes whose gene products protect against a cell progressing towards cancer. Gene products may inhibit cell division or increase the adhesion between cells; they can also induce apoptosis of rapidly dividing cells. Cancer can result from either mutations or inappropriate methylations that inactivate tumor suppressor genes.

Tunica albuginea In mammals, a thick, whitish capsule of extracellular matrix that encases the testis.

“Turing-type” model See Reaction-diffusion model.

Type A spermatogonia In mammals, sperm stem cells that undergo mitosis and maintain the population of Type A spermatogonia while also generating Type B spermatogonia.

Type B cells A type of neural stem cell found in the rosettes of the V-SVZ of the cerebrum; fuel the generation of specific types of neurons in the olfactory bulb and striatum.

Type B spermatogonia In mammals, precursors of the spermatocytes and the last cells of the line that undergo mitosis. They divide once to generate the primary spermatocytes.

Type II deiodinase Intracellular enzyme that removes an iodine atom from the outer ring of thyroxine (T₄), converting it into the more active T₃ hormone.

Type III deiodinase Intracellular enzyme that removes an iodine atom from the inner ring of T₃ to convert it into the inactive compound T₂, which will eventually be metabolized to tyrosine.

Type IV collagen A type of collagen that forms a fine meshwork; found in the basal lamina, an extracellular matrix that lies underneath epithelia.

U

Umbilical cord Connecting cord derived from the allantois that brings the embryonic blood circulation to the uterine vessels of the mother in placental mammals.

Umbilical veins See Omphalomesenteric veins and Vitelline veins.

Undifferentiated zone See Progress zone.

Unipotent stem cells Stem cells that generate only one cell type, such as the spermatogonia of the mammalian testes that only generate sperm.

Unsegmented mesoderm Bands of paraxial mesoderm prior to their segmentation into somites.

3′ Untranslated region (3′ UTR) A region of a eukaryotic gene and RNA following the translation termination codon that, although transcribed, is not translated into protein. It includes the region needed for insertion of the polyA tail on the transcript that allows the transcript to exit the nucleus.

5′ Untranslated region (5′ UTR) Also called a leader sequence or leader RNA; a region of a eukaryotic gene or RNA. In a gene, it is a sequence of base pairs between the transcription initiation and translation initiation sites; in an RNA, it is its 5′ end. These are not translated into protein, but can determine the rate at which translation is initiated.

Ureteric bud tip cells A population of stem cells that form at the tips of the ureteric bud branches during metanephric kidney formation.

Ureteric buds In amniotes, paired epithelial branches induced by the metanephrogenic mesenchyme to branch from each of the paired nephric ducts. Ureteric buds will form the collecting ducts, renal pelvis, and ureters that take the urine to the bladder.

Urodeles Amphibian group that includes the salamanders. Compare with Anurans.

Urogenital sinus In mammals, the region of the cloaca that is separated from the rectum by the urogenital septum. The bladder forms from the anterior portion of the sinus, and the urethra develops from the posterior region. In females, also forms Skene’s glands; in males it also forms the prostate gland.

Uterine cycle A component of the menstrual cycle, the function of the uterine cycle is to provide the appropriate environment for the developing blastocyst.

V

Vagal neural crest Neural crest cells from the neck region, which overlaps the cranial/trunk crest boundary. Together with the sacral neural crest, generates the parasympathetic (enteric) ganglia of the gut, which are required for peristaltic movement of the bowels.

Vas (ductus) deferens Derived from the Wolffian duct, the tube through which sperm pass from the epididymis to the urethra.

Vasa One of the proteins, along with Tudor, Piwi, and Nanos, expressed in germ cells to suppress gene expression. Also involved in anterior-posterior polarity in the Drosophila embryo by localizing Nanos, a posterior morphogen.

Vascular endothelial growth factors (VEGFs) A family of proteins involved in vasculogenesis that includes several VEGFs, as well as placental growth factor. Each VEGF appears to enable the differentiation of the angioblasts and their multiplication to form endothelial tubes. Also critical for angiogenesis.

Vascular tissue The conducting tissue in vascular plants that transports fluids and nutrients; its major components are the xylem and phloem. See Xylem and Phloem.

Vasculogenesis The de novo creation of a network of blood vessels from the lateral plate mesoderm. See also Extraembryonic vasculogenesis.

Vegetal hemisphere The bottom portion of an ovum, where yolk is more concentrated. The yolk can be an impediment to cleavage, as in the amphibian embryo, causing the yolk-filled cells to divide more slowly and undergo less movement during embryogenesis.

Vegetal plate Area of thickened cells at the vegetal pole of the sea urchin blastula.

Vegetal pole The yolk containing end of the egg or embryo, opposite the animal pole.

Vegetal rotation During frog gastrulation, internal cell rearrangements place the prospective pharyngeal endoderm cells adjacent to the blastocoel and immediately above the involuting mesoderm.

VEGF See Vascular endothelial growth factors.

VegT pathway Involved in dorsal-ventral polarity and specification of the organizer cells in the amphibian embryo. The VegT pathway activates the expression of Nodal-related paracrine factors in the cells of the vegetal hemisphere of the embryo, which in turn activate the Smad2 transcription factor in the mesodermal cells above them, activating genes that give these cells their “organizer” properties.

Vellus Short and silky hair of the fetus and neonate that remains on many parts of the human body that are usually considered hairless, such as the forehead and eyelids. In other areas of the body, vellus hair gives way to longer and thicker “terminal” hair.

Ventral (ventrolateral) pathway Migration pathway of trunk neural crest cells that travel ventrally through the anterior of the sclerotome and contribute to the sympathetic and parasympathetic ganglia, adrenomedullary cells, and dorsal root ganglia.

Ventral furrow Invagination of the prospective mesoderm, about 1000 cells constituting the ventral midline of the embryo, at the onset of gastrulation in Drosophila.

Ventricular (ependymal) cells Cells derived from the neuroepithelium that line the ventricles of the brain and secrete cerebrospinal fluid.

Ventricular radial glia (vRG)  Progenitor cells that reside in the ventricular zone. They give rise to neurons, outer radial glia (oRG), and intermediate progenitor (IP) cells. See also Ventricular zone.

Ventricular zone (VZ) Inner layer of the developing spinal cord and brain. Forms from the germinal neuroepithelium of the original neural tube and contains neural progenitor cells that are a source of neurons and glial cells. Will form the ependyma.

Ventricular-subventricular zone (V-SVZ)  Region of the cerebrum that contains neural stem cells and is capable of neurogenesis in the adult.

Vertical transmission In referring to symbiosis, the transfer of symbionts from one generation to the next through the germ cells, usually the eggs.

Vg1 A family of proteins that is part of the TGF-β superfamily. Important in specifying mesoderm in amphibian embryos. See also TGF-β superfamily.

Visceral endoderm A region of the primitive endoderm where the cells contact the epiblast in the mammalian embryo. See Primitive endoderm.

Visceral mesoderm See Splanchnic mesoderm.

Viscerocranium The jaws and other skeletal elements derived from the pharyngeal arches.

Vital dyes Stains used to label living cells without killing them. When applied to embryos, vital dyes have been used to follow cell migration during development and generate fate maps of specific regions of the embryo.

Vitelline envelope In invertebrates, the extracellular matrix that forms a fibrous mat around the egg outside the cell membrane and is often involved in sperm-egg recognition and is essential for the species-specific binding of sperm. The vitelline envelope contains several different glycoproteins. It is supplemented by extensions of membrane glycoproteins from the cell membrane and by proteinaceous “posts” that adhere the vitelline envelope to the membrane.

Vitelline veins The veins, continuous with the endocardium, that carry nutrients from the yolk sac into the sinus venosus of the developing vertebrate heart. In birds, these veins form from yolk sac blood islands, and bring nutrients to the embryo and transport gases to and from the sites of respiratory exchange. In mammals they are called omphalomesenteric veins or umbilical veins.

Vitellogenesis The formation of yolk proteins, which are deposited in the primary oocyte.

Viviparity Young are nourished in and born from the mother’s body rather than hatched from an egg, as in placental mammals. Compare with Oviparity.

Vulval precursor cells (VPCs) Six cells in the larval stage of C. elegans that will form the vulva via inductive signals.

W

White matter The axonal (as opposed to neuronal) region of the brain and spinal cord. Name derives from the fact that myelin sheaths give the axons a whitish appearance. Compare with Gray matter.

Whole mount in situ hybridization A technique designed for staining specific DNA or RNA sequences within intact tissues and whole embryos. This allows researchers to look at entire embryos or their organs without sectioning them. By using dye-labeled RNA probes that target mRNAs expressed by specific genes, researchers can use the technique to show regions of expression of these genes.

Wholist organicism Philosophical notion stating that the properties of the whole cannot be predicted solely from the properties of its component parts, and that the properties of the parts are informed by their relationship to the whole. It was very influential in the construction of developmental biology.

Whorled phyllotaxis In plants, the arrangement of lateral organs in which a set of organs (3 or more) emerges simultaneously in a ring around the stem or apex.

Whorls In plants, a set of leaves, sepals, petals, or branches that have a whorled phyllotaxis. See Whorled.

Wnt pathways Signal transduction cascades initiated by the binding of a Wnt protein to its receptor Frizzled on the cell membrane. This binding can initiate any of number of different pathways (“canonical” and “noncanonical”) to activate Wnt-responsive genes in the nucleus.

Wnt4 A protein in the Wnt family; in mammals it is involved in primary sex determination, kidney development, and the timing of meiosis. It is expressed in the bipotential gonads, but becomes undetectable in XY gonads becoming testes; it is maintained in XX gonads becoming ovaries. See also Wnts.

Wnt7a A Wnt protein especially important in specifying dorsal-ventral polarity in the tetrapod limb; expressed in the dorsal, but not ventral, ectoderm of limb buds. If expression in this region is eliminated, both dorsal and ventral sides of the limb form structures appropriate for the ventral surface, such as ventral footpads on both surfaces of a paw. See also Wnts.

Wnts A gene family of cysteine-rich glycoprotein paracrine factors. Their name is a fusion of the name of the Drosophila segment polarity gene wingless with the name of one of its vertebrate homologues, integrated. Wnt proteins are critical in establishing the polarity of insect and vertebrate limbs, promoting the proliferation of stem cells, and in several steps of urogenital system development.

Wolffian (nephric) duct In vertebrates, the duct of the developing excretory system that grows down alongside the mesonephric mesoderm and induces it to form kidney tubules. In amniotes, it later degenerates in females, but in males, becomes the epididymis and vas deferens.

Wound epidermis In salamander limb regeneration, the epidermal cells that migrate over the stump amputation to cover the wound surface immediately following amputation; later thickens to form the apical ectodermal cap.

X

X chromosome inactivation In mammals, the irreversible conversion of the chromatin of one X chromosome in each female (XX) cell into highly condensed heterochromatin—a Barr body—thus preventing excess transcription of genes on the X chromosome. See also Dosage compensation.

Xylem In vascular plants, the conduits for bringing water and nutrients upward through the plant.

Y

Yellow crescent Region of the tunicate zygote cytoplasm extending from the vegetal pole to the equator that forms after fertilization by the migration of cytoplasm containing yellow lipid inclusions; will become mesoderm. Contains the mRNA for transcription factors that will specify the muscles.

Yolk cell The cell containing the yolk in a fish embryo, once the yolk-free cytoplasm at the animal pole of the egg divides to form individual cells above the yolky cytoplasm. Initially, all the cells maintain a connection with the underlying yolk cell.

Yolk plug The large endodermal cells that remain exposed on the vegetal surface surrounded by the blastopore of the amphibian gastrulating embryo.

Yolk sac The first extraembryonic membrane to form, derived from splanchnopleure that grows over the yolk to enclose it. The yolk sac mediates nutrition in developing birds and reptiles. It is connected to the midgut by the yolk duct (vitelline duct), so that the walls of the yolk sac and the walls of the gut are continuous.

Yolk syncytial layer (YSL) A cell population in the zebrafish cleavage stage embryo formed at the ninth or tenth cell cycle, when the cells at the vegetal edge of the blastoderm fuse with the underlying yolk cell, producing a ring of nuclei in the part of the yolk cell cytoplasm that sits just beneath the blastoderm. Important for directing some of the cell movements of gastrulation.

Z

Zebrabow Transgenic zebrafish used to trigger the expression of different combinations and amounts of different fluorescent proteins within cells, labeling them with a seeming “rainbow” of possible colors that can be used to identify each individual cell in a tissue, organ, or whole embryo.

Zeugopod The middle bones of the vertebrate limb; the radius and ulna (forelimb) or tibia and fibula (hindlimb).

Zona pellucida Glycoprotein coat (extracellular matrix) around the mammalian egg, synthesized and secreted by the growing oocyte.

Zona proteins 1, 2, and 3 (ZP1, ZP2, ZP3) The three major glycoproteins found in the zona pellucida of the mammalian egg; the human zona pellucida also contains ZP4. Involved in binding sperm in a relatively, but not absolutely, species-specific manner.

Zone of polarizing activity (ZPA) A small block of mesodermal tissue in the very posterior of the limb bud progress zone. Specifies the anterior-posterior axis of the developing limb through the action of the paracrine factor Sonic hedgehog.

Zygote A fertilized egg with a diploid chromosomal complement in its zygote nucleus generated by fusion of the haploid male and female pronuclei.

Zygotene Greek, “yoked threads.” In the first meiotic division, it is the second stage of prophase I, when homologous chromosomes pair side by side; follows leptotene.