Developmental Bio lectures 1, 2 & 3

Anterior

towards the head or front end of an organism.

blastula

an early embryonic stage consisting of a hollow sphere of cells surrounding a fluid filled cavity.

blastopore

the opening created when cells invaginate into the blastula during gastrulation.

Chick-Quail Chimeras

Embryos created by grafting tissue between chick and quail embryos to track cell movement using species-specific cellular markers.

cleavage

a series of rapid cell divisions without growth that converts a fertilized egg into a multicellular blastula.

cross section

a slice taken perpendicular to the long axis of an organism or structure.

development

the progressive process of structural and functional changes an organism undergoes throughout its life cycle.

dorsal

towards the back or upper side of an organism.

embryo

an early stage of animal development between fertilization and hatching or birth.

ectoderm

the outermost primary germ layer, giving rise to skin, nervous system, and sensory organs.

embryogenesis

the process by which an embryo forms and develops into a fertilized egg.

embryology

the scientific study of embryonic development from fertilization to birth or hatching.

endoderm

the innermost primary germ layer, giving rise to the lining of the digestive tract and respiratory system.

fate map

a diagram showing which tissues or organs specific embryonic regions will become later in development.

fertilization

the fusion of male and female gametes to form a diploid zygote.

gametogenesis

the process of producing mature haploid reproductive cells (sperm and egg)

gastrulation

the developmental phase where blastula cells rearrange into three distinct germ layers.

genetic labelling

inserting a permanent DNA marker (like GFP) into a cell’s genome to trace its lineage in development.

germ cells

specialized reproductive cells (sperm and egg) that carry genetic information to the next generation.

germ layer

one of the main cell layers (ectoderm, mesoderm, endoderm) formed during early embryonic development.

germ line

the lineage of germ cells that gives rise to gametes and passes genetic material across generations.

germ plasm

cytoplasmic components in the egg that specify cells to become germ cells rather than somatic cells.

growth

the irreversible increase in physical size of cell number of an organism.

larva

an immature, free-living form of an animal that undergoes metamorphosis to reach adulthood.

lateral

located toward or on the sides of an organism away from the central midline.

longitudinal section

a plane cut along the long axis of an organism or structure.

mesoderm

the middle germ layer, giving rise to muscle, bone, blood, and connective tissue.

metamorphosis

a rapid post-embryonic structural transformation from a larval stage to an adult form.

Morphogenesis

the biological process that causes an organism or tissue to develop its characteristic shape and form.

morula

a solid ball of cleavage stage cells before the formation of a blastula cavity.

midsagittal plane

a vertical plane down the exact midline dividing an organism into equal left and right halves.

necessary

a condition/gene required for a biological process; without it, the process cannot occur.

organogenesis

the process of tissue organization into functional organs during embryonic development.

Oviparous

animals that lay eggs that hatch outside the mothers body.

Ovoviviparous

animals that produce eggs that hatch inside the mother’s body, giving birth to live young without a placental connection.

pattern formation

the process by which embryonic cells organize spatially to form structured tissues and body plans.

posterior

towards the tail or rear end of an organism.

regeneration

the reactivation of development to restore lost or damaged tissues, organs, or limbs.

reporter gene

a gene encoding an easily detectable protein (like GFP) used to track gene expression or protein localization.

reporter gene construct

an engineered DNA sequence that combines a target gene’s regulatory region (promoter) with a reporter gene to track where and when that promoter is active.

reproduction

the biological process by which organisms produce new offspring of the same species.

sagittal section

a vertical plane parallel to the midline dividing an organism into left and right portions.

sufficient

a condition/gene that can induce a biological outcome on its own without needing any extra signals.

transverse section

a horizontal cross-cut perpendicular to the main longitudinal axis.

viviparous

animals that develop offspring inside the mother’s body with direct nourishment (like a placenta) and give live birth.

vital dye

non-toxic stains applied to living cells to trace their movements during development without killing them.

autonomous specification

cell fate decision driven internally by inherited cytoplasmic determinants, independent of neighboring cells.

cell potency

the total range of different cell types that a given stem or embryonic cell can differentiate into.

cellularization

the process where plasma membranes form around individual nuclei in a syncytium, converting it into a multicellular structure.

conditional specification

cell fate decision determined by interactions and signals from neighboring cells.

cytoplasmic determinants

maternal molecules (mRNAs or proteins) unequally distributed in the egg cytoplasm that dictate cell fate after division.

determination

the irreversible commitment of a cell to a specific lineage, even if transplanted to a new environment.

differentiation

the process by which a cell acquires a specialized structure and function (ex. neuron, muscle cell).

Ectopic Expression

the expression of a gene in a tissue, location, or developmental stage where it is not normally expressed.

juxtacrine factors

signaling proteins that require direct cell-cell contact between membrane bound ligands and receptors.

ligand

a signaling molecule that binds specifically to a receptor protein to trigger a cellular response.

morphogen

a diffusible signaling molecule that specifies cell fates in a concentration-dependent manner.

mosaic development

early embryonic development where cell fates are fixed early via autonomous specification.

multipotent

stem cells capable of differentiating into multiple, but closely related, cell types within a specific tissue.

paracrine factors

secreted signaling proteins that diffuse over short distances to induce responses in nearby neighboring cells.

physical factors

mechanical forces (tension, shear stress, or matrix stiffness) that influence cell behavior and development.

plasticity

the ability of a cell or tissue to alter its developmental fate or function in response to environmental cues.

pluripotent

stem cells capable of giving rise to almost all body cell types, excluding extraembryonic tissues (like the placenta).

preblastoderm stage

an early stage in insect development before nuclei migrate to the cortex and cellularization occurs.

progenitor cell

a partially differentiated stem-like cell committed to a specific cell lineage with limited self-renewal capacity.

receptor

a membrane or intracellular protein that binds a specific ligand to initiate a signal transduction cascade.

specification

the reversible first stage of commitment where a cell can differentiate autonomously in a neutral environment.

stomodeum

an anterior ectodermal invagination in the embryo that forms the primitive mouth.

syncytial blastoderm

an embryonic stage (common in insects) where multiple nuclei share a single common cytoplasm before cellularization.

syncytial specification

fate determination in a shared cytoplasm, where gradients of morphogens directly instruct free-floating nuclei.

syncytium

a single cell containing multiple nuclei produced by nuclear division without cytokinesis or cell fusion.

totipotent

a cell capable of giving rise to an entire complete organism, including both embryonic and extraembryonic tissues (ex. zygote).

unipotent

a stem cell capable of differentiating into only one specific cell type (ex. spermatogonial stem cells).

yellow crescent

a distinct region of cytoplasm in tunicate embryos containing determinants that specify muscle cell fate.

3’ UTR (untranslated region)

the section of mRNA immediately following the translation termination codon that is not translated into protein; it contains regulatory sequences that influence mRNA stability, localization, and translation efficiency.

5’ UTR (untranslated region)

the section of mRNA directly upstream from the translation initiation codon; it plays a key role in regulating translation initiation and mRNA stability.

alternative 5’ splice sites

a type of alternative splicing where two or more alternative 5’ donor splice sites are recognized, altering the 3’ end of the upstream exon.

alternative 3’ splice sites

a type of alternative splicing where two or more alternative 3’ acceptor splice sites are recognized, altering the 5’ end of the downstream exon.

alternative splicing

a regulated process during gene expression that allows a single pre-mRNA to produce multiple distinct mRNA isoforms by selectively including or excluding specific exons/introns.

alternative transcription start sites

the use of different promoter regions or start positions within a single gene to initiate transcription, resulting in mRNA transcripts with different 5’ ends.

basal apparatus

the complex of basal transcription factors and RNA Polymerase II assembled at the core promoter to initiate basal levels of transcription.

basal transcription factors

general transcription factors required by RNA Polymerase II to bind to the core promoter and initiate baseline transcription.

cell type-specific proteins

proteins expressed only in particular cell types or tissues, giving those cells their specialized structure, function, and identity.

chromatin

the complex of DNA and histone proteins found within the eukaryotic nucleus that package DNA into a compact structure.

coding sequence

the portion of a gene’s DNA or mRNA that directly codes for the amino acid sequence of a protein, bounded by the start and stop codons.

CpG islands

regions of DNA with a high frequency of cytosine-guanine dinucleotide repeats, often located near gene promoters; their methylation status regulates gene silencing.

differential gene expression

the process by which different cell types express distinct subsets of genes despite containing the identical genome.

differential transcription

the regulated synthesis of a specific RNA transcripts in specific cells at specific times, serving as the primary control point for differential gene expression.

enhancer

a DNA sequence element that binds specific activator transcription factors to significantly increase transcription levels of a target gene, regardless of distance or orientation relative to the promoter.

epigenetic modifications

heritable changes in gene expression or chromatin structure that occur without altering the underlying DNA sequence (ex. DNA methylation, histone modifications).

euchromatin

a lightly packed, transcriptionally active form of chromatin accessible to transcription factors and RNA polymerase.

exon

a segment of a gene that is retained in the mature mRNA transcript after splicing and typically codes for protein regions or regulatory UTRs.

exon skipping

the most common pattern of alternative splicing, where a specific exon is deliberately excluded from the mature mRNA transcript.

exportin

a nuclear transport receptor protein that binds cargo molecules (like RNA or proteins) and facilitates their transport out of the nucleus through the nuclear pore complex.

genomic equivalence

the concept that almost all differentiated cells in a multicellular organism an identical, complete set of genetic information.

H1 histones

the linker histone protein that binds to the DNA between nucleosomes, stabilizing the high-order coiling of chromatin fibers.

heterochromatin

tightly packed, condensed chromatin that is transcriptionally inactive and inaccessible to the transcription machinery.

high CpG promoter

a type of gene promoter rich in CpG islands, typically found in broadly expressed housekeeping genes and developmentally regulated genes, regulated mainly by chromatin state.

histone

highly conserved, basic proteins (H2A, H2B, H3, H4) around which DNA winds to form the fundamental structural units of chromatin (nucleosomes).

histone acetylase (HAT)

an enzyme that adds acetyl groups to lysine residues on histone tails, neutralizing their positive charge, relaxing chromatin, and activating transcription.