Chapter 3

Mutants- organisms carrying a mutation

Mutation- change in genomic DNA
Chemical mutagenesis- technique to create of point mutation in which a single DNA base
is changed to another, substitution of one amino acid to another
Frameshift mutation- addition or deletion of a single nucleotide, changing the entire
downstream sequence of amino acids in the protein
X-irridiation- deletion of a whole stretch of DNA
Spontaneous mutation- addition, subtraction, deletion or substitution of DNA including
the addition of transposable elements
Homeotic mutation- conversion of one part to the likeness of another
Homeotic gene- genes that influence homeotic mutation, transcription factors influence
mutation, developmental control gene, states the commitment of cells
Alleles- different versions of a gene
Wild type- normal allele
Genome- totality of nuclear DNA in an organism
Genotype- specific combination of alleles
Phenotype- totality of characteristics of an organism
Loss of function or knockdown- most common mutation, protein products of the mutant
gene is less active than the wild type, recessive mutation
Null mutation- complete loss of function, lack of active gene products
Allelic series- arrangement of severity of abnormal phenotype brought upon by loss of
function
Haploinsufficiency-
- at least 50% is loss but the rest is enough to produce an abnormal phenotype,
genetically dominant loss of function, 100% loss of function (homozygous
phenotype) 50% loss of function (heterozygous phenotype)
Gain of function or overexpression
- dominant mutation, signals are present all the time regardless of the presence of
ligands, involves constitutive normal gene products, dominant due to the
production of gene products made by the allele on the other gene other than the
wild type
Constitutive- gene products that are active all the time
Dominant negative- genetically dominant, gene products has no function but interferes
with the wild type gene product
Pleiotropic - genes with many functions
Dorsal gene- gene of the drosophila that influences the production of the ventral
development, when lost an all dorsal animal is produced (loss of function)
White gene- gene of the drosophila that influence the production of red eye pigment,
when lost a white eyed animal is produced (loss of function)
Dimorphic sex chromosomes- different forms of genetic combination that dictates sex of
an organism
Female mammal, female drosophila- XX
Male mammal- XY
Male bird- ZZ
Female bird- ZW
Male drosophila- XO
Sex-linked mutations present in sex chromosomes, depend on the individuals sex
Autosomes- chromosomes other than sex chromosomes
Maternal effect- phenotype of an individual depends on the genotype of the mother
Stella gene- present in mouse, encodes a chromosomal protein expressed in germ cells
and early embryo blastomeres, if knock out the mother is normal but with defective
embryos
Rescue protocol- when several genes have similar mutant phenotypes, sequences of
action and expression
Nanos- last acting member of the pathway, drosophila
Epistasic- one genes prevents the expression of another
Epistasis analysis- study of repressive pathways, or the effect of one gene to the
expression of the other
Temperature sensitive mutation- dependent on temperature, heat causes
conformational changes to proteins products
Nonpermissive- displays phenotypes, high temperature usually
Permissive- do not display phenotypes, low temperature usually
Poikilothermic organism
- Temperature sensitive mutants are used in C.elegans, Drosphila, and zebra fish,
can be subjected to multiple ranges of temperature, cold blooded,
environmentally influenced
Homeotherms- mouse, maintains an internal temperature, warm blooded
Genetic mosaic- organisms that consists of a mixture of cells with different genotypes

Gynandromorphs- half male and half female tissue, due to loss of sex chromosomes at
the first cleavage
Autonomous- mutation only affects the region where the gene is active
Non autonomous- the gene is affecting a structure outside its domain of expression
Pole-cell transplantation- technique in forming a mosaic
Chimera- embryos made experimentally by cell injection or aggregation of blastocyst
Forward genetics- investigation of an interesting mutant phenotype
Reverse genetics- functional investigation of known genes
Balancer chromosomes- multiple inversions, with recessive lethal mutation, marker
genes
Cloned genes- genes coding sequence is incorporated into a bacterial plasmid or cloning
vector for amplification and purification - reverse genetics
P-element- transposable element that causes mutation, probe to isolate DNA clones in
the library
Positional cloning- mutation is mapped in high resolution using microsatellite
polymorphism or restriction fragment length polymorphism
PCR primers- enable the visibility of polymorphism, bands on DNA gel
Genetic strain or genetic line- subjects to gain or loss of function experiments to produce
many individuals of the same genotype
Transgene or knock in- gene introduced into an organism through transgenesis, has
promoters
Transgenesis- introduction of a new gene to an organism commonly in the germ line0
Enhancer trap- probe the environment, providing genetic lines highlighted expressions or
markers like B-galactosidase and green fluorescent protein (GFP)
Gal4- yeast, enhancer trap, zinc-finger class, binds to upstream activating sequence
Tetracyclin system- E.coli deoxycyclin addition represses or upregulates expression
Homologous recombination- direct replacement of a gene by a modified version made in
vitro
Zinc finger nucleases- artificial proteins constructed using a judicious selection of zinc
finger type DNA binding domains combined with an endonuclease
Morphlino- oligonucleotides replaces sugar phosphate backbone
Dicer- enzyme that cleaves DsRNA to 21-23bp, involve in RNAi, mRNA destruction
Neutralizing antibody- against protein production
Tetraploidization- doubling of chromosome number
Pseudoallele- look like allele also same expression patterns, not alleles because they
occupy specific genetic loci
Redundancy- partial or complete overlap of gene function
Paralog- set of similar genes in the same genome, brought upon by gene duplication
 Chapter 4
Normal development- course of development that a typical embryo follows in standard
laboratory conditions when it is free from experimental disturbances
Anterior or cranial end- front end
Posterior or caudal end- rear end
Dorsal- upper end
Ventral- lower surface
Transverse- across the long axis
Longitudinal- parallel to the long axis
Sagittal- vertical longitudinal
Parasagittal- one side of the midline
Frontal or coronal- horizontal longitudinal section, dorsal and ventral sides
Stage series- describes the course of development as a number of stages which can be
identified by external features under the dissecting microscope
Maternal- development is due to the components that exist in the egg
Zygotic- development due to components newly synthesized by the embryo after
fertilization
Fate map- diagram that shows what will become of each region of the embryo in the
course of normal development; where is will move, how it will change shape and what
structures it will turn into
Fate- commitment to form particular structures or cell types is usually through a series of
intercellular interaction
Mosaic (old) - if experimentally isolated parts develop strictly according to the fate map
Regulative (old) - if experimentally isolated parts forms more structure than expected
from the fate map
Genetic mosaic- organisms consisting of cells of different genotypes
Clonal analysis- form of fate mapping, single cells is labelled and the position and cell
types of its progeny identified a later stage
Compartment- region in an embryo whose boundaries are boundaries of clonal
restriction
Specification or specified cells- become a particular structure if it will develop
autonomously into that structure after isolation
Specification map- map showing that Specification is the same to the fate in normal
development
Determination or determined cells- develop autonomously in isolation but differs in that
the commitment is irreversible, loss of competence
Orthotropic graft-same position of grafting, usual method for fate mapping
Heterotropic graft- grafting to different position, test for determination
Competence- ability to respond to inducing factors
Potency- the range of cell types or structures into which a particular cell population can
develop
Determinant- a substance in the egg which guarantees assumption of a particular state of
commitment by the cells that inherit it during cleavage
Inducing factors-extracellular signals controls regional specification
Nodals- Xenopus, signaling molecules, upregulates transcription factors that define
mesodermal state
Instructive induction- responding tissue has a choice before specification, increases
complexity
Threshold response- series of territories are formed because of difference responses to
different concentration
Morphogen- signal substance with more than one positive outcome
Appositional induction- induction between tissues in contact
Permissive- signal is necessary but cannot influence the development pathway selected
Cytonemes- alternative routes for diffusion, fine intercellular processes
Lateral inhibition- notch delta system, one population of cells follow on pathway of
development while the surrounding follows another, neurogenesis
Epigenetic- understanding of gene expression in terms of chromatin structure
 Chapter 2

Embryonic development- conversion of a single cell, the fertilized egg, into a complex
organism consisting of many anatomical parts
Regional specification- explains how patterns appears in previously similar population of
cells
Blastula or blastoderm- featureless ball or sheet of cells
Determinants- regulatory molecules deposited in particular positions within the fertilized
egg, involved in cell programming
Embryonic induction
- intercellular event, upregulating the different combinations of developmental
control genes in each zone of cells. Chemical signals that control the pathway of
development of cells in the embryo
Differentiation- mechanism whereby different sorts of cells arise, dictated by protein
codes of a gene
Morphogenesis- cell and tissue movement, depends on the dynamics of the cytoskeleton
Growth- overall increase in size of an organism
Developmental time- coordination of development, differs for different species
Meiosis- halving of the number of chromosomes, involves two successive cell division
Fertilization- fusing of the male and female gametes
Zygote- fertilized egg
Gastrulation- morphogenic movement that gives rise to a three-layered structure
consisting of multicellular sheets
Germ layers- ectoderm, mesoderm and endoderm
Extraembryonic structures- generated by the germ layers, it is important for support and
nutrition, establishes different commitments between future anteroposterior body
regions
Transcription factors- upregulates different combinations of gene activity in each region
Symmetry breaking- segregates some substances to one region of the zygote and the
other substances to other regions
Spermatozoan (sperm) - small motile male gamete
Egg or ovum- large, immotile female gamete, after the second meiotic division
Germ cells- bring rise to gametes
Germ line- collective germ cells
Cytoplasmic determinant- present in eggs that dictates it to become a germ cells
Germ plasm- visible specialization of cytoplasm to become germ cells
C.elegans- organism that Inherited polar granules becomes the p lineage then after will
form the germ cell. The germ cells are hermaphrodite or male
Drosophila- organism that inherited pole plasm becomes pole cells then later the germ
cells
Xenopus- has a vegetally located germ plasm rich in mitochondria
Gonad- germ migration site, derived from mesoderm, composed mostly of somatic tissue
Gametogenesis- gamete formation
Hermaphrodite- germ cells producing both male and female gametes
S-phase- chromosomes are replicated to form two identical sister chromatids
Bivalents- four chromatids, homologous chromosomes pairs up, mother and father
chromosomes
Crossing over- recombination of alleles
Oogenesis- formation of egg
Oogonia- female germ cells develop to this
Primary oocyte- oogonia after the completion of the mitotic division
Secondary oocyte- primary oocyte after first meiotic division
Yolk proteins- absorbed material in aid of growth for amphibians and fish , originating
from the liver
Nurse cells- produces materials exported to the oocyte, made by the last 4 mitotic
division of the oogonia of the fruit fly
Ovulation- release of oocyte from the ovary, resumption of the meiotic division
Germinal vesicle- oocyte nucleus
Polar bodies- cell that buds off after meiotic division of an egg, degenerates and plays no
role in development
Spermatogonia- mitotic germ cell in the testis, forms both progenitor and stem cells
Polyspermy- multiple sperm penetration
Inositol triphosphate signal transduction pathway- occurs after penetration, prevents
polyspermy, increase in intracellular calcium
Cortical granules- excreted due to large amounts of calcium, contribute to the
fertilization membrane
Animal hemisphere- upper hemisphere of a zygote, carries the polar bodies
Vegetal hemisphere- lower hemisphere, rich in yolk
Cleavage- early cell division of the zygote, exhibits no growth
Blastomeres- products of cleavage
Maternal effect- maternal mRNA controls the protein synthesis, from messenger proteins
transcribed during oogenesis
Meroblastic- uneven division of the zygote due to large yolk amounts
Holoblastic- complete division of the egg
Macromeres- large blastomeres, yolk rich, vegetal pole
Micromeres- small blastomere, animal pole
Radial- form of cleavage exhibited by echinoderms
Bilateral- form of cleavage exhibited by ascidians
Rotational- form of cleavage exhibited by mammals
Spiral- form of cleavage exhibited by annelids, molluscs and flatworms
Superficial cleavage- form of cleavage observed by insects and crustaceans
Synctium- production of superficial cleavage, many nuclei
Blastocoel- cavity of the blastula
Cadherins- binds the cells of the blastula in tight junctions
Gastrula- three-layered structure
Ectoderm- outer layer, that form the skin and nervous system
Mesoderm- middle layer, forms the muscle, connective tissue, excretory organs and
gonads
Endoderm- inner layer, forms the gut lining
Phylotypic stage- different members of animal groups show similarity in development
Tail bud stage- phylotypic stage of vertebrates, includes notochord, neural tube, paired
somites, brachial arches and tail bud
Extended germ band
Phylotypic stage of insects, six head segments, three appendages, thoracic segments and
abdominal segments
Situs solitus- asymmetrical arrangement
Situs invertus- invertion of arrangement
Isomerism- 2 sides are partly or wholly equivalent
Homeotic gene or selector gene- developmental control gene
Bistable switch- two-discrete states of activity, on and off
Concentration gradients- where inducing factors is distributed
Morphogens- inducing factors in gradients with multiple responses
Source- where morphogens are produced
Sink- region where morphogens are destroyed
Mirror symmetry- 2 similar halves joined in a plane
Homeotic mutation- converts one body part to another
Anteriorization- loss of function mutation, recessive
Posteriorization- gain of function mutation, dominant
Homeobox- DNA sequence encoding a homeodomain
Homeodomain- 60 basic amino acids which forms their DNA binding domain
Hox gene- responsible for specifying anteroposterior identity
Lamellipodium or lamellipodia- flat processes rich in microfilaments, for fibroblast
movement
Integrins- focal attachment points of lamellipodia
Filopodia- embryos processes for movement
Chemokine SDF1 and receptor CXCR4- signal center that establishes the concentration
gradient for individual cell movement
Growth cone- nerve axon movement emits the filopodia
Invagination- cells leave the epithelium and enter the space below, inpocketing
Homophilic adhesion- cells with the same cadherin components (E or N) will bind more to
each other
Condensation-formation of aggregates
Cavitation- hollowing out of fluid-filled spaces
Lumen- structure formed by cavitation
Delamination- cells leave the epithelium and move off as individual cells
Convergent extension- individual cells intercalate in between one another
Planar cell polarity-acquisition of a polarity by cells in an epithelium in the direction of the
plane of the epithelium
Epiboly- sheet of cell surround and enclose another population
Branching morphogenesis- epithelial budding
Checkpoints- where process stops unless the appropriate condition are fulfilled
Cyclins- controls the cell cycle
Asymmetric division- uneven division of the cytoplasm of egg
Apoptosis- programmed cell death
 Chapter 1

Developmental biology- science of how biological forms changes in time

Stem cells-source of continuous differentiation of new functional cells
Molecular and cell biology- study of how individuals genes and cells work
Genetics- study of the function of an individual genes
Morphology- study of anatomical structures
Experimental embryology- study of embryos through microsurgical experiments
Embryonic induction- chemical signals that controls the pathway of development a cell
within an embryo
Frog and sea urchin embryo- most commonly used embryos for experiments
Drosophila- model organism that is an asset to developmental genetics because of mass
genetic screens
Mutagenesis screens- identification of high proportions of genes that control
development, that is common to all animals
Molecular cloning- amplifying simple genes to chemically useful quantities
Nucleic acid hybridization- method that identify DNA and RNA samples
DNA sequencing- determines the primary structure of genes and their protein products
In vitro fertilization (IVF), artificial insemination by donor (AID), egg donation, & embryo
freezing
- Routine procedure that has given infertile couples babies
Robert Edwards- introduces artificial insemination, in vitro fertilization, embryo freezing
& embryo transfer to farm animals
Organogenesis- after general body plan is formed, where individual organs are laid out
(most sensitive event to human embryos)
Teratology- study of how environmental agents such as chemicals, viral infection or
radiation affect the embryo
Down syndrome- a birth defect having an extra chromosome
Amniocentesis or chorionic villi test- test that detects possible birth defects through
gathering and studying samples from the amniotic fluid or chorionic villi
Erythropoietin and granulocyte-macrophage colony- stimulating factor (GM-CSF)
- Hemapoietic growth factors used on patients with depleted blood cells
Fibroblast growth factors (FGFs)- growth factor that assist the healing of wounds
Animal models- organisms used to study pathological mechanism of human diseases, also
for testing new experimental therapies. Example: mice
Stem cell biology- study of the capabilities of stem cells
Therapeutic targets- identified targets with degenerative diseases through studying the
genes and signaling molecules, they are up for intervention
Combinatorial chemistry- the intervention of therapeutic targets through creating a drug
that can specifically augment or inhibit the action of the disease
Prenatal screening- encompasses the whole variety of single-gene disorder
Cell therapy- cell or tissues are transplanted
Pluripotent stem cell- has the ability to differentiate to all cell types and to grow without
limit in tissue culture. Can be induced pluripotent or embryonic
Induced pluripotent stem cells (iPS)- reprogrammed normal fibroblast or any other cell
types to become pluripotent
Pancreatic B-cells- differentiated cells made for the treatment of diabetes
Dopamine neurons- differentiated cells made for the treatment of Parkinson's disease
Cardiomyocyte- differentiated cells made for the treatment of heart diseases
Tissue engineering- the process of generating more complex tissues and organs starting
with constituent cells
Scaffolds- 3-dimensional extracellular matrix where cells grow and interact, this is altered
by tissue engineering
 Chapter 5
Dissecting microscope- 3d image, binocular microscope, aids in microsurgery or
microinjection, x10 to x50
Fiberoptic light- cold but illuminating light
Compound microscope- for viewing series sections, or small whole mounts, x40 to x1000,
invert image because of extra lens
Transmitted light- light for viewing whole mounts
Phase contrast microscope- technique that converts small differences of refractive index
within the specimen into large differences of light intensity, favored for living cells,
isolated gametes, and transparent embryos
Differential interference contrast- also known as nomarski optics, converts small
differences of refractive index into an apparent difference in height, provides sharp
resolution
Fluorochrome- fluorescent substance
Fluorescence microscopy- includes fluorescent antibody staining, fluorescent in situ
hybridization (FISH), and visualization of fluorochromes
Excitation spectrum- showing how the intensity of fluorescence varies with the excitation
wavelength
Emission spectrum- shows how intensity of emitted fluorescence is distributed across the
wavelength spectrum
Dark-field microscopy- depends on illumination from a very oblique angle that only points
within the specimen that scatter light extensively are visible
Polarization microscopy- place specimens across polaroid filters
Birefringence- when components alter the plane of polarization
Confocal scanning microscope- viewing fluorescence with thicker whole mounts, uses a
laser for illumination so excitation is achieved with just the single wavelength
characteristics of the laser
Multiphoton microscopy- provide better optical sectioning of fluorescent specimen than
the confocal light source is less than the required to excite the fluorochrome, two or
more photons strike one fluorochrome simultaneously
Charged coupled devices (CCDs) - cameras that contain array of pixels each of which can
be filled with electrons, 24 bit color image, 8 bit for each color - red, green and blue
Time-lapse imaging- for viewing morphogenic movement of cells
Histological sections- thin slices of the specimens that can be stained for viewing of
structure
Fixation- killing of specimens for slide preparation
Formalin, glutaraldehyde
Dehydration- in order to infiltrate the cells with wax
Ethanol
Microtome- for Sectioning of wax and specimens
Cryostat- microtome in a cooled chambers
Electron microscopy- more magnification, 3 dimensional
Reverse transcription polymerase chain reaction- standard method for detecting and
measuring mRNA
Real time PCR- more quantitative measurement of specific mRNA levels
Northern blotting- 1 Oldest and least sensitive technique
Number and size of mRNA; total mRNA through gel electrophoresis
MicroArrays- eEables examination of large numbers of gene products
RNA-Seq- refers to the ability to measure the composition of the entire transciptome
Proteomics- analysis of proteins
Western blot- shows the content of a specific proteins
Immunoprecipitation- method of isolating the protein recognized by a specific antibody
Chromatin immunoprecipitation- shearing chromatin to fragments of about 500
nucleotides in length, the immunkprecipitating with antibody
In situ hybridization- reveals the region of a specimen where a specific mRNA is present
Epitopes- particular parts of an antigen molecule that are recognized by the antibody
Hybridomas- hybrid cells; capable of both antibody production and also growth without
limit in vitro
Reporter genes- encode some easily detectable products, to monitor some particular
aspects of event in the organism
Perdurance- persistence of a gene activity after the gene expression has stopped
Fusion protein- polypeptide fused to other proteins
Vital dyes- extracellular labels
Fluorescent dextrans- common intracellular labels