Embryology Notes
the embryo relative to one another resulting in
Lecture 1
How many bps are there in a typical Gene?
•1 Mb = 1 000 000 bp
•1 KB = 1 000
•5000bp total 3bp per AA is approx..1667
What’s Wrong with Calculation: You don’t take
into account splicing  introns begone
•transcript needs poly A tail/ 5” modification
•UTR: Untranslated Reg. Cis elm= enhancer
•URR: Upstream, Regulate Region
•Eukaryote 3.2 GB Genome size of animals
•More splicing (alternative)  leads to less
genes needed  1 gene functions as 2 or 3
Dev Bio: Adaption how germline maintained
Embryology: How single cell form entire
organism  only about 200 diff cell types
Morphogenesis: Formation of structures
Evolution: How much change & still function?
Regen: How use stem cells  to reform shit
ENV Integration: Genotype env.  Gives
different phenotype. Ex: turtle sex/catpillar diet
Lecture 2
Dev. Biology: Basic Concepts
Development: Creating more complex
organism via embryogenesis going into adult
form and aging through senescence
Embryology: Study of animal development from
fertilization to hatching or birth
Fertilization: When mommy meets a daddy
Gamete: Specialized reproductive cell
Genome: Complete DNA sequence of indiv. Org.
Cleavage Rapid mitotic cell division following
fertilization  WITHOUT increasing mass
Blastomere: A cleavage- stage cell resulting
from mitosis
Blastula(membrane): Early stage of embryo
consisting of a sphere of cells surrounding an
inner fluid- filled cavity, the blastocoel
Gastrulation: Movement of the blastomeres of
the formation of the 3 germ layer of embryo
Gastrula: Stage of embryo following
gastrulation that contains 3 germ layers that
will interact with the organs of the body
Blastomere  Gastrulation ( movement to form
3 germ layers  Gastrula
Germ Layer
• 1 of 3 layers of vertebrate embryo will
form tissues of body except the germ cells
•Triploblastic: To have 3 germ layers
1.Ectoderm: Nervous system, Neurons, pigment
2. Mesoderm: Muscles & Skeleton, Connective
Tissue; Reproductive organs; kidney; blood
3. Endoderm: Respiratory, Digestive track, Skin
•Organogenesis: Interact between and
rearrang. of the 3 layers Produce tissues
• Metamorphosis: Changing form 1  another
•Germline Cells: Not somatic  gonad cells 
Undergo meitotic division  to generate eggs
•Somatic Cells: Cells that form body ( not germ)
*Separation of germline cells from somatic cells
often one of 1st differentiation in animal dev*
Gametogenesis : Production of gametes
•2ndary spermatocyte/oocyte1 spermatocyte
/ootid  Differenation & maturation = sperm
Aristotle: Recognized 2 dif types of cleavage
1. Holoblastic: Cell 2. Meroblastic : Cell
divison pattern in divison pattern in
embryo containing zygotes containing 1.
entire egg-> divided Large Yolk 2. Portion
into smaller cells of cytoplasm Cleaved
Holo = complete Mero= part
William Harvey: All animals from egg & sperms
1. Blood Tissue formed B4 Heart
2. Observed blastoderm in chick
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Marcello Malpighi: 1st microscopic chick dev
•Epigensis vs Preformation: Made from scratch
(undivided stems) vs Homunculus theory
(organs always present in miniature form)
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Kaspur Fredrich Wolf: Argues against preforma.
•Essential life force creates embryos
• Supports epigenesis but w/o the concept of
cells and the Cell doctrine (all plants and
animals tissue are aggregates of cells emerged)
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Karl Ernst von Baer (1828’s): Cells do
gastrulation & found mammalian egg •found
NOTOCHORD (Transient mesodermal rod in
dorsal of embryo  role in inducting &
patterning in nervous sys.)
•Showing flaw viewed of Recapitulation: As
embryo you were initially fish  newt  lizard
 Chicken  small racoon  then human
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Schwann and schleiden (1839)
•Cell Theory  Virchow added 1858 prexist cell
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Cell are either  Epithelial & Mesenchymal
Epithelial Mesenchymal
Form Sheets Loose organized &
connected by loosely attached
junctional complexes cells (bold indiv.)
Sheets act like barrier Migrate as indv. Cell
Move in Harmony Adhere in 3D clump
Clear polar character
Basal Lamina is Basal lamina may
foundation contacts surround the cells
only 1 surface of cell ( muscle or fat cells)
Morphogenesis: Organization of cells in body
into a functional structure & coordinate such as:
 Cell movement; growth ( smaller cells & big)
egg x sperm ; death (programmed); division
( direction & amount); shape changes ( change
in character from epithelial to mesenchymal) ;
change in composition or secreted products
( ECM influence whether neighbor cells migrate)
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Fate maps Map of developmental fate of a
zygote or early embryo  Shows what organs
will develop given position on the embryo
•In olden days we marked indiv. cell positions
on embryo to see where it would grow later
•Do a thousand and even dumbasses can do <3
Details on fate Map Construction
1. ~Some embryos have few cells & obvious diff
in cytoplasmic pigmentation of early blastomere
•Fate map can be constructed by removal~~
2. ~Vital dye used on living cells w/o killing
3.~ Fluorescent dyes  much better  injected
& then photo-activated using a laser small
group of cells to be tagged  track movement
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Following Cell fate- Chimeric embryos
1. 1920’s- Hilde Mangold and Hans Spemman
•Transplanted embryonic tissues from one
species of newt to another distinguish from
the natural pigmentation
2. 1969. Le Douarins Quail Eggs
•Took nucleus from quail  drive by chick nuc.
•Quail and chicken aspects in embryo
3.Transgenic Chrimer Embryo’s
•Embryo GFP protein  in wild type host= glow
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Homologous Structure Common anc.
Structure ( our arms and bat wings)
Analogous structuresame function (wings) Hybridoma cell lines : recog. By Easiest method visual
used to produce anti-DIG-  Allow detection of
Malformation: Underlying cause is genetic monoclonal AB. antibody activity of enhancer
(can glow)
Piebald Syndrome: Homo gene mutation (petridish goodness) element rather than
FITC-Goat anti-mouse 4. The all of gene expression
Disruption: Abnormality caused by tetragons Primary AB: Raised in mRNA GFP
Tetratogens: Agent disrupting embryo dev. Rabbit defending bands will 1. Observe subcellular
against rabbit protein appear as localization of specific
(chemical, virus, irradiation, hypothermia) 2ndary AB: Raised in stripes  proteins ( you can add
Syndactyly= Malformation bc its genetic Mouse and recognized You can AA to target specific)
all Rabbit AB (amplify track 2. Must be introduced
signal of primary fucking & then expressed to
Lecture Set 2 Intro Dev Bio & Embryo. get live imaging
(mouse- anti goat) transcript.
Genome equiv: Every cell have same genome Slide *32
Dif. Gene exp (DGE)
1. Every cell nucleus contains entire genome Mechanisms for DGE
2. Genes not used aren’t destroyed or mutated
3. Only small % genome expressed in each cell 1) Transcription
& RNA synthesized in particular cell type •Transcription factor  lead to differential gene
Polytene CH (result of DNA rep cont. w/o Mit.) expression by RNA Pol 2
In Drosophila, physical genetic map, shows 2) RNA Processing
genome organized into 5000 bands, (same each •Nascent transcripts must be processed ( spliced,
tissue) early evidence in sup. of genome equiv. capped & tailed, exported from nucleus) to become
mRNA that can be translated in cytoplasm
 Bands: associated with DFG expression 3) Transport and Localization of mRNA
Genome Equiv– Testing- Somatic nuc. Transfer •Cases transport of mRNA out of the nucleus can be
1952:Briggs and King- Make dem young tad pol selective, while localization of mRNA molecules
1975:Jogn Gurdon frog’s- adult nuclei organs within the cytoplasm can determine whether or not
it will be translated
*Old idea: As organism develops its cell become
4) Translation
more restricted in their developmental potential
•not all mRNA’s are translated at the same rate; they
then dolly took a sheepy shit on this* can also be degraded at different rates ( mRNA
1997- Ian Wilmut produce dolly- Dolly pls  stability). Stability of mRNA Is influenced by polyA
FULLY PROVED GENOMIC EQUIVILANCE tail length as well as activity of miRNA (microRNAs)
mature fertile sheep cloned from somatic cells; 5) Post-Translational Modification
may have epigenetic effects of DNA methylation •protein activity and subcellular localization can be
Visualizing Gene Expression influenced by protein phosphorylation, glycosylation
Chromatin Structure (6 slides on this)
Antibodies In Situ Reporter Genes Chromatin- Eukaryotes DNA packed w/ proteins
Hybrid. Histones- Main packaging proteins
Visualizing Protiens : Used to Reporter Gene: Genes
in fixed cells; visualize that encode products Nucleosomes- Basic unit of chromatin structure
Seperated by mRNA : easy detect (LacZ/GFP)  Nucleosome is an histone octamer of 2X each:
electrophoresis// 1. Get the LacZ: detected using
isolating protiens from target H2A. H2B, H3, H4 with 140 bp DNA wrapped around
special substrate &
cells mRNA precipitates product Linker Region: between nucleosomes is ~60bp (find
(immunoprecipitation)
, blocking protein act.
GFP: detected by histone H1 here)
fluorescent microscop
Monoclonal: Rec 1 EP 2. Recog. Compact Nucleosomes- histone h1 can be this
Reporter Construct
Polyclonal: Rec x EP by DIG Inhibited Transcription- H1 dependent compactions
Epitote(EP)- antigen labeled
determi. AA(residue) probe ( transcription factors and RNA pol have no access to
Antiserum: Antibody 3. Now genes
rich blood <3 – made hybridize In general the default conditions of chromatin is a
via antigen injection d will be Can insert in genome repressed state***
Transcriptional Regulation (3 slides)

Transcriptional Factors ( 5slide)

Silencers- Negative Enhancerss ( 1 slide)

Find DNA regulatory Sequences & ChIP-seq (3)

Transcriptional Reg. & DNA methylation (5)

DGE:RNA process; splicing; (3)

Gene Expression control at Translaion (10)

Post-Translational Reg. of gene expression (3)