● Chick

Introduction to ● Frog (Xenopus)

Model Organisms ● Zebrafish

Definition
● Fruit fly (Drosophila)

● Model Organisms: Selected ● Nematode (C. elegans)

animal species used to represent
general principles of animal
development, not just their own
biology. Selection Criteria

Organisms are chosen based on:

● Goal: Understand processes
applicable to many organisms,
especially humans. ● Year-round availability

● Ease of lab domestication

Medical Relevance
● Experimental advantages

● Research is often aimed at

understanding human
Prototypical Strengths
development and disease.

● Many developmental processes

are conserved across species. ● High fecundity:

○ Xenopus, zebrafish,
Drosophila, C. elegans →
The “Big Six” Model Organisms produce many eggs

● Commercial availability:
● Mouse
 ○ Chick embryos bought ● Xenopus: large eggs → ideal for
from hatcheries grafting and injections

● Transparent embryos:

Practical ○ Zebrafish, C. elegans →

observe cell movements
Considerations live

1. Maintenance Costs
4. Genetics
● C. elegans: very cheap, can be
frozen
● Drosophila:
● Mouse: most expensive
(regulations, space, labor) ○ Advanced genetics,
~2-week life cycle

● C. elegans:
2. Embryonic Access
○ Self-fertilizing
hermaphrodite →
● External fertilization: mutations become
homozygous quickly
○ Xenopus, zebrafish →
easy to access and
manipulate embryos

● Internal (mammals):

○ Mouse embryos implant Key Reminders

after ~4 days → hard to
study long-term in vitro
● C. elegans: grown on agar +
bacteria

3. Micromanipulation ● Drosophila: can be cryopreserved

 ● Mouse sperm & embryos: can be Ploidy Issues
frozen

● Access = ease of obtaining

● Xenopus laevis:
embryos at all stages

○ Pseudotetraploid → gene
● Chick: ~60,000 cells during
redundancy
cleavage (double-layered embryo)

○ Pseudoalleles = duplicated
● Mouse embryos
genes with similar function
(post-implantation): survive 1–2
days in vitro only
● Xenopus tropicalis:

● Organogenesis models: mouse

○ Diploid → easier for
& chick (good for studying
genetic studies
organs)

Genomics and Genome Duplication

Evolution
● Zebrafish:

Genome Mapping
○ Ancient duplication → extra
gene copies but
● All Big Six: nearly complete functionally diploid
genomes → easier gene
identification
Relevance to Humans

● Mouse & chick favored because

they are amniotes
Special Genetic Features
● Mouse = mammal → closest
model to humans
● Drosophila:

○ Balancer chromosomes
maintain lethal mutations
Developmental Secondary &
Milestones Niche Models
Time to Maturity Classic Models

● C. elegans: ~3 days
● Sea urchin:
● Xenopus: up to ~9 months
○ Cyclins discovery,
embryonic regulation

Key Stages ● Ascidians & gastropods:

○ Cell lineage, cytoplasmic

● Gastrulation → germ layer
determinants
formation

● Segmentation → body segments

appear Regeneration Models

● Hatching/Birth
● Planarians

● Adult (reproductive maturity)

● Urodele amphibians (axolotl, newt)

Experimental Focus
Unique Systems

● Mostly on early embryonic stages

● Dictyostelium: chemotaxis &
aggregation
● Endpoint = completion of a
specific process (not full
● Physarum: synchronous nuclear
adulthood)
division

● Volvox: morphogenesis
Evolutionary
● Beetle (Tenebrio)

● Silk moth (Bombyx)

Models
● Amphioxus: primitive vertebrate
ancestor REFLECTION

● Hydra: possible ancestor of all

“Big discoveries can come from the
animals
smallest organisms.”

Learning about model organisms

honestly made me excited about how
Specialty / biology works in real research. I used to
think scientists just study humans
directly, but now I see how powerful
Ancillary Models these simple organisms are in
uncovering complex processes. It’s
interesting how each organism has its
● Rat: post-implantation embryo own strengths like transparent embryos
or fast reproduction that make
culture, teratogenicity testing
experiments easier and more effective.

● Quail: grafting experiments with Even though there’s a lot to remember, I

chick enjoyed realizing how everything
connects, especially how these models
● Medaka: used in zebrafish can help us understand human
development. This topic made me feel
transgenics
more curious and motivated to learn,
because it shows how smart choices in
research can lead to big scientific
breakthroughs.
Other Insect
Models
● Dragonfly (Platcnemis)

● Cricket (Acheta)
 ○ Abdomen

DROSOPHILA ● Embryonic body plan visible in

extended germ band stage

MELANOGASTER ● Phylotypic stage: stage where all

insect embryos show maximum
similarity
● First organism whose development
was understood at the molecular
level.

● Developmental biology advanced

DROSOPHILA BODY
through: ORGANIZATION
○ Mutagenesis screens Segmentation
○ Gene cloning
● 3 thoracic segments: T1, T2, T3
○ In situ hybridization (to study
gene expression patterns) ● 8 abdominal segments: A1–A8

○ In vitro studies for ● Two types of segmentation:

mechanistic detail
○ Parasegments (early):
transient, out of phase

GENERAL INSECT BODY ○ True segments (later): adult

PLAN body plan

● Three main regions

Head

● 6 segments:
HTA (remember this):
○ 3 procephalic

○ Head ○ 3 gnathal (form

mouthparts)
○ Thorax
● Gnathal segments initially resemble
leg buds
Thorax Holometabolous development
(Drosophila)
● T1 (prothorax)
● Egg → larva → pupa → adult
● T2 (mesothorax)
● Larva is structurally different from
● T3 (metathorax) adult

● Adult structures arise from:

Functions:
○ Imaginal discs

● Each segment - one pair of legs ○ Abdominal histoblasts

(ventral side)

● T2 and T3 - wings (dorsal side)

Hemimetabolous (contrast)

● Larva resembles adult

Internal Organization
● Develops through nymphal stages
● Ventral nerve cord (main nervous
system)

● Dorsal heart OOGENESIS

● Tracheal system:
16-CELL CYST
○ Oxygen delivered via
tracheae (no blood oxygen
FORMATION
transport)
● One germ cell undergoes 4 mitotic
● Circulatory system:
divisions

○ Open system (hemolymph)

● Produces:

○ No specialized blood vessels

○ 1 oocyte

○ 15 nurse cells
METAMORPHOSIS ● Cells remain interconnected
par1 Gene

● Required for oocyte specification

● If absent:

○ All 16 cells become nurse

cells

○ No oocyte forms

2. EGG CHAMBER
FORMATION

● Components:

○ Oocyte

○ Nurse cells

○ Follicle cells

● Follicle cells:

○ Somatic (not germline)

○ Derived from gonads

○ Surround entire cluster

 REFLECTION
As a third-year biology student, studying
Drosophila melanogaster development
helped me better understand how
complex body structures form from simple
beginnings. At first, the topic felt very
detailed, especially with all the genes and
stages involved, but as I went through it, I
started to see how everything is
connected in a clear and organized way.

One concept that stood out to me was the

syncytial stage, where nuclei divide
without cell membranes. It made me
realize that early development relies
heavily on molecular gradients rather than
physical boundaries. The roles of Bicoid,
Nanos, and Dorsal showed how important
proper distribution of proteins is in
determining body axes.

The genetic hierarchy from maternal

effect genes to Hox genes also helped me
understand how development is
controlled step by step. Each group of
genes has a specific role, and mistakes at
any level can lead to major changes in
body pattern. This made me appreciate
how precise gene regulation needs to be
during development.

Oogenesis was another important part

because it showed that development is
already being set up even before
fertilization. The contribution of nurse cells
and the formation of the pole plasm
highlighted how much the mother’s input
affects the embryo.

Overall, this topic helped me connect

concepts from genetics, cell biology, and
embryology. It also showed me why
Drosophila is such an important model
organism, since it allows scientists to
study these processes in a simpler but
still meaningful way.
Tab 1
AMPHIBIANS NOTES LECTURE PPT

Oogenesis ( Egg Development ) - Triggered by gonadotrophins from

pituitary gland which leads to
= Frog ovary contains many oocytes progesterone release
surrounded by: Progresterone -
● follicle cells activates c- Mos
● blood vessels
Progesterone
Oogonia persist into adulthood → stimulates
continue dividing translation of c-Mos, which
activates the MAPK pathway
and promotes activation of
MPF. MPF directly induces
Last mitotic division → primary oocyte : germinal vesicle breakdown
Oocyte growth takes months ; and meiotic progression.
After meiosis I, c-Mos helps
accumulating food reserves —> for early maintain the secondary
embryo development oocyte in metaphase II
arrest until fertilization.

So; oogonia —> primary oocyte Eggs are ovulated and coated in
Oocyte: jelly as they move through the
oviducts
● Stores - ribosomes, tRNA, yolk
proteins (produced by the
mother’s liver)
● Develops animal-vegetal polarity:
Fertilization
Balbiani body ( mitochondrial cloud ) Natural = male fertilizes egg (occurs in the
● Cluster of organelles including: animal hemisphere ; sperm binds via
● Many mitochondria surface glycoproteins)
● RNA molecules Lab= in vitro
● Proteins
● Germ cell determinants
Marks future vegetal pole and localizes
specific mRNA (e.g., vegT = maternal
mRNA ; located in the vegetal cytoplasm ;
transcription factor that activates genes
involved in = endoderm formation ;
mesoderm induction signals (TGF-B
pathways )

● Animal hemisphere becomes

pigmented (pigmented granules
move towards Animal hemisphere
cytoplasm during egg formation
___________________________________

Maturation (Final Egg Preparation)

AMPHIBIANS NOTES LECTURE PPT

Calcium also causes cortical granule exocytosis ; which PARALLEL STACKS (contributes to
lifts vitelline membrane —-> allow egg to rotate (so
centrosome*)
animal hemisphere is on top)

MICROTUBULES : separate outer cortical

Normal Development in Xenopus
cytoplasm (from yolky internal cytoplasm)
- ESTABLISH the DORSAL VENTRAL
Frog development progresses AXIS by DIRECTING CORTICAL
through: ROTATION (powers movement)

● Cleavage
● Gastrulation
● Neurulation

24 Hours 24 C = stages are

categorized by Nieuwkoop and
Faber

Stage 8: Mid blastula

Stage 9: Early Gastrula Sperm enters the animal hemisphere
Stage 10: Early Gastrula ● Trigger cortical rotation = results in
pigmentation shift = grey crescent (
Stage 13: Early neurula marks the future site of gastrulation )
Stage 20: End of neurulation ● Sperm binds via surface glycoproteins
● A dorsal determinant is relocated from
the vegetal pole to the dorsal side =
Cortical Rotaion and Dorsal Axis establishing the dorsal - ventral axis
Formation
MISCONCEPTION : The vegetal hemisphere is the
dorsal side X

= Before fertilization:
- frog only has animal-vegetal axis
- Where: vegetal hemisphere is yolk-rich
bottom half
- Dorsal determinant molecules are initially
located in the vegetal cytoplasm =

after fertilization:
- cortical rotation moves these
determinants to one side of the egg
opposite sperm entry point = >
becomes dorsal side of embryo

Sperm centriole enters the egg and

ORGANIZES MICROTUBULES into
 AMPHIBIANS NOTES LECTURE PPT

Feature Role in
Development
Sperm Entry Point Defines ventral (belly) side

180 Degrees Opposite of Becomes dorsal (spinal)

Sperm Entry side

Microtubules ● Guide cortical

reaction
● Axis specification

Gray Crescent ● Future

Gastrulation site
● Initiates dorsal
body structures

CLEAVAGE IN XENOPUS Characteristics of Amphibian

DEVELOPMENT Cleavage

CLEAVAGE PATTERN - RADIAL HOLOBLASTIC

CLEAVAGE : whole egg divides
1st Cleavage - VERTICAL (like echinoderms)
- SPLIT : LEFT - YOLK (density) slows cleavage
AND RIGHT in the vegetal hemisphere —>
HALVES
ASYMMETRIC CELL SIZES
- Left and right
halves

2nd Cleavage - VERTICAL ->

CLEAVAGE DIRECTION OUTCOME
RIGHT
ANGLES TO
THE FIRST
1st Meridional BISECTS
- Dorsal/ventral (vertical) GREY
halves CRESCEN
T
3rd Cleavage - Horizontal/Eq
uatorial = Starts at
- Vegetal and animal
Animal pole and
halves moves
slowly to
vegetal

2nd Meridional Divides

(vertical + embryo
perpendicula into 4
AMPHIBIANS NOTES LECTURE PPT

r to the first) blastomer

es FORMATION OF MORULA AND
BLASTULA
3rd Equatorial Creates
(but shifted smaller MORULA ( 16- 64 ) - > mulberry
toward animal - Ball made of many tightly
animal pole) micromer packed blastomeres
es and (cleavage cells)
larger
vegetal Embryo is now called blastula( ~ 128
cells) -> formation of blastocoel
(CENTRAL CAVITY; fluid filled)

BLASTULA FORMATION - Ball made of many tightly

packed blastomeres
(cleavage cells)
- Large Cleavage cells are called blastocoel - separates vegetal
blastomeres and animal cap cells - delaying
- A blastocoel cavity forms in the differentiation
animal hemisphere (cells -Prevents mesodermal induction
divide faster there; yolk slows too early
down cell division = vegetal
cells heavier= fluid cannot
accumulate there), making the
embryo a blastula
REGION FATE
- Outer membrane of blastula is
sealed by TIGHT JUNCTIONS = ANIMAL - ECTODERM
IMPERMEABLE TO MOST HEMISPHERE 1.) Epidermis
SUBSTANCES 2.) Nervous
system
- Internal cells : connected by
VEGETAL - ENDODERM
cadherins (Can be dissociated HEMISPHERE 1.) Gut
by calcium removal) 2.) Interna
l
GAP JUNCTION LINK CELLS (cell organs
communications)
CELLS BENEATH - MESODERM
= DESMOSOMES APPEAR LATER = blastocoel 1.) Muscle
provide stronger mechanical attachment = 2.) Notochord
needed when tissues start experiencing 3.) Blood
physical stress OPPOSITE SPERM 1.) Neural
ENTRY ectoderm
AMPHIBIANS NOTES LECTURE PPT

2.) Notochord
3.) Pharyngeal = DRIVEN BY FACTORS LIKE
endoderm
VegT
= Cell cycle gains GAP
PHASES (G1/G2)
= Blastomere become motile =
MID- BLASTULA FORMATION prepare for GASTRULATION
MBT
CONTROLLED BY
-Occurs after 12 CLEAVAGES CHROMATIN TO
(LATE BLASTULA STAGE) CYTOPLASM RATIO

= as cleavage continues = more nuclei

Key changes: (chromatin/DNA)
- Slower cleavage rate +
loss of synchrony More chromatin = earlier mbt
- Increased cell adhesion
→ smoother looking
blastula
IMPORTANT EVENT OF MID-
BLASTULA FORMATION
= ZYGOTIC GENOME
ACTIVATION (ZGA)

= this activation allows

embryo to begin controlling
processes (cell differentiation, GENE EXPRESSION AND
pattern formation, preparation EARLY CELL FATE
for gastrulation)
= allowing early transcription Mesoderm formation =
of specific genes ● Marked by BRACHYURY GENE -
regulates GASTRULATION
AMPHIBIANS NOTES LECTURE PPT

DORSAL ORGANIZER REGION embryo, but keeping track of each

● SPEMANN’S ORGANIZER movement and its role is challenging.

Characterized by genes: The molecular signals, like VegT,

1.) Siamos Nodal, and the organizer region, also
2.) Goosecoid add another layer of difficulty. I
understand that they control cell fate
3.) Not
and axis formation, but remembering
4.) Lim1 how they interact and what each one
= which control AXIAL specifically does can be
DEVELOPMENT and GASTRULATION overwhelming.

Overall, this topic made me realize

that amphibian development is more
complex than it initially seems. While I
REFLECTION am starting to understand the general
flow, I still need more time and
Trying to understand amphibian practice to fully grasp the details and
development felt like trying to follow a connect all the processes together.
very detailed process without being
able to clearly see what is happening
step by step. As a third-year biology
student, I found this topic more
challenging than expected, especially
when compared to Drosophila.

One of the parts I struggled with the

most is cortical rotation. I understand
that after fertilization, the cytoplasm
shifts and helps establish the dorsal
side, but it is still difficult for me to fully
visualize how this movement leads to
the formation of the gray crescent and
eventually determines the body axis. It
feels like a small change with a very
big effect, which makes it harder to
grasp.

Gastrulation is another area that I find

confusing. There are many types of
cell movements involved, such as
invagination, involution, and
convergent extension, and I
sometimes mix them up. I know these
processes are important for forming
the germ layers and shaping the
 ○ Birds/reptiles → meroblastic
(partial, yolk-dependent)
AMNIOTES
○ Mammals → holoblastic
(complete, adapted for
● Birds and reptiles share
placenta)
developmental patterns; birds are
reptilian clade.

● Amniote egg membranes support

terrestrial life:
Bird Development

○ Amnion → prevents Fertilization & Cleavage

desiccation
● Fertilization in oviduct before shell
○ Yolk sac → nutrient
deposition.
absorption & circulation
● Discoidal meroblastic cleavage:
○ Allantois → waste storage
blastodisc forms on yolk →
blastoderm (~4 cell layers).
○ Chorion → gas exchange
● Subgerminal cavity: forms area
● Model organisms:
pellucida (embryo) vs area opaca
(extraembryonic).
○ Chick (Gallus gallus):
accessible, similar to
mammals.
Gastrulation & Body Axes
○ Mouse (Mus musculus):
genome sequenced, main
mammalian model. ● Epiblast: forms embryo;
hypoblast: extraembryonic
membranes & signals
gastrulation.

Amniotes vs Mammals ● Three phases: EPS

● Eggs: protective shell; mammals: 1. Epiblast/Hypoblast formation

placenta supports gas exchange,
nutrition, waste removal. 2. Primary body (head, neck,
trunk)
● Cleavage:
 3. Secondary body (tailbud →
Mammalian Development
posterior structures)

Challenges & Models

Polarity & Primitive Streak ● Small eggs, internal development.

● Mouse: short cycles, large litters,

● Koller’s sickle → posterior easy manipulation.
thickening → anterior-posterior
axis.

● Posterior Marginal Zone (PMZ): Fertilization & Cleavage

initiates primitive streak; influenced
by gravity.
● Fertilization in ampulla; first
cleavage ~1 day post-fertilization.
● Primitive streak: gastrulation site;
forms mesoderm & endoderm.
● Rotational, asynchronous
cleavage; early zygotic gene
● Hensen’s node: organizer →
activation:
notochord, prechordal plate,
somites.
○ Mouse & goat → 2-cell stage
y
● Streak elongation: convergent
○ Human → 8-cell stage
extension + hypoblast migration.

Axis & Cell Fate Compaction & Blastocyst

● Anterior streak: endoderm, head ● 8-cell: compaction (E-cadherin)

mesoderm, notochord
● 16-cell morula → ICM (embryo) +
● Middle: somites, heart, kidneys trophoblast (placenta)

● Posterior: lateral & extraembryonic ● DNA demethylation →

mesoderm totipotency; genomic imprinting
ensures proper differentiation.
● Left-right axis: Nodal & Pitx2 (left),
BMP4 & Fgf8 (right), Lefty1 midline
barrier
First Cell Fate Decision
 ● ICM vs trophoblast: ● Hox genes regulate A-P
patterning: early genes → anterior,
○ Oct4 → ICM/pluripotency late genes → posterior.

○ Cdx2 → trophoblast

○ Mutual inhibition ensures Left-Right Axis

fate commitment
● Node cilia: leftward flow → left-sided
Nodal → Pitx2

Second ICM Decision ● Cerberus/Lefty inhibit right-sided

Nodal

● Nanog → epiblast (embryo) ● PCP pathway positions cilia; dynein

mutations → heterotaxy
● Gata6 → primitive endoderm (yolk
sac/support)

Tail Development

Blastocoel & Cavitation

● Neuromesodermal progenitors
(NMPs): spinal cord & vertebrae
● Trophoblast secretes fluid →
blastocoel formation. ● Oct4 → trunk; GDF-11 → tail;
Hoxb13 → tail termination
● ICM on one side → key
mammalian feature. ● Apes lost tails via T (Brachyury)
mutation

Gastrulation & Axis Formation

● Primitive streak forms at posterior;

EMT allows epiblast migration. Major Themes of
● Node → anterior structures; AVE
Vertebrate Gastrulation
(anterior visceral endoderm) blocks
Wnt/Nodal → A-P axis. 1. Internalization → mesoderm &
endoderm move inward
● Fgf signaling drives EMT &
mesoderm/endoderm migration. 2. Epiboly → ectoderm spreads
 3. Convergence → internal cells
migrate midline
REFLECTION
4. Extension → body elongation along
A-P axis “Understanding begins with confusion.”

This quote perfectly describes my

experience with the amniotes topic. At the
Key Signals start, everything felt overwhelming,
especially with the number of structures
involved. The extraembryonic membranes
● A-P axis: Nodal, Wnt were the hardest part for me because
they all seemed similar, and I kept mixing
up their functions.
● D-V axis: BMP inhibitors (Chordin,
Noggin) The amnion, chorion, allantois, and yolk
sac were particularly confusing. Even
● Left-right axis: Nodal → Pitx2 when I tried to memorize them, I realized I
didn’t fully understand how each one
works or how they support the embryo in
terms of protection, gas exchange, and
waste management. It felt like I knew the
terms, but not the actual concepts.

Another challenge was visualizing the

process. Since development happens
inside the egg or within the mother, it was
harder to imagine what was going on
compared to other organisms where
development is more visible. I found it
difficult to connect familiar processes like
gastrulation to what is happening in
amniotes.

Overall, this topic made me realize that I

need to focus more on understanding
rather than just memorizing. I still feel
confused about some parts, but I know
that with more practice and reviewing
diagrams, I’ll be able to understand it
better.