ZOO-3202 - Trans 3 - Model Organisms

ZOO 3202: Developmental Biology (Lecture)
A.Y. 2022 - 2023 PAMANTASAN NG LUNGSOD NG MAYNILA

PROF. SARMIENTO, D. COLLEGE OF SCIENCE
BMD 3-2 Department of Biology
TRANS 3: MODEL ORGANISMS
OUTLINE
I. Lesson Outline
II. Objectives
III. Model Organisms
a. C. elegans + Apoptosis
b. Ascaris
c. D. melanogaster
d. Sea urchin
e. Starfish
f. Zebrafish
g. Frog
h. Mouse
IV. Regulator Genes APOPTOSIS
● Programmed cell death or “cellular suicide”
OBJECTIVES o Its difference to necrosis
● To determine why these organisms are commonly (nangingitim) is cell death due to an
used in the study of development. injury. It will happen because the cell
● To know the importance of model organism is already injured.
research. ● A form of orderly process where cell contents are
packed into small packets of membrane for
MODEL ORGANISMS “garbage collection” of immune cells.
o The small packets of cells are seen by
C. ELEGANS immune cells or the WBCs as
● Multicellular organism; a nematode or free-living garbage, thus, engulfing them
roundworm, transparent in appearance. (phagocytosis).
● 2-3 weeks lifespan; new generation every 3 days ● Removes cells during development.
o After being a fertilized egg, it becomes o Most of the time, it is advantageous
a larva already. It grows in size rapidly, because it acts as a survival or
until 3 days. defense mechanism. If the body part
o After 3 days, its maturation is final. must be removed for development, it
● Used by scientist to analyze mechanisms to cell must undergo apoptosis.
suicide (apoptosis) ● Eliminates cancerous and virus-infected cells and
o C. elegans is used in developmental maintains balance in the body.
biology, especially if you are
researching or doing something that
has to do with apoptosis because of its
short lifespan, it can be studied or
obtained easier.
o It can also be studied about ageing.
For example, the extract of mango
leaves has the potential to delay
ageing. It has antiinflammatory
properties that can fight free radicals
that contribute to ageing. ● The developing mouse paw looks generic at first,
o In this case, it can be placed on the then eventually, a distinct structure or fingers or
medium with the extract for it to be digits forms because apoptosis occurs in the cells
studied. If the worm reacts to the between digits, causing it to separate.
antiinflammatory properties of the ● If apoptosis did not occur in hands or paws, it will
extract, it can extend its lifespan. result in syndactyly, a condition for having fused or
● Genome sequences in 1998 with 19,099 genes. webbed digits.
40% resemble humans.
ALABADO, S., DAR SANTOS, M.J., JAMBALOS, Z.H., LUCIDOS, A. & POBLETE, M.J. 1
o Children who play outside can obtain

this, specifically when they bite their
nails. They digest the eggs of worms
and grow them inside their small
intestine, causing diarrhea.
o Once they are eliminated, they are
already mature or white/pale in
appearance.
● Demonstrate sexual dimorphism.
● Used to observe fertilization.
o Presence of male and female genes.
● Cells shrink and form blebs.
o Blebs refer to protrusions or resulting
in an irregular shape of the
membrane.
o The nucleus also condenses.
● DNA in the nucleus is chopped into fragments.
● Cells shrink in small fragments enclosed by a
membrane.
o It needs to be in small fragments to be
digested.
o Apoptotic bodies or little sealed sacs
form, containing information or
substances from dying cells, such as
different organelles.
● Fragments release signal that attract immune cells
o The immune cells are the WBCs. It
can be T-cells, b-cells, or lymphocytes.
● Fragments of dying cells display the lipid molecule
“phosphatidylserine” on the surface.
o This PS tells the immune cells, “kunin
mo ako, kainin mo ako.”
o Basically, it attracts immune cells.
● PS lets the phagocytes bind and eat cell
fragments.
.
o Either matured with an opaque color
when rid from the body.
FRUIT FLY (Drosophila melanogaster)

● Genome sequenced in 2000 with 13,600 genes;
with 50% human equivalence.
o Fewer genes compared to C. elegans.
o There is a research that induced a fly
ASCARIS (Ascaris lumbricoides) with alcohol, and the specimen
● A parasitic worm also known as “small intestinal exhibited minimal side to side flying
roundworms”, commonly seen in soil. motion (as if drunk like a human).
● It can also be found in feces through fecal analysis ● 2-3 months lifespan; new generation every 10
from an infected person or children. days.
o Demonstrates cell stages during

cleavage formation (2 cells, 4 cells,
and so on).
o Embryo
o 1st instar
o 2nd instar
o 3rd instar
o Pupa
o Prepupa
o Adult (3 months maximum, ideally)
● With 61% genes for human diseases and 68%
cancer genes have homologues in D.
melanogaster genome.
● Observed a high degree of conservation in
neurological, cardiovascular diseases (CVD),
endocrine and metabolic diseases.
o For example, if you want to study the
level of cholesterol, to prevent the
development of CVD, D. melanogaster
can be used as a model organism.
o Extracted genes could be those that
can lower lipid profile; ow-density
lipoprotein (LDL) or high-density
lipoprotein (HDL) - responsible for the
development of cholesterol in the
arteries. BIPINNARIA (STARFISH LARVAE)
● Good source of information about neuron activity
and genetics of addiction. ● Demonstrates early body plan of organisms after
o However, due to its small size, it is the gastrulation.
difficult to handle. o After gastrulation, ectoderm,
mesoderm, and endoderm are distinct
SEA URCHIN and will undergo organogenesis. The
plan will then be visible.
● Have a genome that encodes for many vertebrate
o Types of body plans:
immune system-related genes.
● Used to observe early cleavage. ▪ Symmetrical or Bilateral (e.g.
o Favored model organism for studying humans)
cleavage.
▪ Asymmetrical (e.g. sponges)
▪ Radial (e.g. starfishes)
▪ Epiboly stage, wherein the

cells move downward and
later on move upward.
o The 14-somite stage is the last
gastrulation stage.
ZEBRAFISH o It proceeds to organogenesis,
● Has shorter history as a laboratory organism. blastopore, hatching, and so on.
● Lacks sophisticated technology that exists for the ● Zebrafishes or fishes in general, as model
more longstanding models. organisms are costly as they require a maintained
● Lifecycle duration of 4 months. aquarium environment and food (depending on
what is needed to be induced).
WHITEFISH
● Demonstrates the process of mitosis.
o Possible researches involving mitosis:
cancer, cysts, etc.
o Start with fertilization.

o 30 minutes after fertilization, from cell
division. It becomes a meroblastic Question: It is considered as the “senior citizen” of
cleavage. embryological research. It was able to demonstrate
o As it develops, the division of darker embryonic regulation and the existence of vegetal
and animal gradients controlling the body plan.
parts (above) and lighter parts (below)
is visible. In the sphere stage, it Answer: Sea Urchin. It is the first animal that
consists of 1000 cells. demonstrated the existence of vegetal and animal
o Then it proceeds to gastrulation and poles (part of the protoplasm). Among the others, it
epiboly. is part of the first animals that developed. During
those times, limited or there were no options for
vertebrates, sea urchins were abundant and easier
to handle - sessile (not moving).
XENOPUS (Xenopus laevis & tropicalis) ● Ovaries are observed to demonstrate early stages
of oogenesis
● Common Name: Clawed frog
● Genes are unlikely to be sequenced for X. laevis ● Stages of Oogenesis
o Possible researches involving mitosis: o Oogonia → Primary oocyte →
can Secondary oocyte
● Never taken seriously for genetics due to long life
cycle ● Markers for Microscopy
o Takes 9 months to rear until sexual 1. Epithelial Cells - abstract, light colored
maturity 2. Matured egg cells
o Similar to human pregnancy, it takes 9
months before it can be experimented Table 1. Frog and Cat Ovaries
Frog Cat
with
• Frog ovaries largely • Cat ovaries specifically
● X. tropicalis will mature in 4 months demonstrate the early show the stages after the
o Another species with earlier sexual stages in oogenesis non-fertilization of egg
maturity cells
B. Frogs and Grasshoppers: Testis &

Spermatogenesis
● Frog (Xenopus) vs Grasshoppers (Caelifera)
● Testis cross section (transverse) are used to
demonstrate stages of spermatogenesis
● Markers for Microscopy

1. Spermatozoa (matured sperm) -
longitudinal, dark hair-like strands →
represent the flagella of sperm
2. Seminiferous Tubules - outline that
encompasses each region (boundary)
● Neurulation containing developing sperms
o Neurula later develops → Neural plate 3. Cysts - stained circular structures
→ Neural groove → Neural tube 4. Epithelial Cells - lightly-stained,
● Early Structures give rise to organs: absract structures
1. Neural tube: develops into the CNS (brain
and spinal chord) Table 2. Frog and Grasshopper Testis Comparison
2. Notochord: develops into the vertebral Frog Grasshoppers
column • Frog testis show similar • Grasshoppers
3. Somites: develops into dermis, muscles, stages of specifically show the
skeletal system and cartilages spermatogenesis with stages after the
numerous vertebrates non-fertilization of egg
cells
GAMETOGENESIS ANIMAL REPRESENTATIVES
A. Frogs and Cats: Ovary & Oogenesis
● Frog (Xenopus) vs Cat (Felis catus)
pseudotetraploidy. Billions of years ago, during its

evolution, X. laevis had various mutations hence the
double set of chromosomes, resulting to
pseudotetraploidy. That’s why this is not advisable to
be used in sequencing - it would be confusing due
to the presence of pseudoalleles in the set of
chromosomes. For example is the height; it will not
be determined as for the possibility of mimicry in the
allele present for the specific trait. Furthermore,
MOUSE (Mus musculus) there is also a tendency to have a duplication in the
function of genes since there’s the presence of a
● Genome sequenced in 2002 with ~30,000 genes; double allele.
99% human equivalence
o Used in many researches due to high
equivalence
o All to be observed in humans can be
observed in mouse
● ~3 billion bp of DNA same as humans
● 2 years lifespan; new generation every 9 weeks
● >90% of mouse and human genomes can be

partitioned into regions of conserved synteny (see
Figure of Karyotype below)
o Synteny - same genes of the same
order in the chromosome observed in
two different species Figure: Phylogenetic tree showing the positions of the big six
model organisms used in developmental biology (Slack,
● Mouse models have invaluable use in medical Essential Developmental Biology)
trials of new drugs
o Intraperitoneal (viscera), ● All model organisms are bilateral and they are
subcutaneous, intravenous further identified into:
o Ex. Testing vaccines ○ Protostomes - mouth
○ Deuterostomes - anus
● Separation via development of opening.
Experimental advantages and disadvantages of six

model organisms
● For chick, it is referring to the egg only and not
the matured chick.
Karyotypes of Mouse and Human
● In using mice in research, you have to consider
the variant or specific mice - environment and
age, to avoid bias.
Question: Which among the model organisms is a
● Gene inventory = genomic sequence and the
pseudotetraploid?
bioinformatics of the model organisms
Answer: Xenopus laevis is unlikely to be
sequenced since this organism exhibits
● Transcription factor regulates what particular

portion of a gene is transcripted by turning on and
off gene transcription.
● Fly is under Arthropoda, Class Insecta

○ Usually, flies have six legs and its
body segments include head, thorax,
and abdomen.
○ If the homeotic gene is normally
developed - no mutation and
aberration (below is the ideal structure
of the fly produced).
● C. elegans and Drosophila have the shortest

period of generation.
● Xenopus have the longest lifespan.
● Zebrafish also has a relatively short period of
generation for about 1-2 days as compared to
other model organisms.
Homeotic Genes
● Selector genes
● Master regulatory genes that direct the ○ Antennapedia is an example of a
development of particular body segments or homeotic gene; it expresses the gene
structures. for the development of the legs in the
○ Many genes are under control by the thorax.
Homeotic genes like the Hox gene.
○ The determinants and morphogens
are not equally distributed and have
gradients; more concentrated, more
defined morphogenesis and structure
of development, which is usually
caused by homeotic genes.
● Encode transcription factor proteins; central
dogma:
DNA → RNA → polypeptide → protein
(transcription) (translation)
○ If homeotic gene is not normally
develop (due to external environment
factor) mutation may occur or its legs the gene encoding for the
may develop in their head, replacing development of the thorax in a fly is
the antenna. missing, then the thorax region will
also be absent)
Hox Genes
● Aka Homeobox; a region in the homeotic genes.
○ Only a region since the homeotic gene
is the master regulator.
● Turned on by a cascade of regulatory genes.
● Found in many animals.
○ Mutations in human Hox genes cause
genetic disorders.
● It is used as an evolutionary factor to determine
our origin since almost all animals have this kind
of gene and only differ in features. Hox Genes in Humans
● Duplicated over evolutionary history; used in
evolutionary studies since almost all animals have
this kind of gene.
● Exist as 4 similar gene clusters (A to D).
○ Different clusters work together from
head to tail axis (clusters 1 to 4 has
something to do with the upper portion
of the human body, 5-6 has something
to do with the neck, 7-8 is the body
and vertebral column, while 9-13 is the
upper and lower extremities and
appendages);
There are many different homeotic genes that express ○ Ex: if the concern is at the neck
genes for the development of various body parts. region, then the Hox gene that is
responsible for this can be either
Early Developmental Cascade Hox-A6, Hox-B6, or Hox-C6.
● Maternal effect genes. ● Mutations in HoxD13 causes synpolydactyly
○ Placed in egg cell for fertilization.
○ Responsible for head-tail polarity (the
gradient in the head-tail axis has
something to do with the development
of a structure).
○ Encode and regulate transcription or
translation.
● Gap genes
○ Define large, multi-segment regions of
fly.
○ Missing when gene is mutated (such
as in the previous example of
antennapedia in fruit fly)
● Pair rule genes
○ Turned on by interaction between gap
genes.
○ If missing, there is a loss of structure
in the segment region (for example, if
Synpolydactyly
● HoxD13: if mutation occurs, synpolydactyly may
also occur.
○ It is a condition wherein the digits are
joined.
○ Possibly because HoxD13 did not
express this kind of development - the
cell did not undergo apoptosis,
therefore resulting in the digits
remaining fused instead of separated
to each other.
Importance of Model Organism Research

● It offers a cost-effective way to follow the
inheritance of genes through many generations in
a relatively short time.
○ Especially if the budget is limited,
therefore researchers can choose their
target in the study and what are other
options or counterparts that they can
use (aside from mice which are
expensive or above the budget).
Likewise, other model organisms are
also important since their genome can
be used to obtain the generations in a
short time.
● Using comparative genomics, we can gain a
better understanding of how species evolved.
○ Genomics can be further divided into:
lipidomics (lipids), proteomics
(proteins), glycomics
(carbohydrates).
○ We can also know the counterpart
percentage of the human genome
compared to the genome of the model
organism.
● Researchers learned about the function of human
genes by examining their counterparts in other
organisms (e.g. mouse).

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ZOO 3202: Developmental Biology (Lecture)

A.Y. 2022 - 2023 PAMANTASAN NG LUNGSOD NG MAYNILA

TRANS 3: MODEL ORGANISMS

o Children who play outside can obtain

FRUIT FLY (Drosophila melanogaster)

o Demonstrates cell stages during

▪ Radial (e.g. starfishes)

▪ Epiboly stage, wherein the

o Start with fertilization.

B. Frogs and Grasshoppers: Testis &

● Markers for Microscopy

pseudotetraploidy. Billions of years ago, during its

● >90% of mouse and human genomes can be

Experimental advantages and disadvantages of six

● Transcription factor regulates what particular

● Fly is under Arthropoda, Class Insecta

● C. elegans and Drosophila have the shortest

Importance of Model Organism Research

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