CYTO311: CYTOGENETICS

TOPIC: MODEL ORGANISMS

1ST SEMESTER | S.Y 2024-2025
LECTURER: Prof. Pamela Sengson-Sevilla, RMT, ASCPi
TOPIC • The rediscovery of Mendel’s work back in the 1900s
SUBTOPIC using a wide-range of organisms confirmed that the
SUB SUBTOPIC principles of inheritance were able to breakthrough the
significance of animals and plants on researchers.
• The first generation organisms to be used as genetic
MODEL ORGANISM models are Mus musculus (Mouse) or the Drosophila
• Purpose of genetics: to understand human inheritance melanogaster (fruit fly) – because of their well-
and genetic disease. However, humans are not ideal characterized genetics and ease in experimentation
genetic organism because of the uncontrolled mating • In 2003, the human genome project
and their long life-span. Because of that, few model - voyage of biological discovery led by international
organisms are developed to study genetics. group of researchers looking to comprehensively
• A model organism is a non-human species that is study all of the DNA of a select set of organisms
extensively studied to understand basic biological - they are able to sequence the genome of five model
phenomena, with the expectation that discoveries organisms:
made in the model organism can be extrapolated to o Bacteria (Escherichia coli)
other species, Including humans. o Yeast (Saccharomyces cervisiae)
- Extrapolated: what we have learned or what we o Fruit Fly (Drosophila melanogaster)
have experimented from non-human species can be o Roundworm (Caenorhabditis elegans)
extended for the application for humans o Mouse (Mus musculus)
- Aside from these 5, we also have the Danio rerio
TYPICAL CHARACTERISTICS OF MODEL ORGANISMS (zebra fish), Chick embryo and Arabidopsis thaliana
(mustard plant)
• Small adult size
• Rapid development with short life cycles BACTERIA AS A MODEL ORGANISM
• Can be bred in large numbers • The foundations of molecular biology were based on
- Easy to breed studies of bacteria
• Readily available and inexpensive maintenance • Antibiotics
• Similar genes or similar-sized genomes to humans • Recombinant DNA technologies
• Tractability to experimental methodology
• Because of their well characterized genetics and ease • Back in 1884, the German microbiologist and
that they may be manipulated experimentally, these pediatrician, Theodor Escherich, began to study the
infant gut microbes and its role in the digestion and
species are considered to be our model organisms
disease.
• In his study, he discovered a fast-growing bacterium
called ‘Bacterium coli commune’ – now known as
Escherichia coli
• Escherichia coli usually used for recombinant DNA
technology, and used to associate specific disease of
the genome of individual; this discovery led to
invention of drugs and therapies; have been proven
to be a useful model system in which to investigate

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 protein structure and function; cannot be used to [yeast share some genes with humans so, it can
directly study manifestation of human diseases be used to test new drugs – tested on yeasts
• Knowledge gained in the bacteria model can often be containing mutated human gene to know if the
applied to homologous proteins and more complex drug can restore normal human function]
higher organism - Those genes that are most similarity shared with
• E. coli is an excellent model organism for geneticist human and yeasts are MSH2 = Muts Homolog 2
because of variety of reasons: small, take up very and MLH1 = Mut L Homolog 1 – these genes are
little lab space, easy to grow [without the need for involved in hereditary non-polyposis colorectal
expensive supply and equipment], has short doubling cancer in humans and examining these genes
time [15-20 mins] under ideal growth conditions help scientists to know more about the role of
(easy for scientists to obtain large population in a MSH2 and MLH1 in colon cancer
very short period of time); has its genome sequence Caenorhabditis elegans
already and has been studied extensively for many • One of the best characterized multicellular animal at
decades now, providing geneticist a wealth of the level of genomics, genetics, embryology
information for experimental designs and • Its genome is fully sequenced
interpretation of results • C. elegans is unique in that it can be grown and
• Bacteria share many basic biological processes with genetically manipulated with the speed and ease of a
higher organisms. This means, scientists can learn a micro-organism while offering the features of a real
lot from these biological process by studying E. coli. animal
- Easily manipulated genetically [many procedures • C. elegans has a full set of organ systems, has
for genetic manipulation have been developed by complex sensory systems, shows coordinated
scientists over many decades] behavior, and it is possible to trace the lineage of
- E. coli is a haploid [have one copy of every one of its approximately 1000 constituent cells
chromosomes]; scientists don’t have the difficulty
in observing the effects of genetic manipulation • Could be male only or hermaphrodite [have both
because they don’t have issues between female and male reproductive organs, but they are
dominant and recessive traits not female or male only]
YEAST AS A MODEL ORGANISM • Each worm contains 1000 somatic cells – 1/3: nerve
• Eukaryotic system. cells; 1/3: germ cells
• Signaling molecules and cell cycle are nearly similar. • C. elegans can be grown cheaply and in a large
• Good model system to understand many human number of plates containing bacteria, and produce
diseases including cancer over 1000 eggs everyday.
• Ease of genetic manipulation allows its use for - Have short life cycle of 2 weeks [helpful in
analyzing and functionally dissecting gene products studying their development]
from other eukaryotes. - Small organisms [convenient to keep in the
• Last decade four Nobel prizes were awarded for laboratory]
discoveries involving yeast.
• C. elegans Life Cycle and Research
• Baker’s Yeast or Saccharomyces cerevisiae is known - Its provides models for many human diseases
to be among the best experimental organism including neurological disorders, congenital heart
- Commonly used in the bread-making industry diseases and kidney diseases, studying apoptosis,
and studying the biology of the yeast enabled the could hold the key in counteracting aging of
scientists to work out the connections between humans, can provide clues in cancer, diabetes,
genes and proteins, and the function they carry and other diseases.
out in the cell. FRUIT FLY (Drosophila melanogaster)
- Although, it may seem that yeast and human • A versatile model organism that has been used
have little in common, yeast is a eukaryotic extensively for biomedical research.
organism. Like our cells, yeast have nucleus that • Easy-to-manipulate genetic system and can be used
contains DNA packaged inside the chromosome to study development, physiology and behavior.

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• Biological complexity comparable to that of a
mammal
• Many organ systems in mammals have well-
conserved homologues in Drosophila Has provided
new insights into forms of cancer, neurodegenerative
diseases, behavior, immunity, aging, multigenic
inheritance, and development.
• Has provided new insights into forms of cancer,
neurodegenerative diseases, behavior, immunity,
aging, multigenic inheritance, and development.

• Study specific diseases; mutant genes have been • 8-14 days and depending on the environmental
discovered in melanogaster that produces temperature, several generation can be observed in
phenotypes with abnormalities with the nervous just a matter of months
system [abnormal brain structure, adult on-set - Food change regularly every 10-14 days if temp is
degeneration of nervous system, retinal degeneration 25 degrees Celsius and 5-6 weeks if the
(retinitis pigmentosa)] temperature is at 18 degree Celsius
• Study of these mutations is helping to dissect the Danio rerio (ZEBRA FISH)
retinitis pigmentosa and to identify the role of genes • Small size, short life cycle, ease of culture, and ability
involved. to readily produce mutations relevant to human
• Another approach to identifying the nervous system health and disease
is to transfer mutant human disease genes in this • The embryonic development can be seen through its
organism using recombinant DNA technology transparent egg and closely resembles that of higher
[product: transgenic flies – used to studying the vertebrates
mutant human gene] – transgenic organism: • Other shared features with humans include blood,
organism has been modified by introduction of kidney, and optical systems
external DNA sequence in the germline • In addition, its genome is model or of the mouse and
- Used to study dozen human neurodegenerative human genomes, which is valuable in identification of
disease like Huntington disease [rare inherited key vertebrate genes.
disease that causes the degeneration of nerve
cells in the brain], Machado-Joseph Disease or • Used to study vertebrate development
Spinocerebellar Ataxia Type III [rare inherited • Reproduces rapidly
ataxia or lack of muscular control which affect • Development in ex vivo.
the central nervous system and characterized by • Entire initial development is transparent.
slow generation of the hind brain], Myotonic • 48hrs is enough for the development of most of the
dystrophy [characterized by progressive muscle organ systems.
wasting and weakness; can prolonged muscle CHICK EMBRYO
contractions or myotonia and are not able to
• The chick embryo provides an excellent model system
relax certain muscles after use], Alzheimer’s
for studying the development of higher vertebrates
disease [neurologic disorder that causes the
wherein growth accompanies morphogenesis.
brain to shrink and brain cells to die]
- Can be used to observe GFP (Green Fluorescent
Protein) – known as the Roslin Green or
Cytoplasmic GFP
- Powerful tool for developmental biology,
facilitating fate mapping, cell lineage, and tissue
grafting

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• The chicken embryo (Gallus gallus domesticus)
- Extremely valuable model organism in research
because most of their development is in the egg
that is incubated outside of the mother • Laboratory mouse in which one or more genes have
- As a result, early developmental stages can be been turned off. To create knownout mice, scientists
accessed, visualized, and manipulated by simply genetically engineered the animal by disrupting gene
creating a small hole in an eggshell of interest by deleting portion of DNA sequence or
- Its transparency and accessibility and ease of replacing the gene by an altered sequence
manipulation makes it an ideal tool for studying • Used to study what happens to an organism when a
the formation and patterning of the brain, neural particular gene is absent and studying knockout mice
tube, somite, and heart primordia can provide information how the knockout genes
MOUSE (Mus musculus) usually functions, including the biochemical, physical,
• Closest mammalian model organism to humans and behavioral roles.
- Anatomy, physiology, and genetics • Because humans and mice have many similar genes,
- Useful for study of human diseases knockout mice are usually used to discover the
- Cost-effective and easy to look after functions of human genes and study human diseases.
- Adult mice: reproduce quickly, as often as 3 Arabidopsis thaliana (Thale cress or Rock cress)
weeks [mate and give birth – lots of mice to work • Small flowering plant with white flowers (often
with] considered as a week)
- Mice are far better than flies and worms for - Can be found across Europe, Asia, or Africa
studying the complex biological systems found in - Easy to look after compared to animal model
human such as immune, endocrine, nervous, organisms
cardiovascular, and skeletal systems - Produce quickly and produce small seeds
- Mice naturally develop diseases that affect the - Characterized by the volume of work in this plant
system, including cancer and diabetes - Became a model organism through the study of
• Genes that code for proteins responsible for carrying biochemical and molecular processes involved in
out vital biological processes in both the human and human diseases
the mouse share a high degree of similarity. - Named as the ‘premiere model for plant biology’
• Therefore, the mouse has already proven extremely • Has a small genome relative to other plants and is
useful in development, genetic, and immunology easily grown under laboratory conditions
studies • Amenable to some genetics particularly generation of
• Transgenics and KO's possible transgenics
• A great system for studying and understanding • Allows insight into numerous features of plant
human disease, as well as a mechanism for biology, including those of significant value to
investigating new treatment strategies in ways that agriculture, energy, environment, and human health
cannot be done in humans

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 GENE MAPPING recombinants and those named genes (A,a,B,b) will
be transferred]
• The model organisms are very useful for different
- In linkage, meron pa ring A,a,B,b, but after crossing
processes including gene mapping.
over, the recombinants will not be exchanged
• Refers to the mapping of genes to specific locations on o The closer they are, the highly linked they
chromosomes will be
- Loci or locus o The farther they are, the more they are
• The ultimate goal of gene mapping is to clone genes, likely to recombine
especially disease genes - The distance between genes is called
- Determine the DNA sequence and its product “centimorgans” or genetic mapping unit (m.u)
- Example: Cystic Fibrosis (most common lethal o Distance between genes for which 1
inherited disease in US [1985 – gene have mapped product of meiosis per 100 is recombinant
where CF is located; mapped in the chromosome o If 2 genes are 1 centimorgan apart, they are
7q31-q32 through linkage analysis] 1/100 or 1% that meiosis happens, the
- 4 years later, Francis Collins and his co-workers genes will recombine
cloned this gene – defect of chloride channel
[protein product of this disease gene] RECOMBINANT DNA
• 2 Types:
1. Genetic Mapping – using linkage analysis to
determine the relative position between two genes
on a chromosome
- linkage map or recombination map
2. Physical Mapping – using all available techniques or
information to determine the absolute position of a
gene on a chromosome
- Based on the direct analysis of DNA wherein we • Can be done in-vitro. Once made, the recombinant DNA
measure the physical distances between and molecules are introduced in an organism (often
within the loci or locus bacterium)
• Linkage analysis is the genetic mapping that is based on • Cleavage of DNA at specific sites by the restriction
the linkage between “loci” or the locations of genes nucleases (restriction enzymes). Kukunin yung part na
guston i-isolate; then tatanggalin yung part na pagi-
insert-an ng DNA
o Hae III
▪ Haemophilus aegypticus
o Hind III
▪ Haemophilus influenzae
o EcoR1
▪ Escherichia coli
-
Here, if 2 loci are inherited together, they are said - Restriction enzymes are produced by bacteria as a
to be “linked” defense mechanism against infection from viruses.
- 2 loci on different chromosomes are not linked – Prevent viral infection by degrading the DNA of
separated by 2 different independent assortment viruses
[part of Mendel’s law; assorted 2 daugher cells • DNA ligation by ligase
differently in the process of Meiosis] - Seal the phosphodiester backbone of the DNA to
- If the independent assortment often happens, the covalently join the fragments together to form the
duplicated homologous after crossing over meiosis, recombinant DNA molecules
recombination will happen [end up having a
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 - Make it possible to seamlessly join together the - To distinguish host cells that have taken up vectors
DNA molecules from widely different sources from host cells that have not, the vector should
carry a selectable marker gene [usually an antibiotic
resistant gene or a gene that is absent from host
cell]
- Many vectors incorporate specific sequences
[allowed for sequencing]
- The vector and its inserted DNA fragment should be
easy to isolate from the host cell [to recover cloned
DNA for different applications]

• Restriction enzyme – recognizes and binds to DNA at a

specific nucleotide sequence [restriction site]
- Cuts both strands within the sequence by cleaving
the phosphodiester backbone of the DNA
- That process of slicing or cutting the strands are
referred to as ‘digestion of DNA’
- Restriction sites are present randomly in the
genome
- Actual fragment sizes produced by DNA digestion
with a given restriction enzyme vary because the
number and location of recognition sequences are
not always randomly distributed in the DNA
- Most recognition sequences often exhibited a form
of symmetry described as a palindrome –
nucleotide sequences the same on both strands of • Scientists recognized fragments produced by restriction
the DNA [3’ or 5’ direction] enzyme digestion can be cloned.
- The most common recognition sequence are usually • DNA cloning is done by inserting a particular fragment
4 or 6 nucleotides long, but there are 8 or more of DNA in a purified DNA genome of a self-replicating
nucleotides genetic element (plasmid)
- Enzymes such as EcoR1 and Hind III – make off set - The purified plasmid DNA circles are first cut with a
cuts in the DNA strands – producing fragments with restriction nuclease to create linear DNA molecules
single stranded overhanging ends – cohesive ends - To DNA to be cloned is added to the cut plasmid
- Alu-1 – known as blunt ends and then covalently joined using the DNA ligase and
the recombinant DNA circle is reintroduced into the
DNA CLONING bacterial cells
- As cells grow and divide, the recombinant plasmid
• DNA Cloning Vectors – DNA molecules that accept DNA
also replicates to produce enormous copies of DNA
fragments and replicate inserted DNA fragments when
circles containing the foreign DNA
vectors are placed into host cells
- A vector contains several restriction sites VECTORS
- Vectors must be introduced into host cells [to allow
independent replication of vector DNA and other • Plasmids have been extensively modified by genetic
DNA fragments it carries] engineering to serve as cloning vectors. Many

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 commercially prepared plasmids are readily available - Others can be induced in the laboratory to become
with a range of useful feature competent
- Derived from naturally occurring plasmids [extra- • First step of transformation, there will be an entry of
chromosomal double-stranded DNA molecules that DNA, which is thought to occur in limited number of
replicate independently from chromosomes within receptor sites on the surface of competent bacterial cell
bacterial cells] • Second, the passage of the cell that is thought to be an
- Plasmids are introduced to the bacteria in the active process that requires energy and specific
process of transformation [consist of numerous transport molecules
steps that achieve 2 basic outcomes] - This model is supported by the fact that substances
1. Entry of foreign DNA to a recipient cell that inhibit energy production or protein synthesis
2. Recombination of foreign DNA and its also inhibit transformation
homologous region in the recipient • Soon after entry, one of the two strands of the double
chromosome helix is digested or degraded by nucleases, leaving only
- Completion of both outcomes are required for a single strand to participate in the transformation
genetic recombination, the first step of • The surviving DNA aligns with the complementary
transformation can occur without the presence of region of the bacterial chromosome in the process
the second step and results in the addition of involving several enzymes.
foreign DNA in the bacterial cytoplasm, not the - The segment DNA replaces its counterpart in the
chromosome chromosome which is excised or degraded.
• For recombination to be detected, the transformation
of the DNA must be derived from a different strain of
bacteria that bear some distinguishing variation such as
mutation and once this is integrated into the
chromosome, the recombinant region contains 1 host
strand and 1 mutant strand
- Because these strands are from different sources,
the region is referred to as ‘heteroduplex’ which
usually contains some mismatched of sequences.
- That mismatch activates a repair process, and
following repair in 1 round of DNA replication, 1
chromosome is restored to its original DNA
sequence, identical to that of the originial recipient
cells. While the other contains the properly aligned
mutant gene
• Following cell division, one untransformed cell
[nonmutant] and 1 transformed cell [mutant] are
produced.

- In the population of bacterial cell, only those in a

particular physiological state take up DNA and
studies have shown that various kinds of bacteria
readily undergo transformation naturally
[Haemophilus influenzae, Bacillus subtilis, Shigella
dysenteriae, Streptococcus pneumoniae, and
Escherichia coli]

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• DNA Cloning is done through these steps:
1. Insert the particular fragment of DNA into a purified
DNA genome of a self-replicated genetic element
[plasmid]
2. DNA purification [extract genomic or plasmid DNA
in the sample quantities the research requires]
- Purfying the DNA samples from contaminants
extend their shelf life and reduces the probability of
errors in research results
3. The purified plasmid DNA circles are first cut with a
restriction nuclease to create linear DNA molecules
4. The DNA to be cloned are added to the cut plasmid
and covalently joint using the enzyme, DNA ligase
5. After ligation, the recombinant DNA circle is
introduced back into the bacterial cell and as the
cell grows and divides, the recombinant plasmid
also replicates to produce a number of copies of
DNA circles containing the foreign DNA
• Because of DNA cloning, we can now generate many
millions of identical molecules to produce a large
number of copies of a gene or other piece of DNA
• The cloned DNA are used to work out a function of a
gene, investigate gene characteristics such as size and
expression, look at how mutations can affect gene
function, make large concentrations of proteins coded
by that gene

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