Model Organisms

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Model Organisms
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Archaea Bacteria Fruit Flies Retroviruses Yeast Pl
asmodium Dictyostelium Zebra fish C. elegans Mice
Rats Arabidopsis
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What Is a Model Organism?
Over the last century, research on a small number
of organisms has played a pivotal role in
advancing our understanding of numerous
biological processes. This is because many
aspects of biology are similar in most or all
organisms. These much-studied organisms are
commonly referred to as model organisms, because
each has one or more characteristics that make it
suitable for laboratory study.
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The most popular model organisms have strong
advantages for experimental research, such as
rapid development with short life cycles,
small adult size, ready availability and ease
of maintenance. .
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A large amount of genetic information can be
derived from these organisms, providing valuable
data for the analysis of normal human development
and gene regulation, genetic diseases, and
evolutionary processes.
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Archaea
Archaea are unique. They represent the most
primitive organisms yet discovered and have been
found to have a remarkable resemblance to some of
the earliest known fossils. They live in some of
the most extreme environments on earth, hence the
nickname "extremophiles". Uses - bioremediation,
global climate change, biotechnology, and energy
production.
Extremophiles that survive in extremely cold
environments.
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Archaeans resemble bacteria and have some genes
that are similar to bacterial genes. They also
have other genes that resemble eukaryotes and
some genes that appear to be unique. Studies of
these unshared genes may provide new clues to the
evolution of early life on earth.
Sphingopyxis alaskensis
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Evolutionary History
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Archaea genome
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Methanopyrus
Produces methane by combining carbon dioxide with
hydrogen from rocks in geothermal springs and
other hot spots. An "extremophile,"
Methanopyrus grows optimally at temperatures near
and above the boiling point of water.
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Microbes
Microbes are thought to make up more than 60
percent of the earth's biomass. They have
survived and evolved on Earth for over 3.7
billion years and have been found in almost every
environment. The diversity and range of
environmental adaptations mean that microbes have
long ago "solved" many problems for which
scientists are still actively seeking solutions.
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Disease-causing Microbes
1. Giardiasis 2. Influenza 3. Food
poisoning 4. Malaria5. Strep throat 6.
HIV/AIDS 7. Tuberculosis 8. Lyme disease9.
Hepatitis B
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Most microbes are not responsible for diseases in
humans, animals, or plants. Therefore, by
studying and understanding a diverse group of
microbes at the genomic level, researchers may
develop answers to existing challenges in
medicine, agriculture, industrial processes,
energy production and use, and environmental and
waste cleanup.
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Escherichia coli
Prokaryote 22 minute doubling time Grows on agar
plates Millions per plate Small, simple
genome 1/1000 of the eukaryote DNA
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Drosophila Melanogaster
The fruit fly, Drosophila melanogaster, has been
used as a model organism for research for almost
a century and is considered an attractive system
for a number of reasons, including its
easy-to-manipulate genetic system, relatively low
cost, and biological complexity comparable to
that of a mammal.
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Many organ systems in mammals have well-conserved
homologs in Drosophila, and Drosophila research
has already led the way in providing new insights
into forms of cancer, neurodegenerative
diseases, behavior, immunity, aging,
multigenic inheritance, and development.
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Life Cycle
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Drosophila Genome
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Retroviruses
Retroviruses are an unusual form of virus capable
of infecting a wide range of vertebrates and
causing a number of diseases such as pneumonia,
leukemia, and AIDS.
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Viruses are important to the study of molecular
and cellular biology because they provide simple
systems that can be used to manipulate and
investigate the functions of many cell types.
Numerous studies have demonstrated the utility
of animal viruses as probes for investigating
different activities of eukaryotic cells.
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Other examples in which animal viruses have
provided important models for biological research
of their host cells include studies of DNA
replication, transcription, RNA processing,
and protein transport.
HIV
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Yeast
Commonly known as baker's or brewer's yeast, has
been used in research studies for a very long
time.
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The complete genome sequence of the S. cerevisiae
lab strain S288C was obtained in the spring of
1996, making yeast the first eukaryotic organism
to be completely sequenced.
16 chromosomes (haploid) 12 Mb
The complete sequence of its genome has proven
extremely useful as a reference toward extracting
the sequences of human and other higher
eukaryotic genes.
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The ease of genetic manipulation of yeast allows
its use for conveniently analyzing and
functionally dissecting gene products from other
eukaryotes.
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Zebra Fish Danio rerio
The zebrafish, is used as a model organism
because of its small size, short life cycle (3
months), ease of culture, and ability to readily
produce mutations relevant to human health and
disease.
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The embryonic development of the zebrafish can be
seen through its transparent egg and closely
resembles that of higher vertebrates, making it
useful for studying development and mutations.
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Zebrafish Genome
Other shared features with humans include blood,
kidney, and optical systems. In addition, its
genome is half the size of the mouse and human
genomes, which is valuable in identification of
key vertebrate genes.
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Caenorhabditis elegans
3-day generation time 1.5 mm long 300
progeny/brood lt1,000 cells Reproducible,
quantifiable behaviors
Worm eating video
Worm moving video
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C. elegans, A Nematode Worm

• Nematodes are some of the most abundant animals
  on the planet.
• They are found in almost every environment, and
  many are harmful parasites of animals and plants.
  C. elegans however is not a parasite.
• It is a free-living nematode that lives in the
  soil. In a teaspoon of soil from a garden it is
  possible to find many  nematodes, some of which
  may be C. elegans or its relatives. 
• Soil nematodes eat bacteria.

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Hermaphrodites and Males
Hermaphrodite
Male
6 pairs of chromosomes XX hermaphrodite XO male
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C. Elegans Anatomy
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C. elegans Genome

• It is the first animal to have its  entire genome
  sequenced. 
• The genome size of C. elegans is 100 megabases or
  1/30 the size of the human genome. 
• It has six chromosomes, five autosomes and a sex
  chromosome, all of similar size. 
• The chromosomes are  holokinetic, that is, they
  don't have a centromere. 

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• There is little repeated DNA in the genome, which
  makes  it good for sequencing. 
• There are about 18,000 protein coding genes, and
  1000 RNA genes. 
• About half the  genes have similarity to genes in
  other organisms, and some are homologs of disease
  genes in humans.
• Experiments using C. elegans are done by
  thousands of scientists around the world and even
  on the space shuttle

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Cell Lineage
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Mutants of C. elegans have been found that
have altered development, behavior, movement, 
ability to smell and taste, feeding,
defecation, rate of growth, aging and
programmed cell death.
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Locomotion Mutants
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Size Mutants
Various mutants, a.normal, b.dumpy, c.small,
d.long
There are many C. elegans mutants available for
biological research, which is especially
important for genetic study. Some genetically
determined traits, such as motility mutants, are
easy to observe. When a mutant is found, it can
be crossed with worms having a known genetic
background and, further, one can learn where this
mutated gene may be located and define its
function.
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Microinjection
http//www.mcb.arizona.edu/wardlab/injectionvid.ht
ml
Video link
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Gene Expression Studies
video
By observing the worm with the green fluorescent
protein under a microscope, the expression of a
gene can be seen, and its timing, location and
quantity of the gene expression can be monitored.
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Culturing Worms

• The worms eat all the bacteria in a few days,
  get crowded and begin to starve, so we transfer
  them to fresh  plates. 
• In response to crowding, C. elegans can arrest
  development at the end of the second larval
  stage,  and last in that dormant state for months
  to years. 
• When these arrested worms, called dauer
  ("enduring")  larvae, are moved to fresh plates
  with bacteria to eat, they resume development
  where they left off.

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Sub-Culturing Worms
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Research
Blood Pressure
Space Travel
Amyotrophic Lateral Sclerosis ALS
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The Mouse Mus musculus
The mouse is the closest mammalian model organism
to humans. The gene sequences that code for
numerous proteins responsible for carrying out
vital biological processes in both the human and
the mouse share a high degree of similarity.
Lives 1.5 3 years Gestation 21 days Can
reproduce at 7 weeks
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Transgenic Mouse
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The Mouse Genome
The mouse has already proven extremely useful in
development, genetic, and immunology studies.
Elucidation of the mouse genomic sequence
provides a system for studying and understanding
human disease, as well as a mechanism for
investigating new treatment strategies in ways
that cannot be done in humans.
Clues to human genetics
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The Rat Rattus norvegicus
The rat is a principal model organism to link
function to genes. The large number of inbred rat
models and the vast amount of data available for
the rat provide important strengths for the study
of human health and disease.
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In some instances, specific aspects of human
disease are duplicated well only in the rat,
making these animals a unique resource for
studying and identifying genetic pathways
relevant to human disease.
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The rat is also a model of choice for many
physiological studies related to cardiac and
vascular function, pulmonary circulation,
metabolism, neurological control, age- and
gender-related differences, and studies related
to hypertension and signal transduction
3-5 year life span 7-20 rats/litter 6-7 litters
per year
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Arabidopsis Thaliana
Arabidopsis Thalania is a small flowering plant
that belongs to the Brassica family, which
includes species such as broccoli, cauliflower,
cabbage, and radish.
6 weeks from germination to seed
TAIR
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Because Arabidopsis has a small genome relative
to other plants and is easily grown under
laboratory conditions, it has become the organism
of choice for basic studies of the molecular
genetics of flowering plants. Scientists expect
that systematic studies of
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Arabidopsis will offer important advantages for
basic research in genetics and molecular biology
and will illuminate numerous features of plant
biology, including those of significant value to
agriculture, energy, environment, and human
health.
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Mutations
Mutation accumulation in fifth generation of
mismatch-repair-defective Arabidopsis. (A) wt
plants, (B-F) selected morphological mutants,
(G) wt flower, (H) mutant flower.
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Dictyostellium

• Cellular slime molds
• Study of cell communication and
• programmed cell death