iGEM 101: Session 7
4/2/15
4/5/15
Jarrod Shilts
Ophir Ospovat
Purpose of Model Organisms
 Simplified system
 Tiers of complexity
 Evolutionary similarities
 Limitations and advantages
 Coordinating research
 Depth of understanding
 Community of investigators
 Accumulated resources and knowledge
 Databases, pathways, protocols, and tools
 Historical contingency
Uses of Model Organisms
▪ Basic Research
▪ Disease Models
▪ Applied Biology
Model Organism Commonalities
▪ Rapid generation time
– Short life cycle, many progeny
▪ Easy to maintain
▪ Evolutionary conservation
– Pathways of interest
– Homologs for disease genes
▪ Available information
– Prior research, genome sequence,
protocols, et cetera
▪ Unique specialties
– Specific research focuses
– Useful attributes
Overview
▪ Cell-Free Systems
▪ Prokaryotes
– Eschercicia coli
– Bactillus subtilus
– Other specialized strains
▪ Eukaryotes
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Saccharomyces cervisae
Cell lines
Caenorhabditis elegans
Drosophila melanogaster
Mus Musculus
Arabidopsis thalina
Other specialized organisms
Cell-Free Systems
▪ Abiotic conditions
– Cell enzymes
– Cytosolic cofactors and energy sources
– No preexisting genetic material
▪ Control over contents
– Purify enzymes, nucleic acids, and even
available nutrients and precursors
▪ Ongoing refinement
– In vitro transcription and translation
– Biochemical reactions
– Minicells
Eschericia coli
▪ Most common bacterial model
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Gram-negative bacterium
Small genome (1 chromosome, 3000 genes)
Doubling time less than 1 hour
Safe (biosafety level 1)
▪ Many strains available for lab applications
– High efficiency peptide secretion
– Increased rate DNA transformation
– Other specializations
▪ Extensive Synbio use
– Most biobrick parts for E. coli
Bacillus subtilis
▪ Second most common bacterial model
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Gram-positive bacterium
Only 200 essential genes (4k total)
Spore forming
Safe (biosafety level 1)
▪ Natural competence
– DNA transformation without chemical treatment
▪ High enzyme secretion
– 60% of prokaryote-produced enzymes
Other Prokaryotes
▪ Methanococcus
– Methanogenic archae
▪ Mesoplasma florum
– Very small genome (800,000 bases)
– Modified stop codon
▪ Azotobacter
– Aerobic extracellularly, anaerobic
intracellularly (specialized applications)
▪ Mycoplasma
– Artificial genomes
– Minimal cells
Saccharomyces cerevisiae
▪ Budding Yeast
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Single celled eukaryote
Relatively little non-coding DNA
Doubling period of 2 hours
Visible cell cycle
▪ Genetic manipulations
– Capable of transformation
– High rates of recombination
– Integrates plasmid genes
▪ Other fungi
– Schizosaccharomyces pombe
– Neurospora crassa
Mammalian Cells
▪ Immortalized cell lines
– Many strains available from multiple
cell types
– Human cells or from other mammals
– Fibroblasts common
– Eukaryotic, singled celled
▪ Cell culture
– Growth factors
– Possibly ECM
▪ Introduce DNA by virus
Caenorhabditis elegans
▪ Nematode worms
– Multicellular eukaryote (Eutely with just
over 1000 cells)
– Hermaphroditic with hundreds of
progeny per worm
– Simple tissues
▪ Simple nervous system
– Complete connectome
– Development tracked
▪ Genetic manipulations
– Similar in span to Drosophila
Drosophila melanogaster
▪ Fruit flies
– Complex animal with complete organ systems
– Small genome (three chromosomes)
– Life span just over one week
▪ Characterized biology
– Developmental stages
– Nervous and other systems
▪ Genetic manipulations
– Targeted gene modifications
– Genetics-based tools for
studying proteins at high
resolution (ex. GRASP, MARCM)
Mus Musculus
▪ House mouse
– Advanced mammalian model
– High similarity to humans
– Generation time of couple months
▪ Human disease models
▪ Genetic manipulations
– Approaching the level available
for invertebrate models
– Crossing steps like Drosophila,
but significantly longer
▪ Also Rattus norvegicus
Arabidopsis thaliana
▪ Thale cress
– Predominant plant model
– Rapid growth in one month
– Studied plant physiology
▪ DNA transformation by Agrobacterium
Other Eukaryote models
▪ Chlamydomonas reinhardtii
– Unicellular algae
▪ Zea mays
– Maize for agricultural research
▪ Xenopus laevis
– Frog for embryological studies
▪ Danio rerio
– Zebrafish for developmental studies
▪ Macaca mulatta
– Rhessus monkey for disease and
cognition studies