iGEM 101 – Session 7 Presentation
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Transcript iGEM 101 – Session 7 Presentation
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