19/10/2015. Response to environmental manipulation. Its not as simple as it seems!

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Janis Todd
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Common in vivo model species Genetic manipulations (Lecture 2) To catalogue/identify gene function 30,000 protein coding genes <10,000 with

1 Jackie Mitchell Department of Basic and Clinical Neuroscience - IoPPN Why do we need model genetic systems? What does it take to be a good model? Common in vivo model species Genetic manipulations (Lecture 2) To catalogue/identify gene function 30,000 protein coding genes <10,000 with known function Recent identification of functional non-coding RNAs To identify gene/protein role in disease Multiple genes in multiple neurological disorders Often little knowledge of functional relevance Model disease causative and healthy genes Develop models for therapeutic assessment 1

2 Study genetic perturbations under a controlled environment Gene/protein knockouts Gene/protein overexpression Normal Disease mutant Gene/protein point mutations/knock-ins Multiple genetic variations Natural variation (inbred/outbred strains) Trait selection Response to environmental manipulation Its not as simple as it seems! One gene can have several functions Multiple genes can perform the same function What is a model? A small measure A simplified representation used to explain/understand the workings of a real system Two basic types In vitro A controlled environment outside the living organism Test tube Cell culture In vivo A whole living organism Also ex vivo intact tissue from a living organism 2

environmental manipulation Construct Validity How well the model reflects theoretical assumptions (the human condition) Predictive Validity How well a

3 genetic models drug models environmental manipulation models behavioural models Simple genetic system vs. close relatives Breeding capacity and known history Ease of genetic manipulation Quantifiable phenotypes Experimental tractability Ease of environmental manipulation Construct Validity How well the model reflects theoretical assumptions (the human condition) Predictive Validity How well a manipulation in the model being studied predicts performance (again in the human condition) Face Validity Degree of similarity between responses observed in the model and the disorder it simulates in humans 3

4 Reproducibility Relevance Decreases with increasing model simplicity Interpretation (interpretability) Species specific responses Humans are the worst model system!!!! 4

5 Unicellular Organisms Bacteria (Escherischia coli) Yeast (Saccharomyces cerevisiae) Non-vertebrates Worms (caenorhabditis elegans) Flies (drosophila melanogaster) Non-mammalian vertebrates Fish (danio rerio, takifugu rubripes) Frogs (Xenopus laevis) Non-primate mammals Rodents (mus muscularis, rattus norvegicus) Non-human primates Monkeys (macaca mulatta) mammals bacteria archarea eucaryota reptiles and amphibians animalia plants funghi protist birds fish invertebrates arachnids vertebrates urchins corals and anemones insects bivalves jellyfish worms and leeches crustaceans Monotremata Marsupialia Afrotheria Xenarthra snails Laurasiatheria and slugs Euarchontoglires squids, cuttlefish and octopi Humans Primates Rodents Euarchonta Glires 5

Unicellular Organisms Bacteria (Escherischia coli) Prokaryotes (no nucleus) Rapid growth Easily manipulated bacteria archarea eucaryota Used in neuroscience research predominantly to grow proteins or

6 Unicellular Organisms Bacteria (Escherischia coli) Prokaryotes (no nucleus) Rapid growth Easily manipulated bacteria archarea eucaryota Used in neuroscience research predominantly to grow proteins or plasmids expressing genes of interest Unicellular Organisms Baker s yeast (Saccharomyces cerevisiae) First eukaryote to have its genome fully sequenced (1996) Genetic simplicity ~6200 genes (humans have ~20,800) Breeding capacity h (doubling) Genetic manipulations eucaryota Direct cellular transfection Experimental tractability Petri dish cultures animalia plants funghi protist Unicellular Organisms Baker s yeast (Saccharomyces cerevisiae) Quantifiable phenotypes Cell death/dysfunction Protein mislocalisation/aggregate formation Environmental manipulations Chemical or physical (i.e. heat) stimuli can readily be applied to petri dish Other Factors No central nervous system Research use Basic cellular mechanisms of the cell cycle (DNA replication, recombination, cell division, metabolism, cellular proteins). Yeast two hybrid assay (protein-protein/dna interactions) 6

Unicellular Organisms Baker s yeast (Saccharomyces cerevisiae) Protein toxicity/aggregation/misfolding FUS expressed in yeast (Motor Neuron Disease) Ju et al, 2011, PLOS Biology Non-vertebrates Worms

7 Unicellular Organisms Baker s yeast (Saccharomyces cerevisiae) Protein toxicity/aggregation/misfolding FUS expressed in yeast (Motor Neuron Disease) Ju et al, 2011, PLOS Biology Non-vertebrates Worms (caenorhabditis elegans) First multicellular organism to have its genome fully sequenced (1998) Genetic simplicity ~20,500 genes Breeding capacity invertebrates Self-fertilising ~300 progeny vertebrates Development to adult ~2.5 days (egg-egg ~ 3 days) Life span ~ 2-3 weeks Genetic manipulations RNA interference direct application/injection/ ingestion of bacteria Transgenic injection (U.V irradiation integration) worms Non-vertebrates Worms (caenorhabditis elegans) Experimental tractability Grown on E. Coli petri dish (~10,000 worms/dish) Can be frozen and thawed Quantifiable phenotypes Development/Survival Fertility/offspring Motility Lifespan Environmental manipulations Chemical or physical (i.e. heat) stimuli can readily be applied to petri dish Other factors 302 neuron nervous system (humans have ~85,000,000,000) Transparent 7

Non-vertebrates Worms (caenorhabditis elegans) NTg FUS expressed in C.Elegans (Motor Neuron Disease) Murakami et al, 2011. Hum. Mol. Gen.

lifetime) Development to adult 7 to >50 days temp dependent, usually ~10 days at room temp Lifespan ~30 days (at 29 o C) Genetic Manipulation P-element (transposons) microinjection (random) Cre-LoxP

8 Non-vertebrates Worms (caenorhabditis elegans) NTg FUS expressed in C.Elegans (Motor Neuron Disease) Murakami et al, Hum. Mol. Gen. mutantfus Non-vertebrates Flies (drosophila melanogaster) Genome sequenced in 2000 Genetic simplicity ~15,000 genes Breeding Capacity invertebrates vertebrates ~up to 100 eggs/day/female (~2000 per lifetime) Development to adult 7 to >50 days temp dependent, usually ~10 days at room temp Lifespan ~30 days (at 29 o C) Genetic Manipulation P-element (transposons) microinjection (random) Cre-LoxP microinjection (targeted) insects Non-vertebrates Flies (drosophila melanogaster) Experimental tractability Grown in clean bottles with culture media Resilient, but best not to heat or chill to extremes Quantifiable phenotypes Growth/development/survival/appearance Fertility/mating Motor functions/activity Conditioning/spatial learning Environmental manipulations Relatively easy to modify physical conditions No guarantee modifications will affect entire organism Other factors ~75% genes have a human homolog ~100,000 neurons (including a brain) 8

9 Non-vertebrates Flies (drosophila melanogaster) APP+BACE expressed in drosophila (Alzheimer s Disease) APP+BACE Chakraborty et al., 2011, PLOS One Non-mammalian vertebrates Zebrafish (danio rerio) Genome sequenced in 2010 Genetic simplicity >26,000 teleost-specific genome duplication Breeding Capacity Hundreds of eggs/female/clutch/week Development to adult ~3-4 months Lifespan ~2-3 years mammals vertebrates reptiles and birds fish amphibians Genetic Manipulation Embryo injection of morpholino oligomers (gene silencing) Embryo injection of target gene Experimental tractability Kept in aquarium, robust, can be kept in shoals Adults may eat young Susceptible to infection need to be kept clean Non-mammalian vertebrates Zebrafish (danio rerio) Quantifiable phenotypes Growth/development/survival/appearance Fertility/mating Motor functions/activity Conditioning/cognitive learning Anxiety/stress Environmental manipulations Some physical manipulations (e.g. temp) possible No guarantee modifications will affect CNS Other factors ~70% genes have a human homolog (rises to ~80% of human disease genes) ~100,000 neurons (including a brain and spinal cord) Translucent larval form 9

10 Non-mammalian vertebrates Zebrafish (danio rerio) Axonal growth/branching Motor Tracking Atlastin (+/+) Atlastin (-/+) Fassier et al., 2010, Nat. Neurosci. Atlastin (+/+) Atlastin (-/-) Atlastin knockdown in zebrafish larvae (hereditary spastic paraplegia) Non-mammalian vertebrates Mouse (mus muscularis) Genome sequenced in 2002 Euarchontoglires Genetic simplicity Human Primate Euarchonta ~23,000 Breeding Capacity Rodents Glires ~6-8 mice/litter, ~5-10 litters/year (rarely exceed 5 in research) Development to adult ~6-8 weeks Lifespan ~2-3 years (in lab) Genetic Manipulation Embryo injection of plasmid (~2% success rate) Experimental tractability Temperature and humidity controlled environment Large colonies require significant space Adults may eat young Susceptible to infection need to be kept clean Non-mammalian vertebrates Mouse (mus muscularis) Quantifiable phenotypes Growth/development/survival/appearance Fertility/mating Motor functions/activity Conditioning/cognitive learning/problem solving Anxiety/stress Environmental manipulations Some physical manipulations (e.g. food restriction) possible Emotional stress protocols( e.g.restraint) established No guarantee modifications will affect CNS Other factors ~90% genes have a human homolog ~75,000,000 neurons (including a cerebral cortex only found in mammals) 10

Non-mammalian vertebrates Mouse (mus muscularis) Morris

Alzheimer s Disease Non-mammalian vertebrates Mouse (mus

All the model species have benefits and drawbacks, they

11 Non-mammalian vertebrates Mouse (mus muscularis) Morris Water Maze APP (visible) NTg APP APP expressed in mice Alzheimer s Disease Non-mammalian vertebrates Mouse (mus muscularis) NTg APP What question do you want to ask? How well will a model answer it? How easily can you extrapolate back to the human? All the model species have benefits and drawbacks, they must be used together, and in conjunction with in vitro studies, to help piece together the answers 11

Warm Up. What are some examples of living things? Describe the characteristics of living things

Warm Up. What are some examples of living things? Describe the characteristics of living things Warm Up What are some examples of living things? Describe the characteristics of living things Objectives Identify the levels of biological organization and explain their relationships Describe cell structure