Model Systems: Frontiers 1

Week 1

What is a model system?

A non-human organism used to study biological processes. It is smaller, simpler, easier to work with, more manipulable, and captures the main features of the thing you want to study.

Why do we need model systems?

To understand mechanisms of health and disease in humans. They circumvent ethical and technical issues, allow experimental manipulation, and provide in vivo context that cell lines alone cannot.

What are the advantages of model systems?

In vivo phenotyping and gene targeting; fewer ethical/technical issues; allow experimental approaches; probe function better than cell lines; wealth of literature (>100 years); well-developed genome resources.

What factors do you consider when choosing a model system?

Phylogenetic distance, ease of culture/cost, size, fecundity, speed of development, genetic resources, ease of manipulation.

What are the widely used model systems?

Yeast, Streptomyces, C. elegans, Drosophila, Xenopus, zebrafish, chicken, mouse. Man is not a model system.

What is a GWAS?

Genome-Wide Association Study. Profiles the genomes of individuals (controls vs cases) and tests for associations between alleles and a disease.

What is a Manhattan plot?

A plot showing GWAS results. Chromosomes along the x-axis, statistical significance on the y-axis. Spikes indicate genomic regions associated with the trait.

What is the dream result of a GWAS?

A single strong peak where one position in the genome is strongly associated with the condition (e.g., everyone with an A has it, everyone with a C does not).

What are the limitations of GWAS?

Most alleles have small effects; don't explain much variability individually; poor ultimate resolution; mechanisms hard to identify; low power to determine if candidate genes alter risk; uncontrolled variation; gene x environment interactions; difficult to detect trans-acting regulation.

What is a SNP?

Single Nucleotide Polymorphism. A single base pair change in DNA.

What conditions have been associated with genes identified by GWAS?

Age-related macular degeneration, diabetes, rheumatoid arthritis, Crohn's disease, hypertension, cardiovascular disease, cancer, autoimmune disorders, asthma, COPD, gout, stroke, IBD, psychiatric disorders.

Why is the fruit fly a useful model system?

Cheap, easy to keep, short generation time (10 days), high fecundity (80 eggs/day), easily distinguishable sexes, easy genetic crosses, can be sent through the post.

What fundamental genetic principles were worked out using the fruit fly?

Heredity, sex-linked inheritance, epistasis, multiple alleles, gene mapping, crossing over.

Who popularized the use of the fruit fly in genetics?

Thomas Hunt Morgan.

What was the first visible phenotype mutation discovered in Drosophila?

White eye colour, discovered by Thomas Hunt Morgan. It was a spontaneous mutation that bred true.

What is the white gene?

The first gene with a visible phenotype discovered in Drosophila. Located on the X chromosome, controls eye colour (white vs red).

How did Sturtevant use fruit flies to map chromosomes?

By crossing flies with different visible markers and counting recombinant offspring. Recombination frequency relates to the distance between genes.

What are polytene chromosomes?

Giant chromosomes in larval salivary glands. Their banding patterns are visible under a light microscope and used to map chromosome regions and detect inversions.

What genetic resources are available for Drosophila?

Genetic transformation since 1987; genome sequenced in 2000; classical mutants (>100 years); knock-down libraries for virtually all genes; easy CRISPR; precise stage and tissue manipulation.

What is CRISPR/Cas9 used for?

Gene editing. Allows you to edit, replace, or mutate virtually any gene. Requires a gRNA and a PAM sequence (NGG).

What are the limitations of the fruit fly model?

Invertebrate, less closely related to humans; adults largely post-mitotic; limited cell division outside the germline; limits utility for regenerative/cancer studies.

What does post-mitotic mean in the adult fruit fly?

Adult cells largely do not divide or regenerate. Stem cells exist only in the gut and Malpighian tubules outside the germline.

How is the fruit fly used to study eye development?

Both vertebrates and insects require the Pax6 gene (called ey in flies). Mutations cause eye defects — aniridia in humans, eye absent in flies — showing conserved signalling pathways.

What is the eyeless gene?

The Drosophila homolog of human Pax6. Mutations result in absence of eyes.

What is Pax6?

A master regulator gene for eye development, conserved across species. Mutations cause eye defects like aniridia in humans.

What is aniridia?

A human eye condition caused by PAX6 mutations. Characterized by absent iris, opaque cornea, degenerate retina, opaque lens, increased pressure in the eyeball.

How is the fruit fly used to study aging?

Flies are used to study conserved nutrient-sensing pathways (Insulin/IGF signalling and TOR). Manipulating diet or these genes extends lifespan and reduces age-related pathology.

What are the two main nutrient-sensing pathways that influence aging?

Insulin/IGF-like signalling (IIS) and Target of Rapamycin (TOR).

What is the effect of intermittent fasting on Drosophila lifespan?

The 2:5 diet (2 days fast, 5 days feed) extends lifespan and reduces age-related gut pathology.

What are insulin-like peptides (ILPs)?

Peptides released from tissues when the fly has eaten sugar. Flies lacking these are long-lived.

What happens if you manipulate genes in the insulin signalling pathway?

Manipulating more or less any gene in this pathway can extend lifespan. The pathway is highly conserved across taxa.

What is the relationship between the insulin signalling pathway and aging?

Flies lacking insulin-like peptides are long-lived. The pathway is conserved from yeast to human

What is an 'inversion'?

A chromosomal rearrangement where a segment of a chromosome is reversed end to end. Detected by changes in polytene chromosome banding patterns.

What is 'crossing over'?

The exchange of genetic material between homologous chromosomes during meiosis. Discovered using Drosophila.

What is 'sex-linked inheritance'?

Inheritance of genes located on the sex chromosomes. Discovered using the white-eye mutation in Drosophila.

What is 'epistasis'?

When one gene masks or modifies the expression of another gene. One of the genetic principles worked out using Drosophila.

What is 'multiple alleles'?

The existence of more than two alleles for a gene in a population. One of the genetic principles worked out using Drosophila.

What is 'gene mapping'?

Determining the location of genes on a chromosome. Worked out using Drosophila by Sturtevant.

What percentage of disease-associated genes are shared between humans and Drosophila?

Approximately 70%.

What is the 'fruit fly' species name?

Drosophila melanogaster.

What is the 'nematode worm' species name?

Caenorhabditis elegans (C. elegans).

What is the 'zebrafish' species name?

Danio rerio.

What is the 'Xenopus' species name?

Xenopus laevis (or other Xenopus species).

What is the 'yeast' species name?

Saccharomyces cerevisiae (commonly).

What is the 'Streptomyces' species?

A genus of bacteria, including Streptomyces coelicolor and others.

What is the 'mouse' species name?

Mus musculus.

What is the 'chicken' species name?

Gallus gallus domesticus.

What is the 'human' species name?

Homo sapiens.

What is the significance of the 'Man is not a model system' statement?

Humans are the focal organism that model systems are trying to understand, not a model system themselves.

What is the 'Streptomyces' model system used for?

Streptomyces is a microbial model system used for producing antibiotics.

What is the 'Yeast' model system used for?

Yeast is a widely used microbial model system for studying fundamental cellular processes, including aging.

What is the 'C. elegans' model system?

A nematode worm, widely used as a model system for studying development, genetics, and aging.

What is the 'Xenopus' model system?

A frog, widely used as a model system for studying development (has large eggs).

What is the 'Zebrafish' model system?

A small fish, widely used as a model system for studying development, genetics, and disease (has transparent embryos).

What is the 'Chicken' model system?

A bird, used as a model system for studying development (has large, accessible embryos).

What is the 'Mouse' model system?

A mammal, closely related to humans, widely used as a model system for studying disease, genetics, and physiology.

What is the 'Drosophila' model system?

The fruit fly, a widely used model system for studying genetics, development, and aging.

What is the 'Phylogenetic distance' factor in choosing a model system?

How closely related the model system is to humans. Mouse is closer than yeast, streptomyces, or fruit flies.

What is the 'Ease of culture / cost' factor in choosing a model system?

How easy and expensive it is to maintain the organism. Mice require in vivo facilities and Home Office regulations; fruit flies do not.

What is the 'Size' factor in choosing a model system?

How big the organism is. Xenopus has large eggs, making it easier to study gastrulation than fruit flies with tiny eggs.

What is the 'Fecundity' factor in choosing a model system?

How many offspring the organism produces. Fruit flies can lay 80 eggs per day; some organisms lay only 1 egg per year.

What is the 'Speed of development' factor in choosing a model system?

How quickly the organism develops. Fruit flies go from egg to adult in 10 days.

What is the 'Genetic resources' factor in choosing a model system?

The availability of genome sequences, mutant lines, and other genetic tools for the organism.

What is the 'Ease of manipulation' factor in choosing a model system?

How easy it is to perform genetic experiments, such as CRISPR, knock-downs, and transgenic techniques.

What is the 'GWAS' abbreviation for?

Genome-Wide Association Study.

What is the 'SNP' abbreviation for?

Single Nucleotide Polymorphism.

What is the 'IIS' abbreviation for?

Insulin/IGF-like Signaling.

What is the 'TOR' abbreviation for?

Target of Rapamycin.

What is the 'ILP' abbreviation for?

Insulin-like Peptide.

What is the 'Detect inversions' slide about?

The use of polytene chromosome banding patterns to detect chromosomal inversions (where parts of chromosomes have been moved around).

What is the 'Knock down gene libraries' slide about?

Examples of Drosophila lines where gene expression has been reduced (knocked down), showing visible phenotypes like altered eye or bristle patterns.

What is the 'Eyeless' phenotype in the knock down examples?

A fly with reduced or absent eyes, caused by knocking down the 'eyeless' gene.

What is the 'Flamingo' phenotype in the knock down examples?

A fly with altered bristle pattern, caused by knocking down the 'Flamingo' gene.

What is the Drosopholia as Utility as a model system' ?

cheap, easy to keep, short generation time, high fecundity, easily distinguishable sexes, easy genetic crosses. AND can be sent easily between labs in the post.

What is the 'trans-acting regulation' problem in GWAS?

It is difficult for GWAS to detect when a gene is regulated by something on a different chromosome (trans-acting), as opposed to something on the same chromosome (cis-acting).

What is the 'cis-acting regulation' in genetics?

Regulation of a gene by something on the same chromosome. GWAS can more easily pick this up.

What is the 'trans-acting regulation' in genetics?

Regulation of a gene by something on a different chromosome. GWAS struggles to detect this.

Why do GWAS need enormous sample sizes?

Because most alleles identified have small effects, and there is a lot of uncontrolled variation (gene x environment interactions) that needs to be overcome statistically.

What is the 'case-control' design in GWAS?

A study design that compares a group of people with a condition (cases) to a group without the condition (controls) to identify genetic associations.

What is the 'trio' design in GWAS?

A study design that uses family groups (e.g., two parents and an affected child) to identify genetic associatio

What is the 'knock down' technique in Drosophila?

A method to reduce the level of expression of virtually any gene. Examples include lines affecting the eye and bristle pattern (e.g., Eyeless, Flamingo).

What is the 'Flamingo' gene in Drosophila?

A gene that, when knocked down, affects the bristle pattern on the fly.

What is the significance of the 'bristle pattern' in Drosophila research?

It is a visible phenotype used to study gene function and development. Knock-down lines can alter the number, size, and distribution of bristles.

What are the advantages of using cell lines versus model organisms?

Cell lines are simpler and easier to maintain, but they don't behave in a way that has all the tissue and cellular context. Model systems provide in vivo context.

How is the fruit fly used to study aging?

Flies are used to study conserved nutrient-sensing pathways (Insulin/IGF signaling and TOR). Manipulating diet (intermittent fasting) or these genes can extend lifespan and reduce age-related pathology.

What are the limitations of the fruit fly model?

Invertebrate (not as closely related to humans as other model systems); adults are largely post-mitotic; limited cell division outside the germline; can limit utility for regenerative or cancer studies. However, stem cells are known in the gut and Malpighian tubules.

What is a Genome-Wide Association Study (GWAS)?

A study that profiles the genomes of individuals (e.g., controls versus cases) and tests for associations between particular alleles and a disease or trait.

What is a 'Manhattan plot' in the context of GWAS?

A type of scatter plot used to display GWAS results. The x-axis shows chromosomes, and the y-axis shows the statistical significance (-log10 p-value) of associations. Spikes indicate genomic regions associated with the trait.

What is the 'dream result' of a GWAS?

A single strong peak where one particular place in the genome is strongly associated with the condition (e.g., everybody with an 'A' at that position has the condition and everybody with a 'C' does not).

What are the main limitations of GWAS?

Most alleles identified have small effects; don't explain much of the variability in disease individually; poor ultimate resolution; pathways/mechanisms hard to identify; often low power to determine if candidate genes alter disease risk; low statistical power ('uncontrolled'); gene x environment interactions are a problem (need huge samples); difficult to detect trans-acting regulation.

What is a SNP?

Single Nucleotide Polymorphism. A single base pair change in the DNA sequence.

What were some early GWAS successes?

Age-related macular degeneration (2005); diabetes, rheumatoid arthritis, Crohn's disease, hypertension (2007); cardiovascular disease, cancer, autoimmune disorders, asthma, COPD, gout, stroke, IBD, psychiatric disorders (later studies