Model Organisms and Human Health

Course Announcements and Learning Objectives

Final Course Schedule and Assessments: * Exam 4: Scheduled for Tuesday, May 12, at $11:30\,am$ . * Comprehensive Final Exam: Scheduled for Thursday, May 14, from $10:30\,am$ to $12:30\,pm$ . * Preparation Materials: Practice exams are available on Blackboard (Bb). Teaching Assistants (TAs) will host review sessions with times posted on Bb. * Instructor Availability: Dr. Green's office hours are Mondays from $11\,am$ to $12\,pm$ . Wednesday office hour times are to be determined (TBA). * Course Evaluations: Students are urged to complete evaluations. A incentive of $+2$ bonus points will be awarded to the entire class if $75\%$ of students finish evaluations by May 12.
Global Learning Objectives: * Articulate general motivations for utilizing model organisms in biomedical and human disease research. * Explain the specific biological characteristics that make certain organisms advantageous for research. * Describe the experimental procedures used to discover cell cycle regulators in budding yeast and identify their role in cancer. * Explain how genetic studies in nematodes identified apoptosis genes and the relationship between apoptosis and cancer progression.

Introduction to Model Organisms

The Concept of a "Model": A model organism is a non-human species used in research to understand biological processes, with the expectation that discoveries will provide insight into the workings of other organisms, particularly humans.
Categorization of Models via NIH (National Institutes of Health): * Mammalian Models: Mouse (Mus musculus), Rat. * Non-Mammalian Models: * Saccharomyces cerevisiae (budding yeast). * Saccharomyces pombe (fission yeast). * Neurospora (filamentous fungus). * Dictyostelium discoideum (social amoebae). * Caenorhabditis elegans (roundworm). * Daphnia (water flea). * Drosophila melanogaster (fruit fly). * Danio rerio (zebrafish). * Xenopus (frog). * Gallus (chicken). * Other Models: Arabidopsis (plant model).
The Utility of Model Organisms: * Feasibility: They offer rapid growth, abundant reproduction, and allow for extensive genetic and biochemical manipulation. * Ethics and Cost: They avoid the ethical complications and high costs associated with human experimentation. * Evolutionary Conservation: Fundamental biological processes are highly conserved across species. Approximately $50\%$ of genes associated with human diseases have counterparts in yeast, and $60\%$ have counterparts in flies and worms.
Biological Pathways Characterized in Models: * DNA replication and repair. * Transcription and gene expression regulation. * Translation. * Protein trafficking. * Cell division (mitosis and meiosis). * Signal transduction. * Cell death pathways (apoptosis).

Profiles of Specific Model Organisms

Budding Yeast (Saccharomyces cerevisiae): * Pros: Rapid generation time; easy long-term storage; simple genetic manipulation; extensive research toolsets; small genome; recapitulates fundamental cellular processes. * Cons: Unicellular (cannot model complex tissue interactions); small size; genomic conservation varies.
Roundworm (Caenorhabditis elegans): * Pros: Short life cycle ( $3\,days$ ); easy propagation/storage; genetic manipulation; transparent body; invariant cell lineage (every cell's fate from embryo to adult is mapped). * Cons: Lacks circulatory and respiratory systems; possesses only innate immunity; difficult to insert transgenes.
Fruit Fly (Drosophila melanogaster): * Pros: Short lifespan ( $10\,days$ ); complex systems including nervous, innate immune, circulatory, and epithelial; contains germline and somatic stem cells; easy genetic manipulation; used for clonal analysis to study early cancer events; suitable for behavior assays. * Cons: Cannot be frozen (storage is labor-intensive); short lifespan means they do not naturally develop traditional cancers.
Mouse (Mus musculus): * Pros: Lifespan of approximately $2\,years$ ; relatively small for storage; can be bred to genetic homogeneity; allows for gene knockouts and knockins; models the full range of disease progression including tumor initiation and metastasis. * Cons: High expense for feeding and housing; genetic techniques are lengthy/difficult; mouse studies sometimes fail to reflect human outcomes (rats are occasionally better models for certain human physiological responses).
Emerging Model - Tardigrades ("Water Bears"): * Value: Studied for survival mechanisms. * Resilience Factors: Can survive temperatures from $-328\,^{\circ}F$ up to $300\,^{\circ}F$ ; can withstand $6\times$ the pressure of the deepest ocean; resistant to high radiation and the vacuum of space.

Case Study #1: The Cell Cycle, Yeast, and Cancer

The Cell Cycle Phases: * G (Gap) Phases: Growth and preparation. * S (Synthesis): DNA replication ( $[H^3]\,thymidine$ is incorporated into DNA during this phase). * M (Mitosis): Physical cell division. * Regulation: The cycle is unidirectional, precisely timed, and highly regulated.
Molecular Regulators (CDKs and Cyclins): * Cyclin-Dependent Kinases (CDKs): Control progression. In S. pombe, the cdc2 mutant arrests division ( $cdc28$ in S. cerevisiae). * Cyclins: Control kinase activity; different cyclins partner with specific CDKs. * Maturation Promoting Factor (MPF): Discovered in Xenopus, this complex permits passage past checkpoints. * Conservation: Yeast has one major CDK, while higher organisms have many. * Human Equivalence: $CDC28$ in yeast is orthologous to $CDK1$ in mammals.
The Nobel Prize (2001): Awarded to Paul Nurse, Leland Hartwell, and Timothy Hunt for their discoveries of key regulators of the cell cycle (CDKs, specific genes, and cyclins) and checkpoints.
Experimental Methodology (Genetic Screen): 1. Treat haploid cells with a mutagen. 2. Spread cells on nutrient plates at $22\,^{\circ}C$ (permissive temperature). 3. Imprint colonies onto two plates: one at $22\,^{\circ}C$ and one at $36\,^{\circ}C$ (restrictive temperature). 4. Identify temperature-sensitive mutants that grow at $22\,^{\circ}C$ but arrest at $36\,^{\circ}C$ .
Cancer Implications: * Cancer is characterized by the loss of cell cycle control. Hallmarks include self-sufficiency in growth signals, insensitivity to anti-growth signals, and limitless replicative potential. * Drug Discovery: Models are used to screen inhibitors for targets like Polo kinases, Aurora kinases ( $A$ and $B$ ), and Eg-5. Inhibitors like Taxol or Vincas target these pathways to arrest cancer cell growth.

Case Study #2: Worms, Apoptosis, and Cancer

Apoptosis Defined: Programmed cell death involving a signal transduction cascade. It is distinct from necrosis (traumatic death). * Characteristics: Nucleus condensation (pyknosis), cell shrinkage, blebbing, and fragmentation.
C. elegans as a Model for Apoptosis: * In the developing embryo, there are $1090$ cells. In the adult, there are only $959$ cells. * Exactly $131$ cells are programmed to die during development.
The Nobel Prize (2002): Awarded to Sydney Brenner, Bob Horvitz, and John Sulston for discoveries concerning genetic regulation of organ development and programmed cell death.
Genetic Screen for Apoptosis: * Worms are mutagenized and allowed to self-fertilize (as hermaphrodites) to create homozygous diploids. * Researchers screen for "loss of apoptosis" (too many cells) or "too much apoptosis" (loss of essential cells).
Pathway Conservation: * C. elegans Genes: $EGL-1$ $\rightarrow$ $CED-9$ $\rightarrow$ $CED-4$ $\rightarrow$ $CED-3$ . * Mammalian Orthologs: $BH3-only$ proteins $\rightarrow$ $BCL-2$ $\rightarrow$ $APAF-1$ $\rightarrow$ $Caspases$ . * $CED-9$ / $BCL-2$ act as inhibitors of the death process, while others promote it.
Cancer Connection: Cancer cells frequently evade apoptosis. Inhibiting apoptosis allows for the initiation and proliferation of tumors despite oncogene activation.

Case Study #3: Flies and Circadian Rhythms

The Nobel Prize (2017): Awarded to Jeffrey Hall, Michael Rosbash, and Michael Young.
Mechanism: Fruit flies were instrumental in identifying the transcription-translation feedback loop that governs the circadian clock.
Relevance: This system controls physiological rhythms that respond to environmental cues, impacting everything from sleep to metabolic health.

Using Models for Drug and Gene Discovery

Gene Discovery: Overlapping gene sets between worms and human phenotypes (e.g., breast cancer) help identify novel candidate genes.
Drug Discovery Examples: * Thiabendazole: Originally identified in yeast as a drug affecting cell-wall maintenance (antifungal), it is now known to prevent angiogenesis (vascular growth) in humans, making it a candidate for cancer therapy. * Screens: Potential inhibitors are added to yeast expressing a human target protein; if the inhibitor restores normal growth or induces the desired phenotype (like apoptosis), it is identified as a candidate lead.

Questions & Discussion

Q: Which model would you choose to study a gene expressed in neurons potentially involved in vesicle targeting in a neurodegenerative disorder? * A: While yeast (vesicle targeting) or worms/flies (neurons) are possible, the best model for neurodegenerative systems often spans between flies, worms, and mice, but the specific question context often favors flies or worms for rapid genetic screening and transparent observation of neurons.
Q: If you identify a human cell cycle protein that, when expressed in yeast, causes faster division, which scenario suggests you found an inhibitor of the human protein? * A: Identify a drug that causes yeast cells expressing the protein to grow normally (Scenario C). This indicates the drug is counteracting the accelerated growth caused by the human protein.
Q: If you had 100\ to support research, where should it go? * Discussion: Choices include a direct cure for cancer, drug screens in models, basic research in models, patient samples, or basic human cell research. The lecture emphasizes that basic research in model systems often provides the foundational knowledge necessary for all other options.