I_Animal Experimentation Techniques and Questions

Slide 3: Why Animal Experiments?

Key Points:

• Justification for using animals in research based on three reasons.

• 1) Knowledge gain in biology and medicine:

  • Goal: Expand understanding of physiology and disease.

  • Example: Investigating biological functions at organism level.

Explanation of Visuals:

• Bullet points summarize foundational rationale for animal experimentation (highlighted with ethical context).

Glossary:

• Physiology: The study of how living organisms function.

• Basic research: Scientific study that aims to improve understanding without immediate practical application.

Key Takeaway:
Animal experiments help answer fundamental biological questions not possible with in vitro or computer models alone.

Slide 4: Basic Research – Zoology

Key Points:

• Example from zoology: How prey animals detect predators.

• Investigations into sensory-motor response using animal models (e.g., tadpoles).

• Visual data from predator avoidance experiments.

Explanation of Visuals:

• Images show tadpoles reacting to predator presence.

• Graph demonstrates measurable response behavior.

Glossary:

• Predator-prey interaction: Relationship where one animal hunts and the other avoids.

• Stimulus-response: A reaction triggered by a specific external event.

Key Takeaway:
Animal models reveal critical survival strategies, like escape behavior, that are shaped by evolution and sensory processing.

Slide 5: Why Animal Experiments? (Part 2)

Key Points:

• 2) Investigation of specific questions in life sciences:

  • Understanding functions of organs, systems, and disease mechanisms.

• Research examples include immune response, metabolism, and therapy development.

Explanation of Visuals:

• Bullet points emphasizing need for whole-animal context to study complex biological interactions.

Glossary:

• Organismal level: Studying the entire living being rather than isolated parts (e.g., organs or cells).

Key Takeaway:
To answer specific biomedical questions, animal models provide the necessary complexity that cell cultures lack.

Slide 6: Animal Experiments for the Animal

Key Points:

• Animal experiments also benefit veterinary medicine.

• Example: Development of rabbit anesthesia methods for humane care.

• Applications in wildlife conservation and livestock treatment.

Explanation of Visuals:

• Photos of rabbits and lab animals used in medical research.

• Data plots showing outcomes of anesthetic dosage optimization.

Glossary:

• Veterinary medicine: Medical care and treatment for animals.

• Anesthesia: A method to reduce pain during surgery or procedures.

Key Takeaway:
Research with animals also leads to improved treatment methods for other animals, not just humans.

Slide 7: Why Animal Experiments? (Part 3)

Key Points:

• 3) Preclinical testing of treatments and medications:

  • Vital step before human clinical trials.

• Ensures safety and efficacy of therapies.

• Regulatory requirement before approval of new drugs.

Explanation of Visuals:

• Emphasis on legal and scientific necessity of animal models in drug development.

Glossary:

• Preclinical testing: Research phase before trials on humans.

• Efficacy: The ability of a treatment to produce the desired effect.

Key Takeaway:
Animal experiments are a critical step in evaluating new medical treatments for both safety and therapeutic value.

Slide 8: The Mouse for the Cause

Key Points:

• Mice are commonly used due to:

  • Genetic similarity to humans.

  • Ability to breed quickly and in large numbers.

• Example shown: Immune system study using mouse models.

Explanation of Visuals:

• Graph data supports consistent biological response in mouse models.

• Text links mouse use to research efficiency and relevance.

Glossary:

• Model organism: A species extensively studied to understand particular biological phenomena.

Key Takeaway:
Mice are a preferred model organism due to their genetic tractability, short generation time, and physiological relevance.

Slide 9: Why Animal Experiments? (continued)

Key Points:

• Continued justification under point 3: Preclinical testing of therapies.

• b) Translation of findings to humans:

  • Studies on animals can predict how treatments may perform in people.

  • Helps bridge basic science to clinical application.

Explanation of Visuals:

• Continuation of previous points in a text-based format.

Glossary:

• Translational research: Applying laboratory findings to clinical settings.

• Preclinical phase: Research in models before testing in humans.

Key Takeaway:
Animal models act as a necessary step to ensure the safe and effective translation of medical discoveries to human treatments.

Slide 10: Hypothermic Oxygenated Perfusion – Organ Transplant Quality

Key Points:

• Comparison of organ perfusion techniques in different species:

  • Rat, pig, and human.

• Example of preclinical research: Testing organ preservation methods.

• Aim: Improve quality and outcomes in organ transplantation.

Explanation of Visuals:

• Images of experimental perfusion setups in rat, pig, and clinical human settings.

Glossary:

• Perfusion: The process of delivering blood or oxygenated fluid through organs.

• Hypothermic perfusion: Cooling organs while supplying oxygen during storage.

Key Takeaway:
Animal models are essential in refining organ preservation protocols before applying them in human transplant surgery.

Slide 11: Animal Models (Title Slide)

Key Points:

• Introduction to the next topic block: Animal models.

• Sets the stage for discussing:

  • Definitions

  • Model choice

  • Advantages and limitations

Explanation of Visuals:

• Slide title only.

Glossary:

• (Covered on later slides)

Key Takeaway:
Understanding animal models is fundamental to designing ethical and effective experiments that yield meaningful biological insights.

Slide 12: Examples of Animal Models

Key Points:

• Broad range of animal models shown, including:

  • Rodents, pigs, monkeys, birds, frogs, and fish.

• Visual demonstration of diversity depending on research goal (e.g., genetics, development, behavior).

Explanation of Visuals:

• Collage of different animal species used in biomedical and basic research.

Glossary:

• Model organism: A species studied to gain insight into biology that is often applicable to humans.

Key Takeaway:
Different animals are used as models depending on the biological system or disease being studied.

Slide 13: Animal Models – Overview of Topics

Key Points:

• Lists the subtopics that will be addressed:

  • Definition

  • Classification of models

  • Criteria and practical aspects in model choice

  • Examples and translational value

  • Ethical considerations

  • Mouse-human differences

Explanation of Visuals:

• Text outline indicating structure of the upcoming lecture section.

Glossary:

• Translational value: Relevance of research findings in animals to human medicine.

Key Takeaway:
A structured framework will guide discussion of how and why animal models are used in research, including ethical and biological factors.

Slide 14: Animal Model – Definition

Key Points:

• A laboratory animal model is a non-human animal used to:

  • Study biological processes.

  • Understand disease mechanisms.

  • Predict responses in humans.

• The model should mirror the target species (e.g., humans) in the relevant process.

Explanation of Visuals:

• Definition text explaining the rationale behind animal modeling.

Glossary:

• Target species: The species for which the findings are ultimately intended (often humans).

Key Takeaway:
An animal model is used to simulate aspects of human biology, providing insights that are not achievable by other means.

Slide 15: Mammals Used for Disease Models

Key Points:

• Lists common mammalian species used in disease modeling:

  • Mouse: Most frequently used; genetically modifiable, small size, low cost.

  • Rat: Larger, suitable for surgical models; used in toxicology, behavior, neurobiology.

  • Pig: High physiological similarity to humans; ideal for cardiovascular and skin research.

  • Dog: Used in pharmacokinetics, cardiovascular, and muscular diseases.

  • Primate: Closest human analog; used in neuroscience, immunology, and vaccine testing (limited by ethical issues).

Explanation of Visuals:

• Purple vertical bar grouping species by relevance or frequency of use.

Glossary:

• Pharmacokinetics: Study of how drugs move through the body.

• Toxicology: Study of the harmful effects of substances.

Key Takeaway:
Different mammals are chosen based on their biological similarity to humans and the research question being addressed.

Slide 16: Classification of Animal Models

Key Points:

• Two major categories:

  • Explanatory models: Help understand biological or disease mechanisms.

  • Predictive models: Forecast treatment outcomes or disease behavior.

• Model types under each include:

  • Induced

  • Spontaneous

  • Genetically modified

  • Negative

  • Disease-specific

Explanation of Visuals:

• Clear split between model types and their function in research.

Glossary:

• Predictive model: Indicates how a treatment or condition may progress or respond.

• Explanatory model: Clarifies the mechanisms underlying a disease.

Key Takeaway:
Animal models are selected based on whether the goal is to explain a disease process or predict a treatment’s effect.

Slide 17: Animal Models – Induced Model

Key Points:

• A disease is experimentally induced in an otherwise healthy animal.

• Common techniques:

  • Surgery (e.g., heart infarct)

  • Chemicals (e.g., toxins)

• Example: Stroke model induced by artery occlusion.

Explanation of Visuals:

• Diagram showing a pink rodent, surgical procedure, and resulting stroke outcome on a graph.

Glossary:

• Induced model: Disease created deliberately in the animal for study.

• Stroke model: Simulates blockage in brain blood vessels.

Key Takeaway:
Induced models allow tight control of disease timing and progression, enabling reproducible studies.

Slide 18: Animal Models – Spontaneous Model

Key Points:

• Disease arises naturally due to a genetic mutation.

• These models reflect real-world pathology better.

• Example: Zucker Diabetic Fatty (ZDF) rat for obesity and diabetes.

Explanation of Visuals:

• Photos of animals with inherited metabolic disorders.

Glossary:

• Spontaneous mutation: A natural genetic change that results in disease.

• ZDF rat: A well-known model for type 2 diabetes.

Key Takeaway:
Spontaneous models offer high clinical relevance by mimicking human disease development without external induction.

Slide 19: Animal Models – Genetically Modified Models

Key Points:

• Created by manipulating DNA to:

  • Knock out (disable) or

  • Knock in (insert/change) specific genes.

• Enables targeted studies of gene function.

• Can be designed to model human mutations.

Explanation of Visuals:

• Genetic diagrams showing homozygous and heterozygous knockout and knock-in offspring.

Glossary:

• Knockout model: A gene is turned off completely.

• Knock-in model: A gene is inserted or modified at a specific site.

Key Takeaway:
Genetically modified animals are essential tools for linking genes to biological functions and disease mechanisms.

Slide 20: Animal Models – Negative Model

Key Points:

• These animals do not develop a disease that normally affects others.

• Used to study resistance and protective mechanisms.

• Example: Some rodent strains resist atherosclerosis unless genetically altered.

Explanation of Visuals:

• Bar graph comparing disease rates between susceptible and resistant species.

Glossary:

• Negative model: Does not show expected disease symptoms despite exposure to triggers.

• Atherosclerosis: Hardening of arteries due to cholesterol buildup.

Key Takeaway:
Negative models help uncover why some species are naturally protected, offering clues for human disease prevention.

Slide 21: Animal Models – Disease Models

Key Points:

• Disease models replicate human diseases in animals.

• Two types:

  • Species-specific disease model: Disease occurs only in one species (e.g., BSE in cows, FIV in cats).

  • Non-species-specific disease model: Disease also occurs in humans and animals (e.g., epilepsy, diabetes).

Explanation of Visuals:

• Photos and illustrations of species linked to specific or shared diseases (e.g., cow for BSE, cat for FIV, child for epilepsy).

Glossary:

• Species-specific model: A disease naturally occurs only in one species.

• Non-species-specific model: Disease naturally occurs in both animals and humans.

Key Takeaway:
Disease models are essential for studying conditions either unique to one species or shared across species, enabling therapeutic insights.

Slide 22: Animal Models – Orphan Animal Model

Key Points:

• Orphan models arise unexpectedly—animals show disease-like traits without deliberate design.

• These can mimic rare or human diseases when studied closely.

• Example diseases linked to orphan models:

  • BSE (Bovine Spongiform Encephalopathy)

  • Papillomavirus-related models

Explanation of Visuals:

• Graphic of protein (e.g., prion-related to BSE).

• Animal and protein illustration highlighting incidental model discovery.

Glossary:

• Orphan model: An accidentally discovered animal with human disease-like characteristics.

Key Takeaway:
Unexpected disease traits in animals can uncover valuable research models and reveal new disease mechanisms.

Slide 23: Choice of Model

Key Points:

• Model selection depends on:

  • The research question

  • Target organ, cell type, or disease

• Factors influencing model choice:

  • Species, cost, ethical considerations, genetic similarity, translational value

• Decision often balances:

  • Scientific benefits

  • Practical constraints

  • Animal welfare

Explanation of Visuals:

• Flowchart showing steps and factors involved in model selection (e.g., species, handling, availability).

Glossary:

• Translational value: How well an animal model reflects human disease processes.

Key Takeaway:
Choosing the right animal model requires careful evaluation of biological relevance, ethics, and practicality.

Slide 24: Example – Oral Polio Vaccine

Key Points:

• Polio vaccine testing was done in primates, leading to human protection.

• Preclinical success led to effective vaccination strategies.

• Transgenic mouse models are now used instead of primates.

• Example of model replacement in line with ethical 3R principles.

Explanation of Visuals:

• Virus illustration.

• Timeline-style explanation of model transition from primates to mice.

Glossary:

• Transgenic: Organism with genes inserted from another species.

• 3Rs (Replace, Reduce, Refine): Guiding principles for ethical animal research.

Key Takeaway:
Successful human vaccines like the polio vaccine highlight the importance—and evolution—of animal models in research.

Slide 25: Example – Alzheimer’s Model

Key Points:

• Alzheimer’s modeled using transgenic mice that develop:

  • Amyloid plaques

  • Memory deficits

• Tables comparing mouse models based on mutations, onset, and symptoms.

• Used to test therapies, understand disease progression.

Explanation of Visuals:

• Data table summarizing transgenic mouse models.

• Small rodent image to represent the Alzheimer model.

Glossary:

• Amyloid plaque: Protein buildup in the brain, characteristic of Alzheimer’s.

• Transgenic mouse: Mouse genetically altered to express human disease genes.

Key Takeaway:
Genetically modified mouse models allow detailed study of neurodegenerative disorders like Alzheimer’s.

Slide 26: Example – Sheep/Pig for Improved Skin Transplants

Key Points:

• Large animal models like sheep and pigs are used in skin transplantation research.

• Used in pediatric burn care for:

  • Larger surface area for grafts

  • More human-like skin structure

• Shown to improve outcomes in skin healing and graft quality.

Explanation of Visuals:

• Clinical images of transplanted skin and surgical application.

• Comparisons of graft surface and integration.

Glossary:

• Skin graft: Transplantation of skin to cover damaged or burned areas.

• Pediatric: Relating to children.

Key Takeaway:
Large animal models provide critical insights into surgical techniques and skin regeneration for burn patients.

Slide 27: Example – Experimental Autoimmune Encephalomyelitis (EAE)

Key Points:

• EAE is an animal model for Multiple Sclerosis (MS).

• Induced by immunization with CNS (central nervous system) antigens.

• Shows relapsing-remitting disease pattern, similar to human MS.

• Helps understand:

  • Autoimmune mechanisms

  • Inflammatory cell migration in the CNS

Explanation of Visuals:

• Diagram of a mouse with CNS immunization.

• Graph showing disease severity over time, illustrating relapsing-remitting progression.

Glossary:

• EAE (Experimental Autoimmune Encephalomyelitis): Mouse model for MS.

• Relapsing-remitting: Pattern of recurring symptoms alternating with periods of improvement.

Key Takeaway:
EAE is a widely used and controllable model for studying multiple sclerosis and testing immune-modulating therapies.

Slide 28: Example – Humanized Mice

Key Points:

• Humanized mice are immunodeficient mice transplanted with human immune cells.

• Used for research in:

  • Infectious diseases

  • Cancer

  • Transplantation

• Mimic human-specific immune responses (e.g., HIV, hepatitis studies).

Explanation of Visuals:

• Illustration of immune cell transfer into mice.

• Immunofluorescence image showing human cell markers in mouse tissue.

Glossary:

• Humanized mouse: Mouse with functioning human-like immune system.

• Immunodeficient: Lacking parts of the immune system.

Key Takeaway:
Humanized mice bridge the gap between traditional animal models and human studies, especially in immune-related research.

Slide 29: Example – Study of HIV-2 in Monkeys

Key Points:

• Non-human primates are used for HIV research due to immune system similarity to humans.

• HIV-2 studies in monkeys show:

  • Disease progression

  • Immune cell depletion (CD4+ T cells)

• Useful in vaccine and antiviral development.

Explanation of Visuals:

• Photos of monkeys used in studies.

• Text highlights use in studying immune response and disease progression.

Glossary:

• HIV-2: A type of human immunodeficiency virus, less common than HIV-1.

• CD4+ T cells: Immune cells targeted and destroyed by HIV.

Key Takeaway:
Primate models are crucial for studying HIV pathogenesis and testing interventions due to their immune similarity to humans.

Slide 30: Extrapolation to the Target Species (Humans)

Key Points:

• Goal: Transfer knowledge from animals to humans.

• Challenges include:

  • Species-specific differences

  • Variability in drug response and toxicity

  • Metabolic, immune, and genetic differences

• Decision trees and systematic assessments help minimize translational gaps.

Explanation of Visuals:

• Infographic showing various species and their relevance to different biomedical research areas.

Glossary:

• Extrapolation: Applying animal findings to human biology or medicine.

• Translational research: Bridging experimental and clinical medicine.

Key Takeaway:
Extrapolating data from animal models to humans requires understanding interspecies differences and careful interpretation.

Slide 31: Mouse–Human Differences

Key Points:

• Important differences include:

  • Size, metabolism, and organ function

  • Immune system differences

  • Variability in gene expression

• Mouse models must be carefully interpreted, especially for:

  • Toxicology

  • Pharmacokinetics

  • Immune disease models

Explanation of Visuals:

• Bullet points listing physiological and genetic differences.

Glossary:

• Pharmacokinetics: How a drug is absorbed, distributed, metabolized, and excreted.

Key Takeaway:
Mouse models offer many advantages but must be used cautiously due to biological differences from humans.

Slide 32: Mouse–Human Differences (Immunology Focus)

Key Points:

• Differences in immune function:

  • Mice lack certain T-cell subtypes.

  • Differences in cytokine responses and immune memory.

• Example: Mice do not express IL-8, affecting inflammation modeling.

• Important for choosing appropriate disease models (e.g., sepsis, allergy).

• Mice can convert uric acid (Harnsäure) by oxidation with urate oxydase (not possible in humans)

Explanation of Visuals:

• Outline of immune differences.

• Mouse and human figure comparison.

Glossary:

• IL-8 (Interleukin-8): A cytokine involved in inflammation and immune cell recruitment.

• Cytokines: Small proteins that regulate immune responses.

Key Takeaway:
Understanding mouse–human immunological differences is critical when studying immune diseases or testing immunotherapies.

Slide 33: Common Animals in Research

Key Points:

• This is a title slide introducing the upcoming section.

• The next few slides will describe frequently used animal species in biomedical research.

Key Takeaway:
Understanding common model organisms helps in selecting appropriate species for specific scientific purposes.

Slide 34: Species Used for Animal Experimentation in CH (Switzerland)

Key Points:

• Statistics show mice are by far the most used species.

• Top species used (2022 data):

  • Mice: 320,944

  • Rats: 10,623

  • Zebrafish: 2,857

  • Others: rabbits, guinea pigs, dogs, cats, primates (in much smaller numbers)

• Non-mammalian species like fish and birds are also included.

Explanation of Visuals:

• Table listing number of animals per species used in Switzerland in 2022.

Glossary:

• Zebrafish (Danio rerio): A small tropical fish commonly used in developmental biology and genetics.

Key Takeaway:
Mice dominate research use in Switzerland, with other species used in specialized fields such as toxicology or surgery.

Slide 35: The Zebrafish

Key Points:

• This is a title slide introducing the zebrafish (Danio rerio) as a model organism.

Key Takeaway:
Zebrafish are an important vertebrate model due to their transparency, rapid development, and suitability for genetic studies.

Slide 36: Danio rerio (Zebrafish) – Basic Info

Key Points:

• Zebrafish are tropical freshwater fish and lay external eggs.

• Key advantages:

  • Transparent embryos

  • Rapid development (organogenesis complete within 5 days)

  • Cost-effective

  • Robust and easy to hold

    • 5 fish per liter

• Used for:

  • Developmental biology

  • Genetics

  • Drug screening

Explanation of Visuals:

• Photos of zebrafish and embryos in tanks.

• Bullet points highlighting rapid growth and ease of observation.

Glossary:

• Organogenesis: Formation of organs during embryonic development.

Key Takeaway:
Zebrafish are a powerful and economical model for developmental and genetic studies due to their external fertilization and transparency.

Slide 37: Danio rerio – More Details

Key Points:

• Key features for research:

  • Embryos develop ex utero and are genetically manipulable.

  • Early expression of GFP (green fluorescent protein) allows visualization of organs.

• Commonly used in:

  • Cancer models

  • Toxicology

  • Vascular research

• Zebrafish offer insights into vertebrate development with real-time imaging.

• Emryos are transparent from the wall.

Explanation of Visuals:

• Diagrams showing fertilized eggs, embryo stages, and fluorescent labeling.

• Table comparing zebrafish traits with other models.

Glossary:

• Ex utero: Outside the uterus.

• GFP: A protein used as a marker to visualize biological processes in living organisms.

Key Takeaway:
Zebrafish embryos provide unique advantages for studying dynamic biological processes due to their transparency and genetic accessibility.

Slide 38: The Rat – Long-Evans (Hooded Rat)

Key Points:

• The Long-Evans rat is a common lab strain used in behavioral, toxicological, and cardiovascular research.

• Compared to mice, rats:

  • Are larger → better for surgical and pharmacological studies.

  • Show more complex behaviors → useful for neuroscience.

Explanation of Visuals:

• Photos of Long-Evans (hooded) and Wistar rats.

• Text highlights their relevance for cognitive, toxicological, and pharmacokinetic studies.

Glossary:

• Wistar rat: Another common laboratory rat strain.

• Long-Evans: A pigmented rat strain used especially for behavioral experiments.

Key Takeaway:
Rats are essential in research that requires advanced behavioral testing, larger body size, or detailed pharmacological analysis.

Slide 39: Rat Outbred Stocks

Key Points:

• Outbred rats are genetically diverse, suitable for general-purpose studies.

• Common stocks:

  • Wistar: Most widely used; calm temperament.

  • Sprague-Dawley (SD): Used in toxicology, pharmacology, surgery.

  • Han:Wistar (RccHan): Used in regulatory testing.

  • Long-Evans: Pigmented; used for behavioral studies.

• Traits: good fertility, growth rate, and general robustness.

• In-breed → meaning mouses are the same family (stammbaum), so they are genetically very homogenous.

• Out-breed: mouses from different families.

Glossary:

• Outbred stock: A population with genetic variability, mimicking natural populations.

Key Takeaway:
Outbred rats like Wistar and SD are widely used for their reliability in diverse experimental settings.

Slide 40: Rat Inbred Strains

Key Points:

• Inbred strains are genetically identical; used for specific research areas.

• Created through ≥20 generations of sibling mating.

• Common inbred strains:

  • LEW (Lewis): Transplantation, immunology.

  • BN (Brown Norway): Allergy, nephrology.

  • F344 (Fischer 344): Aging, cancer.

  • SHR (Spontaneously Hypertensive Rat): Hypertension studies.

  • ZDF (Zucker Diabetic Fatty): Obesity, diabetes.

Glossary:

• Inbred strain: A genetically uniform population, useful for controlled experiments.

Key Takeaway:
Inbred rat strains allow disease-specific studies with reproducible outcomes due to genetic consistency.

Slide 41: Breeding Parameters – Rat

Key Points:

• Rats reach sexual maturity at ~50–60 days.

• Reproductive details:

  • Estrous cycle: ~4–5 days

  • Gestation: ~21–23 days

  • Litter size: ~6–12 pups

  • Weaning: ~21–23 days

  • Females enter postpartum estrus quickly, enabling fast re-mating.

• Males are removed after mating to prevent aggression.

Glossary:

• Postpartum estrus: Period shortly after giving birth when females can conceive again.

Key Takeaway:
Rats have short breeding cycles and high fertility, ideal for rapid colony expansion.

Slide 42: The Mouse

Key Points:

• Title slide introducing the laboratory mouse as the next model organism to be discussed.

Key Takeaway:
Focus shifts to mice, which are the most commonly used species in biomedical research globally.

Slide 43: The Mouse in Research

Key Points:

• Mice are the most used animals in biomedical research.

• Advantages:

  • Share 95–98% of their genes with humans.

  • Genome is well-studied and fully sequenced.

  • Fast reproduction and low maintenance costs.

  • Rich toolbox for genetic manipulation (e.g. knockouts).

• Versatile for research in immunology, cancer, behavior, and genetics.

Key Takeaway:
The mouse is the gold standard model for genetic, biomedical, and translational research due to its genetic similarity to humans and experimental versatility.

Slide 44: Physiological Data and Breeding Data – Mouse

Key Points:

• Key physiological and reproductive metrics:

  • Lifespan: 1.5–2.5 years

  • Body temp: 36.5–38 °C

  • Gestation period: 19–21 days

  • Litter size: 6–8 pups

  • Weaning: 21 days

• Mice are sexually mature at ~6 weeks.

• Weigh about 20–40g as adults.

Explanation of Visuals:

• A table showing physiological norms relevant to lab use.

Key Takeaway:
Mice are small, fast-breeding, and well-documented, making them ideal for high-throughput biomedical research.

Slide 45: Physiological Data and Breeding Data – Mouse

Key Points:

• Important baseline data for laboratory mice:

  • Gestation period: 18–21 days

  • Litter size: ~6 pups

  • Birth weight: 1.5g

  • Weaning weight: ~10g

  • Age at weaning: ~21 days

  • Sexual maturity: 6–8 weeks

  • Productive breeding life: ~8 months

  • Lifespan: 1.5–2.5 years

• These parameters help in planning breeding schemes and managing colonies.

Key Takeaway:
Mice have short lifespans, fast reproduction, and small size—traits that make them efficient and scalable model organisms.

Slide 46: Inbred Strains

Key Points:

• Created through ≥20 generations of brother-sister mating.

• Result in genetic uniformity:

  • Low variability in traits and responses

  • Useful for reproducible studies

• Advantages:

  • Defined genetic background supports clear results

  • Better suited for disease models (e.g. immunodeficiency)

• Traits remain stable across generations.

• Mice from inbred strains all share the same genotype.

Glossary:

• Inbred strain: A population of genetically identical animals used for controlled studies.

Key Takeaway:
Inbred mice ensure consistency in research by minimizing genetic variation, which is crucial for precise experimental outcomes.

Slide 47: Inbred vs. Outbred (Graph Comparison)

Explanation of Visuals:

• Plots show different physiological traits (e.g. weight, blood values) comparing inbred and outbred mice.

• Inbred mice show smaller variability across samples.

• This improves reproducibility and reliability in controlled experiments.

• Like this you can measure the effect fo the environment, since genetically same mice.

Key Takeaway:
Inbred strains show less variability, making them better for experiments where reproducibility and genetic consistency are critical.

Slide 48: Inbred vs. Outbred (Violin Plot)

Explanation of Visuals:

• Violin plots compare the distribution of biological values (e.g. behavior, immune response) in inbred vs. outbred strains.

• Despite the assumptions, variability is not always lower in inbred strains—depends on the trait.

• "Identical variance between inbred and outbred" is noted for some parameters.

• what has come out was that outbread mouse are not actually so much different form inbread mouse.

Key Takeaway:
While inbred mice often reduce variability, this is not universal—trait-specific variation can still occur and must be considered when choosing a model.

Slide 49: Classical Inbred Mouse Strains

Key Points:

• Lists several commonly used inbred mouse strains with associated research applications:

  • C57BL/6: Most commonly used; genetics and immunology.

  • BALB/c: Immunology (especially antibody production).

  • 129/Sv: Source of embryonic stem (ES) cells.

  • FVB: Transgenics (pronuclear injection).

  • DBA/2: Hearing loss studies, neurology.

• Inbred strains are chosen based on genetic stability and defined traits.

Key Takeaway:
Different inbred mouse strains serve as specialized tools in biomedical research, each suited for specific experimental goals.

Slide 50: Classical Mouse Outbred Strains

Key Points:

• Outbred strains are genetically diverse and not bred through strict sibling mating.

• Examples include:

  • CD-1 (ICR): Used in toxicology and pharmacology.

  • Swiss Webster: Common in general-purpose research.

  • NMRI: Neuroscience, behavioral studies.

• These mice are often used in preclinical testing due to their genetic diversity.

Key Takeaway:
Outbred strains represent genetically diverse populations, which can make findings more generalizable but less reproducible.

Slide 51: Standardisation – The Background

Key Points:

• Title slide introducing the topic of standardisation in animal models.

• Sets the stage for understanding how experimental variability can be reduced through controlled genetic and environmental conditions.

Key Takeaway:
Standardisation is critical in animal research to enhance reproducibility and comparability across studies.

Slide 52: Inbred vs. Outbred (Trait Comparison Plot)

Explanation of Visuals:

• Graphs comparing performance traits (e.g. immune response, physiology) in inbred vs. outbred mice.

• Trends show that inbred strains often have less variance, but not always.

Key Takeaway:
Inbred strains often reduce experimental variability, but differences are trait-specific—standardisation doesn’t guarantee uniformity for all outcomes.

Slide 53: Inbred vs. Outbred (Violin Plot Extension)

Explanation of Visuals:

• Violin plots demonstrate trait distribution across strains.

• Finding: Despite being genetically distinct, inbred and outbred mice can show similar variances depending on the trait.

Key Takeaway:
Genetic homogeneity ≠ consistent variance. Both inbred and outbred mice can show trait variability; context matters.

Slide 54: Influence of Genetic Background on Mutation Effects

Key Points:

• The same genetic mutation may lead to different outcomes in different strains.

• Influencing factors:

  • Penetrance: How often a trait appears.

  • Expressivity: Degree of expression (mild to strong).

  • Phenotype: Can shift depending on background genes.

• Example: Phenotypes like behavior or immune function may vary with strain.

Glossary:

• Penetrance: The percentage of individuals showing a trait.

• Expressivity: The severity or degree of trait expression.

Key Takeaway:
A mutation’s effect depends on the mouse’s genetic background, impacting study interpretation and model selection.

Slide 55: Example: Ctr1 Knock-Out Mice

Key Points:

• Describes the generation of Ctr1 knock-out mice, which lack the copper transporter protein.

• Two different genetic backgrounds:

  • C57BL/6 → shorter survival (2–3 weeks).

  • CD1 → longer survival (up to 9 weeks).

• This example shows how genetic background affects phenotypic outcomes.

Key Takeaway:
Genetic background has a major influence on phenotype — even for the same mutation — highlighting the need for careful model selection.

Slide 56: Standardisation – Beyond Genetics

Key Points:

• Title slide introducing the topic that standardisation must also address non-genetic variables.

Key Takeaway:
To improve reproducibility, researchers must consider not only genetics but also environmental and procedural factors.

Slide 57: Phenotypic Variation

Key Points:

• Phenotype is determined by both:

  • Genotype (fixed) and

  • Environment (variable factors like housing, diet, handling).

• Their interaction shapes biological outcomes.

Key Takeaway:
The phenotype = genotype × environment principle emphasizes the need to control or document both genetic and environmental conditions.

Slide 58: Environmental Factors (Photos)

Explanation of Visuals:

• Photos of animal facilities showing differences in:

  • Cage types, equipment, storage, layout.

  • Handling, feeding, housing environments.

Key Takeaway:
Even subtle environmental differences between labs or rooms can significantly influence animal outcomes, underscoring the need for careful standardisation.

Slide 59: Environmental Factors (Text Overview)

Key Points:

• Lists various environmental variables affecting research outcomes:

  • Housing: temperature, humidity, light cycle.

  • Enrichment: nesting, toys.

  • Handling & care: frequency, technique.

  • Diet, microbiota, cage density, ventilation, transport stress, and more.

• These factors can alter immune, metabolic, and behavioral traits.

Key Takeaway:
Numerous environmental parameters influence experimental results. Controlling or reporting these is crucial for reproducibility and comparability.

Slide 60: Factors Affecting the Laboratory Animal

Explanation of Visuals:

• Graphs showing how housing or location affects animal data (e.g., behavior, physiology).

• Example: mice in different facilities show different anxiety or activity levels.

Key Takeaway:
Even within the same strain, variability in lab conditions can lead to different results — replication requires environmental standardisation or careful documentation.

Slide 61: How Mice Are Kept – Filter Tops, Open Caging

Key Points:

• Shows standard mouse housing setups:

  • Open cages with filter tops are commonly used.

  • Includes photos of standard racks and group housing.

• Filter tops reduce contamination but do not control airflow.

Explanation of Visuals:

• Images show mice housed in open cages with bedding, food, and enrichment.

• Emphasis on variability of housing systems.

Key Takeaway:
Standard cage setups (like open cages with filter tops) are simple and cost-effective, but lack advanced environmental control.

Slide 62: How Mice Are Kept – Individually Ventilated Cages (IVC)

Key Points:

• IVC cages provide:

  • Filtered air flow (in/out), minimizing contamination.

  • Standardized cage environment.

  • Reduced pathogen transmission.

• Cages are changed under laminar airflow hoods to maintain sterility.

Explanation of Visuals:

• Diagram showing the modular IVC system and cage design.

Key Takeaway:
IVCs offer superior biosecurity and environmental control, making them ideal for modern lab animal facilities.

Slide 63: How Mice Are Kept – Germ-Free/Axenic

Key Points:

• Axenic (germ-free) housing used for specialized research:

  • Isolators and sterile conditions.

  • Mice lack any microbiota (completely germ-free).

• Enables study of the microbiome and immune development.

Explanation of Visuals:

• Photo of isolator system housing axenic mice.

Key Takeaway:
Germ-free systems allow high-control experiments but require complex infrastructure and handling.

Slide 64: Hygiene

Key Points:

• High hygiene standards are critical in lab animal facilities:

  • Daily monitoring.

  • Bedding/cage cleaning protocols.

  • Health checks and hygiene scoring.

• Mice can be assigned FELASA status based on microbial screening (specific pathogen free vs. germ-free).

Explanation of Visuals:

• Bullet-point summary with references to Swiss and European (FELASA) hygiene practices.

Key Takeaway:
Maintaining hygiene through regular health monitoring ensures the health, welfare, and validity of research results.

Slide 65: Enrichment

Key Points:

• Enrichment improves animal welfare:

  • Reduces stress.

  • Encourages natural behavior.

  • If the mice get bored and have no enrichment, the just start to run in circles without any sense and this might have impact on your phenotype.

• Can include nesting material, shelter, gnawing blocks, etc.

Explanation of Visuals:

• Photo of a mouse cage with environmental enrichment materials.

Key Takeaway:
Enrichment is a crucial part of humane housing that also positively influences experimental outcomes.

Slide 66: Environment vs. Development – NMDA Receptor Knockout Mouse

Key Points:

• Study of NMDA receptor knockout mice shows:

  • Environment can partially rescue developmental deficits.

  • Example: enriched vs. impoverished housing affects brain structure and behavior.

• Demonstrates gene × environment interactions.

Explanation of Visuals:

• Schematic comparing enriched and impoverished cages and effects on brain development.

Key Takeaway:
Environmental enrichment can significantly impact brain development, especially in genetically modified models.

Slide 67: Reproducibility and Replicability Crisis

Key Points:

• A major reproducibility crisis exists in science.

• Only ~40% of scientific findings are successfully replicated.

• Particularly severe in biomedical and preclinical research.

Explanation of Visuals:

• A pie chart shows that over half of researchers think science is facing a crisis.

Key Takeaway:
Concerns about reproducibility undermine trust in research and highlight the need for more rigorous experimental design.

Slide 68: Replicability as a Cornerstone of the Scientific Process

Key Points:

• Science depends on replication of results.

• The Reproducibility Project revealed that many published studies fail replication.

• Emphasis on open science practices (data sharing, pre-registration, transparency).

Explanation of Visuals:

• Image of researchers restaging experiments.

• Quote from Science magazine underlining the problem.

Key Takeaway:
Reliable, replicable results are essential for scientific credibility and progress.

Slide 69: Replicability in Practice – Survey Results

Key Points:

• Surveys (e.g., by Bayer and Amgen) show:

  • Only ~20–25% of published results can be replicated.

  • Most scientists agree that reproducibility is a widespread problem.

• Differences in replication rates among disciplines.

Explanation of Visuals:

• Pie charts and a bar graph summarizing survey responses.

Key Takeaway:
Reproducibility problems are widespread across disciplines and are acknowledged by the scientific community.

Slide 70: Reproducibility and Replicability Crisis – Consequences

Key Points:

• Scientific consequences:

  • Slows down progress.

  • Hinders innovation.

• Economic losses:

  • Estimated at $28 billion per year in the USA.

• Public trust is eroded by failed replication attempts.

Explanation of Visuals:

• Icons illustrating the impact on science, economy, and public perception.

Key Takeaway:
The reproducibility crisis has far-reaching consequences beyond the lab, including public distrust and wasted resources.

Slide 71: Reproducibility Crisis and Scientific Rigor

Key Points:

• Replicability requires:

  • Transparent methods and materials.

  • Detailed experimental protocols.

  • Accessible data.

• Lack of these leads to poor generalizability.

Explanation of Visuals:

• Comparison of published work vs. replicable work.

• Red warning signs highlight gaps in reporting and execution.

Key Takeaway:
Insufficient documentation and openness limit the value and reliability of scientific studies.

Slide 72: Reproducibility and Translational Validity of Preclinical Research

Key Points:

• Low replicability affects:

  • Translational success (from animal model to human trials).

  • Development of effective therapies.

• Improving reproducibility supports more reliable biomedical advancements.

Explanation of Visuals:

• Diagram shows the chain from replicability → generalizability → translation.

Key Takeaway:
Better reproducibility and design practices are essential for turning research into meaningful medical therapies.

Slide 73: Reproducibility Crisis and Ethical Aspects in Animal Research

Key Points:

• The public is increasingly critical of animal experiments.

• Failed reproducibility raises ethical concerns:

  • Animals may be used in studies that yield unreliable or irreproducible data.

• Example: Switzerland rejected animal testing in a referendum, showing public distrust.

Explanation of Visuals:

• A map of Switzerland and media headlines highlighting public opposition to animal testing.

Key Takeaway:
Unreproducible animal experiments not only waste resources but also undermine ethical justifications for using animals in science.

Slide 74: The Causes of Irreproducible and Irreplicable Research

Key Points:

• Major journals (e.g., PLOS Medicine, PLOS Biology) emphasize the importance of transparent and reproducible practices.

• Increasing focus on:

  • Sharing raw data

  • Publishing negative results

  • Describing experimental conditions in detail

Explanation of Visuals:

• Journal covers and quotes calling for better reproducibility standards.

Key Takeaway:
Scientific publishing must support transparency and open data to improve reproducibility.

Slide 75: Causes of Irreproducibility – Multi-Level Factors

Key Points:

• Reproducibility issues stem from several levels:

  • Individual level: poor training, bias, lack of skills

  • Institutional level: reward systems, lack of quality control

  • Journal level: publication bias

  • Funding level: pressure to produce results

• These factors create a cycle of flawed research.

Harking: Hypothesizing after the results are known.

Explanation of Visuals:

• Circular diagram illustrating different sources of irreproducibility.

Key Takeaway:
Reproducibility issues are systemic and involve many actors in the research ecosystem.

Slide 76: Find 5 Problems – Data Transparency

Key Points:

• First focus area: data availability.

• Without access to raw data, studies cannot be independently verified or reanalyzed.

• Many published studies do not share their full datasets, even when required.

Explanation of Visuals:

• A text-based slide that explains the importance of data sharing.

Key Takeaway:
Lack of data sharing is a major barrier to reproducibility.

Slide 77: Causes – Scientific Publishing Practices

Key Points:

• Journal practices can contribute to irreproducibility:

  • Preference for positive results

  • Lack of enforcement on data/code sharing

• Cartoon illustrates the absurdity of overconfidence in results without transparency.

Explanation of Visuals:

• Humorous cartoon panels showing how scientists might manipulate or selectively report data.

Key Takeaway:
Publishing culture often incentivizes poor practices over reliable science.

Slide 78: Find a Problem – Code Availability

Key Points:

• Analysis code is often not shared, making replication impossible.

• Many studies use custom scripts or workflows that aren’t published.

• Even when code is “available upon request,” it often isn’t provided.

Explanation of Visuals:

• Text emphasizing how lack of code availability hinders reproducibility.

Key Takeaway:
To support transparent science, both data and code must be accessible and reusable.

Slide 79: The Causes of Irreproducible and Irreplicable Research – Example 3

Key Points:

• A third common problem: lack of methodological detail.

• Example: Western blot experiments often lack:

  • Precise protocols

  • Control groups

  • Detailed reagent or sample descriptions

• These missing details make it impossible for other labs to repeat the study.

Explanation of Visuals:

• Image of incomplete Western blot data and a centrifuge to highlight inadequate reporting.

Key Takeaway:
Without clear methodology, even high-quality data becomes irreproducible.

Slide 80: The Causes – Example 4: Reporting Bias

Key Points:

• Many publications omit species names in titles and abstracts.

• This creates confusion and hinders reproducibility across species.

• A study from eLife showed that over 50% of animal studies do not mention the species in the abstract or title.

Explanation of Visuals:

• A screenshot from an eLife article that analyzed animal study reporting trends.

Key Takeaway:
Clear species identification is essential for reproducibility and cross-study comparison.

Slide 81: Biological Variation and Phenotypic Differences

Key Points:

• Variation is caused by genetics and environment.

• Even animals of the same genotype can behave differently depending on housing and handling.

• This biological variability contributes to poor reproducibility across labs.

Explanation of Visuals:

• Illustration of a population of animals and the interaction between genotype and environment.

Key Takeaway:
Phenotypic variability is normal and must be accounted for in experimental design and analysis.

Slide 82: Environmental Background Affects Outcomes

Key Points:

• Studies show that even small environmental differences (e.g. cage type, bedding, noise) can impact experimental results.

• A PLOS Biology paper emphasizes the need to report environmental factors.

• Example: differences in behavioral or immune responses depending on housing conditions.

Explanation of Visuals:

• Animal housing images and a graphical summary of environmental influence on outcomes.

Key Takeaway:
Environmental conditions must be standardized or at least documented to ensure findings are reproducible.

Slide 83: Measures to Improve the Reproducibility and Replicability of Research Findings

Key Points:

• Clearly describe the study design, protocols, and statistical methods.

• Specify all reagents used (antibodies, compounds, cell lines).

• Ensure the inclusion of positive and negative controls.

• Provide biological and technical replicates.

• Standardize:

  • Type of animals (strain, sex, age, weight, etc.)

  • Environmental conditions (light, temperature, diet)

  • Housing and handling conditions

• Consider key variables: species, strain, setting, and sex.(most important feature)

Explanation of Visuals:

• Visual of a mouse and pipette with a checklist of critical reproducibility factors.

Glossary:

• Replicates: Repeated measurements to ensure consistency of data.

• Controls: Known conditions used to validate experiment reliability.

Key Takeaway:
Reproducibility begins with detailed documentation and standardized conditions.

Slide 84: Sex as a Biological Variable

Key Points:

• Most research is done on male animals only.

• Ignoring sex leads to biased or incomplete results.

• Sex differences affect:

  • Physiology

  • Drug metabolism

  • Disease manifestation

• Every study should consider sex as a factor, even if not the main focus.

• Many diseases show sex-dependent prevalence and response.

Explanation of Visuals:

• Four text boxes showing consequences of excluding sex as a variable.

Glossary:

• Biological variable: A factor like sex that can influence biological outcomes.

Key Takeaway:
Including both sexes in research leads to more accurate and applicable findings.

Slide 85: Biology (Sex) and Socio-Cultural Factors (Gender) Influence Health

Key Points:

• Sex is a biological trait (chromosomes, hormones, organs).

• Gender involves identity, roles, and social constructs.

• For laboratory animals:

  • Only sex is relevant — they have no gender roles.

• Experimental designs should disentangle sex-based effects from social factors in human studies.

Explanation of Visuals:

• Diagram separating sex (biology) from gender (social factors).

Glossary:

• Sex: Biological classification as male or female.

• Gender: Social identity and roles.

Key Takeaway:
In animal studies, only biological sex matters — and it should be systematically reported and analyzed.

Slide 86: The Causes of Irreproducible and Irreplicable Research

Key Points:

• A bar chart shows major reasons for irreproducibility:

  • Poor study design

  • Lack of standardization

  • Incomplete reporting

  • Low statistical power

  • Uncontrolled variability

• Each bar reflects how frequently each issue contributes to irreproducibility across fields.

Explanation of Visuals:

• Stacked bar graph comparing different scientific disciplines and key factors of poor reproducibility.

Key Takeaway:
A combination of design flaws, missing data, and uncontrolled variation fuels the reproducibility crisis.

Slide 87: Consequences of One-Sex Bias in Preclinical Research for Drug Development

Key Points:

• Most animal studies historically used only male animals.

• This bias affects clinical research, where both sexes receive treatments.

• Consequences include:

  • Misinterpretation of sex-specific effects

  • Delayed recognition of sex-related side effects

  • Higher drug withdrawal rates (especially for women)

• Balanced representation is crucial in preclinical research for safe and effective translation to humans.

Explanation of Visuals:

• Diagram comparing research using only males vs. using both sexes and highlighting consequences in clinical outcomes.

Glossary:

• Preclinical research: Studies using models (e.g., animals) before testing in humans.

• Sex-related side effects: Adverse reactions that differ between males and females.

Key Takeaway:
Excluding female animals from research undermines the safety and efficacy of new treatments for women.

Slide 88: Sex as a Biological Variable (SABV) in Basic and Practical Research

Key Points:

• Sex differences influence:

  • Behavior

  • Physiology

  • Immune response

  • Drug metabolism

• Both sexes must be included in studies to reflect biological reality.

• Applies across species: mice, rats, zebrafish, humans.

Explanation of Visuals:

• Visual shows a progression from lab animals to humans, highlighting sex diversity in all research stages.

Glossary:

• SABV: Sex as a biological variable; considering sex differences in study design and analysis.

Key Takeaway:
Including both sexes improves scientific accuracy and relevance across species.

Slide 89: What Are the Main Reasons for Single-Sex Studies?

Key Points:

• Slide is a transition slide asking a reflective question.

• Prepares audience for discussion on why female animals are often excluded.

• Implies upcoming content will address logistical, biological, or biased assumptions.

Key Takeaway:
This slide sets the stage to challenge common justifications for using only one sex in animal research.

Slide 90: Common Misconceptions About Female Animals

Key Points:

• Misconception 1: Female animals have more variable outcomes due to hormonal cycles.

• Reality: Studies show no greater variability in females than males.

• Misconception 2: Female data are more complex or difficult to interpret.

• Reality: Complexity is not a valid reason for exclusion.

• PLOS Biology study confirms:

  • Excluding females leads to biased conclusions.

  • Including females does not increase variability.

Explanation of Visuals:

• Graph comparing variability in male vs. female outcomes; showing comparable variance.

Glossary:

• Estrous cycle: Hormonal cycle in female animals, often used (incorrectly) as a justification for exclusion.

Key Takeaway:
Scientific evidence refutes the myth that female animals are more variable — they must be included for valid, unbiased results.

Slide 91: Implementation of SABV Policy

Key Points:

• The NIH introduced a policy requiring researchers to consider Sex As a Biological Variable (SABV).

• Graphs show increased inclusion of both sexes in publications after the policy.

• Despite improvements, male-only studies still dominate in many fields.

Explanation of Visuals:

• Bar graphs per research field (e.g., neuroscience, pharmacology) show the proportion of studies using:

  • Both sexes

  • Only males

  • Only females

Glossary:

• SABV: A policy promoting inclusion of both male and female animals in research to ensure sex-based validity.

Key Takeaway:
Although progress has been made, sex inclusion remains uneven, with males still overrepresented in preclinical research.

Slide 92: Most Papers Did Not Use Sex-Based Analyses (Even if Both Sexes Were Included)

Key Points:

• Including both sexes is not enough — data must be analyzed by sex.

• Many papers combine male and female data or ignore potential sex differences.

• Failure to analyze sex-specific effects limits scientific value.

Explanation of Visuals:

• Graphs show low percentages of papers using sex-based statistical analyses, even when both sexes were studied.

Key Takeaway:
Just including both sexes is insufficient — sex-specific data analysis is crucial for meaningful results.

Slide 93: Implementation of SABV Policy – Summary of Study Designs

Key Points:

• Most studies using both sexes still do not test for sex effects.

• Designs vary:

  • Some balance sexes but don’t analyze separately.

  • Others use unbalanced samples (more males than females).

• Few studies fully comply with SABV policy (balanced design + sex analysis).

Explanation of Visuals:

• Bar graphs are grouped into colored boxes showing:

  • Balanced sex design with/without sex analysis.

  • Unbalanced sex ratios.

  • Male-only or female-only designs.

Glossary:

• Balanced design: Equal numbers of males and females.

• Unbalanced design: One sex is overrepresented.

Key Takeaway:
There is a gap between inclusion and proper analysis of sex in research, limiting the impact of SABV policy.

Slide 94: SABV Policy Progress from 2009 to 2019

Key Points:

• From 2009 to 2019:

  • Studies using both sexes increased.

  • However, only a small fraction analyzed data by sex.

• Barriers include:

  • Lack of training.

  • Misconceptions about complexity or cost.

• Despite policy change, full implementation remains low.

Explanation of Visuals:

• Flowchart shows progress in sex inclusion and analysis over a decade.

• Emphasis on knowledge gap in applying SABV correctly.

Key Takeaway:
Policy adoption improved inclusion, but training and awareness are essential to close the gap in proper SABV implementation.

Slide 95: Integration of SABV into Study Design – Default Option: Not Testing for Sex-Specific Effects

Key Points:

• Many studies include both sexes but don’t test for sex-specific responses.

• This can mask meaningful differences between male and female responses.

• Separate analysis by sex is crucial to identify diverging patterns.

Explanation of Visuals:

• Schematics contrast control (where both sexes are pooled) vs. sex-specific analyses.

• Right panel shows how training and testing sexes separately leads to clearer interpretations.

Glossary:

• SABV: Sex as a Biological Variable – the policy to include and analyze both sexes in research.

Key Takeaway:
Pooled analyses hide sex differences—to improve discovery, sex-specific effects must be tested explicitly.

Slide 96: Integration of SABV – How to Make It Meaningful

Key Points:

• Use historical data to guide study design and sample sizes.

• Perform power analysis separately for males and females when relevant.

• Use validation datasets to confirm observed sex effects.

Explanation of Visuals:

• Visual contrast between:

  • Combining data blindly vs. using sex-aware power estimation.

  • Graph showing validation of findings in separate datasets.

Key Takeaway:
Meaningful SABV inclusion requires careful design, analysis, and validation—not just including both sexes.

Slide 97: If You Look, Chances Are You Will Find It

Key Points:

• Studies that analyze by sex often find sex-specific differences.

• Many still don’t perform sex-specific tests (even with both sexes included).

• Data shows a significant portion of sex-aware studies report differences.

Explanation of Visuals:

• Two pie charts:

  • Left: 80% of studies including both sexes did not perform sex comparisons.

  • Right: Of the 20% that did, 72% found sex differences.

Key Takeaway:
Sex differences are commonly found when tested—suggesting they are biologically meaningful and should not be ignored.

Slide 98: SABV in Single Experiments – Design & Analysis Examples

Key Points:

• Left: Incorrect approach – pooled data masks sex effects.

• Right: Correct approach – sex-aware design with interaction terms.

• Interaction effects can reveal or hide treatment effects depending on sex.

Explanation of Visuals:

• Diagrams compare common flawed designs with statistically robust ones.

• Show how statistical power and interpretation change with sex-aware analysis.

Glossary:

• Interaction effect: When the effect of a treatment differs by sex.

Key Takeaway:
SABV must be considered during both study design and statistical analysis to avoid misleading results.

Slide 99: Four Types of Sex Differences

Key Points:

1. Sexual Dimorphism: Trait appears in only one sex.

   1. Agression cna be increased btw

2. Opposite Direction Effects: A treatment improves one sex but worsens the other.

3. Same Direction, Different Magnitude: Effect seen in both, but stronger in one.

4. One Sex-Only Effect: Effect present in one sex, absent in the other.

Explanation of Visuals:

• Each panel depicts a unique pattern of sex differences in experimental outcomes.

Glossary:

• Sexual Dimorphism: Biological trait present in only one sex due to inherent differences.

Key Takeaway:
Recognizing the type of sex difference is key to interpreting experimental outcomes correctly and tailoring interventions.