M4. L6. 

In scientific experiments, the main living material used to test a hypothesis is called the study organism. These organisms are usually grouped based on how complex they are, where they come from, and how they are used in research.

1. Model Organisms

These are non-human species studied closely to understand basic biological principles. The idea is that what is learned from them can also apply to other living things, including humans. They are popular due to their affordability, ease of maintenance, short life cycles, and ease of genetic manipulation.

• Microorganisms. These are organisms too small to be seen clearly with the naked eye, requiring a microscope. They include single-celled life forms and simple multicellular clusters. Microorganisms are fundamental model organisms because they reproduce rapidly and are easy to manipulate genetically. 

Examples are:

• • • bacteria

    • yeasts

    • viruses

    • protozoa

• Invertebrates. Animals that lack a backbone or spinal column. They represent over 95% of all animal species and range from simple sponges to complex insects. Simpler invertebrates are widely used as model organisms because they share many genes and biological pathways with humans, but are much easier and cheaper to maintain than vertebrates. 

Examples are:

• • • insects

    • nematodes

    • mollusks

    • arachnids

• Vertebrates. Animals that possess a backbone or spinal column, belonging to the subphylum Vertebrata. This group includes fish, amphibians, reptiles, birds, and mammals. Vertebrates are used when the biological process being studied is too complex or specific to be modeled in invertebrates. 

Examples are:

• • • mammals

    • fish

    • amphibians

• Plants. Multicellular, typically photosynthetic eukaryotes that form the kingdom Plantae, including trees, herbs, grasses, and shrubs.

2. Specimen Collections (Standard Strains)

These are well-characterized and maintained strains, often pathogens, obtained from official biological repositories. They serve as consistent standards for experiments worldwide. 

• Standard strains (e.g., bacteria, yeast, cell lines) are organisms maintained by official collections (like ATCC) that serve as universal, unchanged benchmarks for experiments. They ensure researchers are using the exact same biological entity. 

• Genetically Modified Organisms (GMOs) are organisms intentionally altered in laboratories to study specific genes, pathways, or disease states, often requiring specialized handling and permits. Examples are:

  1. • Knockout strains. Strains where a specific gene has been entirely removed to understand what that gene does. 

     • Reporter strains. Bacteria modified to glow green (fluoresce) when they sense a specific chemical or are under stress. 

     • Transgenic animals. Mice engineered to carry a human gene associated with a disease (e.g., Alzheimer's) to model the condition. 

3. Primary Isolates and Environmental Samples

These organisms are directly collected from nature—soil, water, air, or from patients—rather than from long-term laboratory stocks. They are crucial for ecological and medical research. Clinical isolates are bacteria or viruses taken from infected individuals, used to study real-world issues such as antibiotic resistance or disease outbreaks. Environmental isolates, including microbes, fungi, and plants gathered from local ecosystems, are essential for biodiversity and community health studies.

• Clinical Isolates. Bacteria or viruses taken directly from an infected person are used mainly to study real-world issues such as antibiotic resistance or current disease outbreaks. Clinical isolates are microorganisms collected from human or animal patient samples (e.g., blood, sputum, wounds). Due to the high risk of encountering pathogens, working with any primary clinical isolate is usually restricted to BSL-2 or BSL-3 facilities and is not allowed for senior high school students.

• Environmental Isolates. Microbes, fungi, or plants collected from local ecosystems are essential for biodiversity studies and research related to local issues, such as testing local plants for medicinal properties. The context of the collection (e.g., "isolated from a specific river in the Philippines") is crucial. Environmental isolates are microbes gathered from natural sources like soil, water, air, or plants. Their BSL level is determined by the potential risk of the collection site and the organism's inherent nature.

4. Cultured Cells and Tissues

These living cells or tissues taken from an organism and grown in controlled environments outside the body are known as cell cultures. Cell lines are cells capable of growing indefinitely, commonly used in drug testing and research. Primary cell cultures are freshly derived from living tissues and grown temporarily, offering a closer representation of how cells behave in the body.

• Cell Lines. Cells capable of indefinite growth in a lab (immortalized cells, such as cancer cells). They are used for high-throughput screening, toxicology studies, and basic cell function research.

• Primary Cell Cultures. Cells freshly taken from a living organism (e.g., human skin cells or neurons) and grown for only a limited time. They are valued because they more closely mimic native tissue function than cell lines.

5. Based on Specific Purpose

These are grouped depending on their role in experiments. 

• Wild Type (WT). The natural strain with no genetic changes. It always serves as the control or baseline for comparing results from genetically modified or treated specimens.

• Indicator Organisms. Species whose presence, absence, or change in health status is used specifically to monitor an environment or process. For example, using the presence of E. coli to signal fecal contamination in water.

• Host/Parasite Systems. Used in disease research, where one organism (the host) is necessary to maintain or grow the other (the parasite, virus, or pathogen). The specific type of host and its maintenance are crucial descriptive details.

The Classification by Functional Role in Testing is a critical framework for understanding the use of study organisms in prototype research, as it categorizes organisms based on the specific contribution they make to the validation of an engineered system or device. Unlike traditional biological classification, this system focuses on the organism's action or role within the research design.

1. Indicator Organism

The Indicator Organism serves as a measurable proxy to gauge the condition, safety, or sanitation of the system being tested. Researchers do not examine the organism itself but instead use its presence, absence, or population size as an early warning sign. The concept of the indicator organism depends on its easy detectability and a strong, established link between its state and the possible presence of a more dangerous or harder-to-measure condition. For example, coliform bacteria are used to test a prototype water filter; their removal indicates the filter's ability to eliminate not only coliforms but also potentially more harmful pathogens from the same source. This function is vital in environmental and food safety engineering prototypes.

2. Target Organism

The Target Organism is the specific living entity that the prototype is primarily designed to affect, interact with, or eliminate. This organism represents the real-world challenge the prototype aims to address. Whether the prototype is a surgical robot, a new pesticide, or a pest control drone, the target organism sets the performance parameters of the system. For example, a snail is used to test a pest control robot because the robot's success depends on its ability to locate and manage the specific physical characteristics (size, shape, movement) of that snail. The study evaluates the prototype's effectiveness against its intended target.

3. Surrogate Organism

The Surrogate Organism is a non-hazardous substitute chosen to represent a dangerous or highly regulated target, such as a virulent pathogen, bioweapon, or resistant pest. The surrogate is selected because it shares important characteristics—like size, surface structure, or chemical resistance—with the actual target. Its main purpose is to enable researchers to safely and cost-effectively test the effectiveness of a prototype device or process (e.g., sterilization, decontamination, or filtration) without requiring high-level biocontainment. For example, a non-virulent bacterial spore might be used to test a new autoclave; its destruction offers a safe and reliable way to measure the autoclave's ability to sterilize the most resistant life forms.

4. Efficacy Organism

The Efficacy Organism is selected because it exhibits a specific, measurable biological response or trait that directly verifies the prototype's main function. This role is often performed by a clinical or engineered isolate. The organism is used to confirm the accuracy or specificity of a device. For example, a drug-resistant bacterial strain (an isolate) is employed to test a prototype diagnostic kit; the kit’s ability to accurately identify the resistance mechanism in that particular strain confirms its core function and clinical usefulness. The emphasis is not just on affecting the organism but on the organism demonstrating the prototype's intended capability.

The ethical considerations for Study Organisms in research, especially for senior high school students in the Philippines, revolve around respect for life, minimizing harm, safety, and regulatory compliance.

1. Minimizing Harm

This is the core principle, especially important when working with animals. Student-researchers should prioritize methods that lessen distress, pain, and the number of organisms used.

• Replacement. Use non-living methods whenever possible. Example: Use computer simulations, virtual dissections, or cell cultures instead of whole animals.

• Reduction. Use the fewest organisms necessary to achieve valid results. Example: Implement proper statistical design to avoid waste, reducing the number of specimens needed.

• Refinement. Improve procedures and housing to reduce pain and suffering. Example: Ensure specimens are kept in clean, suitable environments (correct temperature, food, water) and that any needed euthanasia is performed humanely and swiftly by a trained adult.

2. Regulatory Compliance and Safety

All research involving living organisms must strictly adhere to institutional, local, and national guidelines, which are put in place to protect the student-researchers, the public, and the environment.

• Institutional Review and Approval. Student-researchers must secure written approval from the Research Area and the Center for Research and Development before beginning any experiment involving vertebrates or high-risk invertebrates.

• Permits for Collection. Suppose the study involves collecting wild organisms (especially endangered or endemic species). In that case, the necessary permits from government agencies (e.g., DENR) must be obtained. Unauthorized collection is illegal and unethical.

• Containment and Disposal. Procedures must be in place to prevent the accidental release of study organisms, especially non-native or engineered microbes, into the environment. All biological waste, including culture plates and deceased specimens, must be autoclaved or chemically treated and disposed of safely, following standard laboratory protocols.

• Student Safety. Student-researchers must be trained on the proper handling of all organisms, especially potential pathogens or venomous animals, and always use appropriate Personal Protective Equipment (PPE).

3. Respect for Life and Environment

This principle goes beyond the laboratory to recognize the inherent value of the organism and its function within the ecosystem.

• Humane Treatment. All organisms must be cared for with proper housing, food, water, and veterinary attention throughout the study. Neglecting their needs and causing suffering is unacceptable.

• Restoration. If organisms are temporarily removed from their natural habitat, protocols must guarantee their safe and prompt return to the collection site, reducing disruption to the local ecosystem.

• Non-Maleficence. Research must be planned to prevent causing significant, irreversible harm to wild populations or ecological communities. The integrity of the environment must be maintained.

4. Special Considerations for Plants and Microorganisms

While plants and microorganisms usually need less strict ethical oversight than animals, unique considerations still apply, especially in terms of environmental impact.

• Introduction of Non-Natives. Student-researchers must never introduce non-native plant species, genetically modified organisms (GMOs), or microbial strains into the local environment, as these can become invasive and harm local biodiversity.

• Biotechnology and GMOs. Research involving genetic modification must be performed under strict containment to prevent gene flow. Ethical considerations of creating new life forms or modifying existing ones must be carefully discussed and documented in the research proposal.

• Suitable Collection. When collecting plant or fungal material, student-researchers must practice sustainable harvesting, making sure enough of the population remains to regenerate and that the habitat is not harmed.

• Biosecurity. When working with microorganisms, including common soil bacteria, students must follow sterile techniques to prevent contamination that could impact human health or other experiments.

NOTE:

Animal and human testing are prohibited in SHS research at Adamson University. 

Filling out a detailed table about study organisms is crucial for ensuring research is reproducible and ethically sound. It provides a complete biological context for the research.

1. Species (Scientific Name)

This column requires the organism's binomial nomenclature—the internationally recognized two-part name (Genus species). This standardized system prevents confusion. It must be written in italics, with the Genus capitalized and the species in lowercase (e.g., Mus musculus).

2. Strain/ Cultivar/ Breed or Race (If applicable)

This indicates particular genetic lines within a species. For bacteria, it is the strain (for example, K-12). For plants, it is the cultivar or variety (such as 'Sinandomeng'). For animals, it can be the breed or specific laboratory line (like CD-1). If a common wild-type organism is used and no particular line is known, enter "Wild-Type" or "NA."

3. Origin/ Source (Supplier or Collection Details)

Traceability is crucial for reproducibility. This column must specify where the organism was obtained. If purchased, include the supplier's name and lot or catalog number. If collected, provide precise geographic coordinates (GPS), collection date, and method (e.g., net collection, hand-picking). Note: It may be helpful to research how a specific species is normally collected to accurately describe the collection process method. 

4. Special Considerations for Plants and Microorganisms

These conditions are maintained to keep the organism healthy and reduce environmental stress before and during the experiment. Key variables include temperature, humidity, light cycle (for animals/plants), and culture medium (for microbes). Any deviation from standard conditions must be recorded. 

TYPICAL LIGHT CYCLE ENTRY

• Standard/ Normal Cycle (12:12 L:D). Twelve hours of light followed by twelve hours of darkness. This mimics a common equatorial day-night cycle and is the most frequently used standard in laboratory research.

• Long-Day Cycle (14:10 L:D). Longer photoperiod, often used to simulate spring/summer conditions, which can influence reproductive cycles and energy storage.

• Short-Day Cycle (8:16 L:D). Shorter photoperiod, often used to simulate autumn/winter conditions, which can trigger hibernation or metabolic slowing.

• Atypical/ Constant Light (24:0 L:D). Continuous light exposure, usually only employed if the prototype specifically requires it or to induce certain physiological stress responses.

• Atypical/ Constant Dark (0:24 L:D). Continuous darkness, typically used for nocturnal species or to study light-independent physiological processes.

SOME COMMON CULTURE MEDIUM ENTRIES FOR MICROBES

• Luria-Bertani (LB) Broth. A standard, rich, general-purpose liquid medium for cultivating a wide variety of non-fastidious (not demanding) bacteria, particularly E. coli.

• Potato Dextrose Agar (PDA). A solid medium rich in carbohydrates (from potato) used primarily for the cultivation of yeasts and molds/fungi.

• Tryptic Soy Broth/ Agar (TSB/TSA). A highly nutritious, general-purpose medium often used for the culture and enumeration of a wide range of bacteria, including some pathogens.

• Minimal Media. A chemically defined medium containing only the essential salts and a single carbon source (e.g., glucose). Used when studying specific metabolic pathways or genetic circuits.

• Selective/ Differential Media. A medium that favors the growth of certain organisms while inhibiting others, or one that makes certain species visibly distinct.

5. Life History/ Distribution

This section provides context for why the organism was chosen as a study subject. It includes details such as natural habitat, lifespan, reproductive strategy, and ecological niche. This helps readers understand the reasons behind selecting a particular species for research.

Scenario:

To explain why Pila luzonica (an indigenous snail) was chosen for a mechanical harvesting prototype.

Possible Entry in the Compendium:

Native to Southeast Asia; herbivorous; reproduces rapidly via fragmentation.

Scenario:

To justify using the laboratory rat as a general mammalian model for a human physiological prototype.

Possible Entry in the Compendium:

Average lifespan 2-3 years; nocturnal; omnivorous; common laboratory rodent.

6. Handling Before Experiment

This outlines the final procedures carried out immediately before the organism undergoes the prototype. This step is essential for standardization, making sure all subjects are in the same state (e.g., fasted, synchronized development stage) when the experiment starts.

Scenario/ Example:

Pre-experiment handling for fish used to test a new oral medication prototype.

Possible Entry in the Compendium:

Acclimatized for 48 hours in experimental tanks; Fasted for 12 hours prior to dosage.

Scenario/ Example:

Preparing a bacterial suspension for inoculation into a prototype culture medium.

Possible Entry in the Compendium:

Centrifuged and washed twice with sterile Phosphate-Buffered Saline (PBS).

Scenario/ Example:

Preparing plant specimens for an agricultural prototype test.

Possible Entry in the Compendium:

Seedlings transplanted into experimental pots 7 days prior to prototype fertilizer application.

7. Size/ Weight/ Length

Using quantitative metrics is crucial for reducing variability and improving reliability. For animals, weight and length are common measurements. For plants, height or leaf area may be used. For microorganisms, optical density (OD) or colony-forming units (CFU) are the standard size metrics.

Scenario/ Example:

Specifying the size of mice used in a prototype drug efficacy study.

Possible Entry in the Compendium:

18-22 grams (standard deviation 0.8g); 8-10 weeks old.

Scenario/ Example:

Specifying the developmental stage of plants used in a growth enhancement prototype.

Possible Entry in the Compendium:

Stem height: 15 ± 2 cm; 5-7 true leaves.

8. Diet/ Feeding Regimen

Diet greatly influences an organism's physiology, which in turn impacts experimental results. The diet must be consistent and thoroughly documented, including the type of feed, feeding frequency, and amount.

Scenario/ Example:

Standard diet for laboratory rats.

Possible Entry in the Compendium:

Commercial rodent chow (Purina); ad libitum (fed freely).

Scenario/ Example:

Controlled feeding regimen for fish in an aquaculture prototype.

Possible Entry in the Compendium:

Commercial Tilapia pellets (2% body weight/day); fed twice daily at 8:00 AM and 4:00 PM.

Scenario/ Example:

The nutrient medium used for cultivating fungal cultures.

Possible Entry in the Compendium:

Potato Dextrose Agar (PDA).

9. Cost (₱)

This section lists the cost of each item or batch (for example, cost per mouse, cost per bag of seeds, or cost per vial of bacterial culture). It is important for project budgeting and for evaluating the feasibility and scalability of the research prototype.

10. Notes (Special Considerations, Ethical Approvals)

This section includes all additional information, especially required regulatory and ethical details. It is essential for studies involving animals or hazardous materials.