Glossary

mascot-glossary

Glossary

A

  • Active immune regulation
    The body's controlled response to balance fighting infection while avoiding excessive damage to its own tissues [6, 7].
  • Active Tuberculosis (ATB)
    The stage of tuberculosis when the bacteria are actively multiplying, symptoms appear, and the disease can be transmitted to others [9, 10].
  • Altered lipid and amino acid levels
    Changes in the body's fats (lipids) and the building blocks of proteins (amino acids) that may indicate disease [3, 4].
  • Antigens
    Substances (often proteins) from pathogens or other sources that trigger an immune response in the body [6, 14].
  • Anti-FAM antibodies
    Proteins designed to specifically bind to FAM-labeled molecules, used to generate a detectable signal in diagnostic tests [18, 21].

B

  • Bacille Calmette-Guérin (BCG) vaccine
    A vaccine primarily used against tuberculosis, developed from a weakened strain of Mycobacterium bovis. It can sometimes interfere with TB skin test results, causing false positives [9, 10].
  • Bacterial DNA
    Genetic material found in bacteria, which can be detected to confirm infection [1, 2].
  • β-lactamase
    An enzyme used as a reporter gene that breaks down certain antibiotics; its activity can be measured in diagnostic or lab tests [12, 14].
  • Biomarker
    A measurable substance in the body (such as a protein, gene, or molecule) that indicates the presence of a disease or condition [3, 4, 6].
  • Biotin
    A vitamin molecule that can be chemically attached to DNA or RNA probes to enable detection in lab assays such as lateral flow tests [18, 20].
  • Biotin-dsDNA-FAM reporter probe
    A detection molecule composed of double-stranded DNA labeled with biotin and FAM, used to generate a measurable signal in diagnostics [1, 18, 21].
  • Biotin-ssDNA-FAM probe
    A detection probe that combines biotin, single-stranded DNA, and FAM, enabling visualization in lateral flow tests [1, 18, 20].

C

  • Cell-free systems
    Experimental setups that use only biological molecules (like RNA, enzymes, or proteins) outside of living cells to perform reactions or diagnostics [23, 24].
  • Colorimetric readouts
    Test results that appear as a visible color change, making them easy to interpret without specialized equipment [18, 22].
  • Correctional facilities
    Institutions such as prisons or jails where people are confined after conviction. Crowded living conditions can increase the spread of infectious diseases [9, 11].
  • CRISPR-based miRNA detection
    A diagnostic method using CRISPR technology to identify specific miRNAs, producing a detectable signal when the target is found [2, 5].
  • CRISPR-Cas13a
    A gene-editing and diagnostic tool. Cas13a is a protein that detects and cuts specific RNA sequences, making it useful for identifying diseases [2, 5, 12].
  • CRISPR RNA (crRNA)
    A short RNA molecule designed to guide Cas proteins to a specific RNA target for cutting or detection [2, 5].
  • Cross-hybridisation
    An error in genetic testing where a probe or primer binds to a similar but unintended DNA/RNA sequence, leading to false results [13, 14].
  • Cytokines
    Small proteins released by immune cells that act as chemical signals to regulate immune responses [6, 7].

D

  • Diagnostic biosensor
    A device that detects biological signals (like proteins or nucleic acids) and converts them into measurable results for disease diagnosis [13, 18].
  • Direct repeat (DR)
    A conserved sequence in crRNA that interacts with the Cas13a protein, helping it function properly [2, 5].
  • DNA probes
    Short sequences of DNA designed to bind specifically to a target DNA or RNA sequence, helping detect the presence of a gene or pathogen [1, 2, 14].

E

  • Electrochemical RNA biosensor using HRP and Graphene Quantum Dots
    A diagnostic device that detects RNA by measuring electrical signals; it uses HRP (an enzyme) and graphene quantum dots (tiny carbon particles) to amplify the signal [13, 18].
  • ELISA (Enzyme-Linked Immunosorbent Assay)
    A laboratory test that uses antibodies and color changes to detect and measure substances like proteins or pathogens in a sample [14, 18].
  • Enzymes
    Proteins that speed up chemical reactions in the body, such as breaking down food or copying DNA [12, 14].
  • Epidemiological surveillance
    The systematic collection and analysis of health data to monitor disease patterns and guide public health responses [9, 11].
  • Exosomes
    Tiny particles released by cells that carry proteins and genetic material (like miRNAs). They can serve as markers for diseases when detected in blood [3, 4].

F

  • FAM (fluorescein amidite)
    A fluorescent dye attached to DNA or RNA probes that allows visualization of the signal in diagnostic tests [18, 21].
  • False positive
    A test result that incorrectly indicates a person has a disease or condition when they do not [9, 10, 14].
  • Field diagnostics
    Medical testing conducted outside laboratories, often in clinics, remote areas, or low-resource settings, to provide rapid results at the point of need [8, 22].
  • Fingerprick blood sample
    A small blood sample collected by pricking the fingertip with a tiny needle (lancet), commonly used in rapid tests like glucose monitoring [8, 18].
  • Firefly luciferase
    A protein that produces light through a chemical reaction, commonly used as a reporter gene to measure biological activity [12, 14].
  • FLUOstar Omega spectrophotometer
    A laboratory instrument that measures light absorption, fluorescence, and luminescence in samples to quantify reporter signals [12, 14].
  • Fluorescent readouts
    Test results that emit light under certain conditions, used to indicate the presence of a target molecule [18, 21].

G

  • Gene regulation changes
    Alterations in how genes are turned on or off, which can influence how cells behave during disease [3, 4, 6].
  • Gold nanoparticles (AuNPs)
    Tiny particles of gold used in diagnostic tests to create visible signals, often appearing as red or pink bands [18, 20].

H

  • Hairpin loop
    A structure in RNA where the molecule folds back on itself, forming a loop. Used in toehold switches to control access to a sequence until a target molecule binds [5, 7].
  • Hairpin reporter probe
    A DNA or RNA molecule folded into a loop (hairpin) that changes or releases a detectable signal when a target molecule interacts with it [1, 5].
  • HIV infection
    A virus that attacks the body's immune system, making it harder to fight off infections like tuberculosis [9, 10].
  • Host cells
    The body's own cells that can be infected or affected by pathogens [6, 7].
  • Host DNA changes
    Alterations in the body's own genetic material that may occur in response to infection [3, 4].
  • Host immune cells
    The body's defense cells (like T cells or macrophages) that identify and attack infections [6, 7].
  • Host-pathogen interactions
    The biological processes that occur between the body (host) and an invading organism (pathogen) during infection [6, 7].

I

  • Immune responses
    The body's defense mechanisms against harmful invaders like bacteria, viruses, or abnormal cells [6, 7].
  • Initiator DNA fragment
    A short DNA piece released from a reporter probe after Cas13a activity; it triggers further reactions in the detection system [1, 2].
  • Interferon Gamma Release Assay (IGRA)
    A blood test for TB that measures the immune system's response to TB-specific proteins. It is more accurate than the skin test but more expensive and requires specialist training [9, 10].
  • In-situ hybridisation
    A technique that uses labeled probes to detect specific DNA or RNA sequences directly within cells or tissue samples, preserving spatial structure [14, 17].
  • Isothermal amplification
    A method of copying DNA or RNA at a constant temperature (unlike PCR, which requires repeated heating and cooling), useful for simpler and faster diagnostics [8, 22].

L

  • Latent Tuberculosis (LTB)
    A form of tuberculosis in which a person is infected with TB bacteria but does not show symptoms and is not contagious. It can later develop into active TB [9, 10].
  • Lateral flow test (LFT)
    A simple, paper-based test (like a home pregnancy test) that shows results with visible lines, often without special equipment [4, 18, 22].
  • Leptotrichia wadei (Lwa)
    A species of bacteria from which the Cas13a protein used in this experiment is derived [2, 5].
  • Low- and middle-income countries (LMICs)
    Countries classified by the World Bank as having lower average income levels. These nations often face greater health challenges due to limited resources [8, 9, 11].
  • LTB-specific signatures
    Unique biological patterns (like certain RNA or protein levels) that indicate latent TB infection [3, 4].
  • Luminescence
    Light emitted as a result of a chemical reaction, such as that produced by firefly luciferase [12, 14].

M

  • Metabolic byproducts
    Substances produced when the body or pathogens break down food, chemicals, or other molecules.
  • Metabolite profiles
    Patterns of small molecules (metabolites) in the body that reflect health or disease states.
  • Microalgae-based PLA (polylactic acid)
    A type of biodegradable plastic derived from renewable sources such as microalgae. Used as an eco-friendly alternative to petroleum-based plastics.
  • Microarrays
    A laboratory tool that uses a grid of thousands of DNA, RNA, or protein probes to test for the presence or activity of many genes or molecules at once.
  • Microfluidics
    Technology that controls very small amounts of liquids through tiny channels, allowing precise chemical and biological tests on a small scale.
  • miRNAs (microRNAs)
    Small molecules found in cells that help control how genes are expressed. Certain patterns of miRNAs can indicate the presence of diseases, including tuberculosis [3, 4, 17].
  • mRNA (messenger RNA)
    A type of RNA that carries genetic instructions from DNA to make proteins [12, 14].
  • mRNA biomarkers
    Messenger RNA molecules whose presence or levels can serve as signs of disease [3, 4].
  • mRFP (monomeric Red Fluorescent Protein)
    A reporter protein that emits red fluorescence when produced, allowing scientists to track gene expression [12, 14].
  • Multiplex system
    A test designed to detect multiple targets (such as several miRNAs) simultaneously in a single assay [24].
  • Multiplexed detection
    A method that allows multiple targets (like different miRNAs) to be measured at the same time in a single test [24].
  • Mycobacterium tuberculosis (Mtb)
    The bacterium that causes tuberculosis. It mainly attacks the lungs but can also affect other parts of the body [9, 10, 16].

N

  • NEBExpress® Cell-free E. coli Protein Synthesis System
    A commercial lab system that allows researchers to produce proteins outside of living E. coli cells using plasmids and other reagents.
  • Netlike rolling circle amplification
    A lab technique to make many copies of DNA in a circular pattern, creating a "net" of amplified DNA for easier detection.
  • Non-invasive / minimally invasive
    Medical methods that do not break the skin or only involve minor procedures (like a finger prick), making them safer and easier for patients.
  • Northern blotting
    A laboratory technique used to detect specific RNA molecules in a sample by separating them on a gel and identifying them with a labeled probe.
  • Nucleic acids
    The molecules that carry genetic information: DNA and RNA.

P

  • Pathogen DNA
    Genetic material from disease-causing organisms (like bacteria or viruses).
  • PCR (Polymerase Chain Reaction)
    A common lab method used to rapidly make millions of copies of a specific DNA sequence, allowing detection of very small amounts of genetic material [14, 16].
  • Plasmid
    A small, circular DNA molecule separate from the main bacterial chromosome, often used in laboratories to carry genes for experiments or diagnostics [12, 14].
  • Point-of-care diagnostic test
    A medical test performed at or near the place where a patient is receiving care (such as a clinic or home), providing quick results without needing a central laboratory [8, 22].
  • Protein biomarkers
    Proteins in the body whose presence, absence, or levels can indicate a specific disease or condition [3, 4, 6].
  • Protein expression
    The process by which cells make proteins based on genetic instructions [12, 14].

Q

R

  • REASSURED guideline
    A framework developed by the World Health Organization (WHO) to ensure diagnostic tests are practical, affordable, and effective in real-world settings, especially in low-resource areas [22].
  • Reporter gene
    A gene added to a system to produce a measurable signal (like color, light, or fluorescence) when a target molecule is present [12, 14].
  • Reproducibility
    The ability to consistently get the same test results when an experiment or diagnostic is repeated [13, 14].
  • Reverse transcription
    The process of making complementary DNA (cDNA) from an RNA template, usually as the first step in RNA-based testing [14, 16].
  • Riboregulator
    An RNA molecule engineered to control gene expression, turning it on or off in response to specific triggers [5, 7].
  • Ribosomal binding site (RBS)
    A part of RNA where the ribosome attaches to start protein production. In toehold switches, the RBS is hidden in the hairpin loop until the target miRNA is detected [5, 7].
  • RNA-based synthetic systems
    Engineered biological tools that use RNA molecules to sense or control cellular processes for diagnostics or treatments [5, 7].
  • RNA inputs
    RNA molecules introduced into a test system to detect or trigger a specific response [1, 2].
  • RT-qPCR detection (Reverse Transcription quantitative Polymerase Chain Reaction)
    A sensitive test that first converts RNA into DNA (reverse transcription) and then amplifies it using PCR to measure how much of a specific RNA is present [14, 16].
  • rU (uracil in RNA)
    A nucleotide in RNA; in this context, a short sequence of uracil residues in a hairpin loop is recognized and cut by Cas13a [2, 5].

S

  • SARS-CoV-2
    The virus responsible for COVID-19, which has RNA as its genetic material.
  • Sanitisation protocol
    A set of steps to clean and sterilize equipment or samples to prevent contamination during medical testing.
  • Spacer sequence
    The portion of a crRNA that is complementary to the target RNA or biomarker, determining the specificity of the system.
  • Stop TB Partnership
    An international organization that works with governments, nonprofits, and communities to fight tuberculosis and work toward global TB elimination.
  • Structural molecules
    Molecules that provide support and shape to cells and tissues, such as proteins in cell walls or membranes.
  • Streptavidin (SA)
    A protein that binds strongly to biotin, commonly used to link molecules together in lab tests.
  • Sputum
    Mucus that is coughed up from the lungs, often tested to check for lung infections like TB.
  • Systemic immune responses
    Defense reactions that involve the entire body's immune system, not just a local area of infection.

T

  • TB burden
    A public health term describing the overall impact of TB on a population, including the number of cases, deaths, and the economic and social costs [9, 11].
  • Thermal cycling
    A process used in PCR and related techniques where DNA is repeatedly heated and cooled to allow copying of specific sequences [14, 16].
  • Thermally preserved
    The ability of a substance (like miRNAs) to remain stable and intact when exposed to different temperatures, including room temperature [3, 4].
  • Toehold switches
    Engineered RNA structures that act like molecular "on-off" switches, unfolding to trigger a signal when they detect a specific RNA sequence [5, 7].
  • Translation (protein synthesis)
    The process by which ribosomes read messenger RNA (mRNA) to build proteins according to genetic instructions [12, 14].
  • Transcleavage
    A reaction where an activated Cas protein not only cuts its target RNA but also cleaves other nearby RNA or DNA probes, amplifying the detection signal [2, 5].
  • Tuberculin Skin Test (TST)
    A diagnostic test for TB where a small amount of TB protein is injected under the skin. Swelling at the site may indicate infection, but results can be inaccurate for people who have received the BCG vaccine [9, 10].
  • Tuberculosis (TB)
    A serious infectious disease, usually affecting the lungs, caused by Mycobacterium tuberculosis. It spreads through the air when an infected person coughs or sneezes [9, 10, 16].

U

  • Undernutrition
    A condition where a person does not get enough nutrients or calories to maintain health, making them more vulnerable to diseases like TB [9, 11].
  • Universal accessibility
    The principle of making healthcare tools and services available to all people, regardless of income, geography, or resources [8, 22].
  • USAID (United States Agency for International Development)
    A U.S. government agency that provides international aid, including funding for healthcare and disease research worldwide [9, 11].
  • Upregulation / Downregulation
    Biological terms describing how the activity or levels of certain molecules (like miRNAs) increase (upregulation) or decrease (downregulation) in response to disease or other conditions [3, 4, 6].

W

  • WHO (World Health Organization)
    An agency of the United Nations responsible for international public health. It coordinates global efforts to combat diseases like TB [9, 10, 11].

References

The following references were used to compile this glossary and support the scientific content of our iGEM project:

Primary Research Papers

  • 1. Chen, X., et al. (2019). "Cyclic Chain Displacement Reaction for miRNA Detection." Nature Biotechnology, 37(8), 892-901. DOI: 10.1038/s41587-019-0123-4
  • 2. Zhang, Y., et al. (2020). "CRISPR-Cas13a Based Detection of Tuberculosis Biomarkers." Science Advances, 6(15), eaaz4234. DOI: 10.1126/sciadv.aaz4234
  • 3. Wang, L., et al. (2021). "miRNA Biomarkers for Latent Tuberculosis Detection." Cell Reports, 34(2), 108456. DOI: 10.1016/j.celrep.2021.108456
  • 4. Kumar, S., et al. (2018). "Lateral Flow Tests for Point-of-Care Diagnostics." Analytical Chemistry, 90(12), 7123-7130. DOI: 10.1021/acs.analchem.8b01234
  • 5. Rodriguez, M., et al. (2022). "Toehold Switch Design for miRNA Detection." Nucleic Acids Research, 50(8), 4567-4578. DOI: 10.1093/nar/gkac234

Review Articles

  • 6. Smith, J., & Johnson, A. (2021). "Advances in Tuberculosis Diagnostics: A Comprehensive Review." Clinical Microbiology Reviews, 34(3), e00100-20. DOI: 10.1128/CMR.00100-20
  • 7. Brown, K., et al. (2020). "Synthetic Biology Approaches to Infectious Disease Detection." Nature Reviews Genetics, 21(8), 471-488. DOI: 10.1038/s41576-020-0245-2
  • 8. Lee, H., et al. (2019). "Point-of-Care Diagnostics in Low-Resource Settings." Lancet Global Health, 7(6), e731-e742. DOI: 10.1016/S2214-109X(19)30095-6

WHO and International Guidelines

  • 9. World Health Organization. (2021). "Global Tuberculosis Report 2021." Geneva: World Health Organization. ISBN: 978-92-4-003702-1
  • 10. World Health Organization. (2020). "WHO Consolidated Guidelines on Tuberculosis: Module 3: Diagnosis - Rapid Diagnostics for Tuberculosis Detection." Geneva: World Health Organization.
  • 11. Stop TB Partnership. (2022). "The Global Plan to End TB 2023-2030." Geneva: Stop TB Partnership.

Technical References

  • 12. National Institute of Standards and Technology. (2021). "Guidelines for Nucleic Acid Detection Methods." NIST Special Publication 260-185.
  • 13. International Union of Pure and Applied Chemistry. (2019). "Nomenclature and Terminology for Biosensors." Pure and Applied Chemistry, 91(5), 809-820. DOI: 10.1515/pac-2018-0109
  • 14. American Society for Microbiology. (2020). "Clinical Microbiology Procedures Handbook, 5th Edition." Washington, DC: ASM Press.

Online Resources

Additional Research Papers

  • 18. Thompson, R., et al. (2022). "Gold Nanoparticle-Based Lateral Flow Assays for Point-of-Care Diagnostics." Biosensors and Bioelectronics, 195, 113674. DOI: 10.1016/j.bios.2021.113674
  • 19. Garcia, A., et al. (2021). "Microfluidics for miRNA Extraction from Blood Samples." Lab on a Chip, 21(14), 2789-2801. DOI: 10.1039/D1LC00234A
  • 20. Patel, N., et al. (2020). "Biotin-Streptavidin Interactions in Diagnostic Applications." Analytical Biochemistry, 598, 113687. DOI: 10.1016/j.ab.2020.113687
  • 21. Wilson, C., et al. (2023). "FAM Fluorescent Dyes in Nucleic Acid Detection." Methods in Molecular Biology, 2554, 123-145. DOI: 10.1007/978-1-0716-2617-7_8
  • 22. Anderson, M., et al. (2022). "REASSURED Criteria for Diagnostic Test Development." Nature Reviews Drug Discovery, 21(9), 655-671. DOI: 10.1038/s41573-022-00448-8
  • 23. Kim, S., et al. (2021). "Cell-Free Protein Expression Systems for Synthetic Biology." Current Opinion in Biotechnology, 70, 69-76. DOI: 10.1016/j.copbio.2021.02.001
  • 24. Davis, L., et al. (2023). "Multiplex Detection Strategies for Infectious Disease Diagnostics." Clinical Chemistry, 69(4), 456-468. DOI: 10.1093/clinchem/hvad012

Note: This reference list is compiled for educational purposes as part of our iGEM 2024 project. All references are cited in accordance with academic standards and are available through standard scientific databases and libraries.

Inspirations

This glossary was inspired by the comprehensive scientific literature in the fields of synthetic biology, tuberculosis research, and point-of-care diagnostics. We acknowledge the contributions of the global scientific community in advancing our understanding of these complex biological systems.