Chapter 9-Molecular Diagnostics

1. Chapter 9-Molecular Diagnostics Enzyme-Linked Immunosorbent Assay (ELISA) Monoclonal Antibodies DNA Diagnostic Systems (DNA fingerprinting) Molecular Diagnosis of Genetic Disease (RFLPs, SNP genotyping, genotyping by sequencing)

2. Old vs. New Molecular Diagnostics • Old: grow cells/pathogen->test • Such growth can be a problem as it is sometimes slow, costly, and specific • New: direct test (either immunological or DNA based) • Detection must be: specific, sensitive, and simple (fast and automatable are also nice)

3. E E E E Y Y Y Y Fig. 9.1 Enzyme-Linked Immunosorbent Assay (ELISA): immunological detection A. Bind sample to the support (commonly plastic or a membrane) B. Add primary antibody; wash C. Add secondary antibody-enzyme conjugate; wash D. Add substrate enzyme linked secondary antibody bound primary antibody antigenic site Y Y colorless substrate Y Y Target molecule colored product i i i i i i i i i i i i i i i Support

4. Fig. 9.2 Target antigens and polyclonal versus monoclonal antibodies 4 3 2 Target antigen with various antigenic determinants (epitopes) 5 1 7 6 Polyclonal antibodies are made against and react with multiple antigenic sites (epitopes) on a target antigen. Monoclonal antibodies are directed against a particular antigenic site.

5. Fig. 9.4 Procedure for producing a monoclonal antibody to protein XNote: B lymphocytes or B cells produce antibodies but do not reproduce in culture. Some B cells can become cancerous and are known as myelomas which can reproduce in culture.See animationshttp://bcs.whfreeman.com/lodish7e/#800911__811944__https://www.youtube.com/watch?v=O-SrPqJuEVghttps://www.youtube.com/watch?v=0A99pk6kpS4

6. Fig. 9.3 Explanation of how HAT medium works Myeloma cells are HGPRT- and will die on HAT media having hypoxanthine, aminopterin (an antifolate), and thymidine. Spleen cells are HGPRT+ , so spleen-myeloma (hybridoma) cells can grow on HAT. (Note: spleen cells by themselves cannot grow in culture.)

7. Table 9.2 Targets for diagnostic monoclonal antibodies • Polypeptide hormones (human chorionic gonadotropin (hCG), growth hormone) • Tumor markers (Prostate-specific antigen) • Cytokines (interleukins 1-8) • Drug monitoring (cyclosporin) • Miscellaneous targets (Vitamin B12) • Infectious diseases (Chlamydia, Herpes, Rubella, Hepatitis B, Legionella, HIV) See examples of hCG pregnancy test: https://www.youtube.com/watch?v=aOfWTscU8YM http://www.sumanasinc.com/webcontent/animations/content/pregtest.html

8. Fig. 9.6 DNA diagnostic systems • Bind ssDNA (target) to membrane • Hybridize to labeled ssDNA or RNA (probe) • Wash membrane to remove unbound probe • Detect hybrid sequences formed between the probe and target DNA (concern: false +s & -s) membrane

9. DNA based diagnosis of Malaria and Typanosomacruzi • A DNA probe from a highly repeated DNA sequence of Plasmodium falciparum, the parasite that causes malaria, is used to screen blood samples via hybridization assays • DNA primers are made against the ends of a 188 bp repeated sequence contained in the protozoan parasite Typanosoma cruzi, the causative agent of Chagas disease and used in a PCR/polyacrylamide gel electrophoresis detection method • Other examples of DNA-based detection: Salmonella typhi (food poisoning), certain E. coli (gastroenteritis), Mycobacterium tuberculosis (tuberculosis), etc.

10. Nonradioactive Hybridization Procedures • Use of biotin-labeled nucleotides in DNA probes instead of 32P, then add avidin (streptavidin) which binds to biotin, and then add biotin attached to an enzyme like alkaline phosphatase for detection (see Fig. 9.11) • Note that fluorescent dyes can also be attached to DNA primers for detecting amplified DNA products (see Fig. 9.12)

11. Nonradioactive Hybridization Procedures

12. Molecular beacon probe . Fig. 9.13 Nonradioactive Hybridization Procedures: Molecular Beacons Target DNA (No Fluorescence) Hybridization Quencher Fluorophore Fluorescence!!!

13. DNA Fingerprinting & Forensics History Uses of DNA Profiling Hypervariable DNA sequences examined (RFLPs, VNTRs, STRs, SNPs, mitochondrial DNA, Y chromosomal DNA) Methods (Southerns & PCR) Statistical considerations Technical considerations Databases and Privacy

14. DNA Fingerprinting • You're 99.9% identical • But of course, you are unique--in a genome of three billion letters, even a 0.1 % difference translates into three million differences. • These differences (or polymorphisms) reside in several places in the genome, often in microsatellites • Examples of such polymorphisms include VNTRs, STRs, RFLPs and SNPs

15. DNA Fingerprinting • Focuses on the 0.1-1.0% of human DNA that is unique • First described in 1985 by Dr. Alec Jeffreys in England • DNA evidence is admissible in courts • Labs such as Cellmark Diagnostics and Lifecodes Corporation are examples of companies which provide such DNA evidence to courts, but states and many U.S. cities have labs for DNA fingerprinting • Have any of you worked in a crime lab?

16. Uses of DNA fingerprinting • Paternity testing • Identification of criminals (e.g. murderers, rapists, letter bombers) • Immigration disputes (family relationships) • Identification of deceased individuals with mutilated or decomposed bodies (e.g., the military, 9/11 victims) • Identifying the sperm donor who “decorated” Monica Lewinsky’s blue dress

17. How is DNA fingerprinting done? • DNA obtained from hair, semen, blood, sweat, saliva, bone or any other tissue (often found at a crime scene) • Can be done by southern blotting with an appropriate probe or by a PCR method using appropriate primers • Can use single locus probes/primers or multilocus probes/primers • DNA can be resolved on a gel or by a capillary electrophoresis system

18. Sequences examined in DNA fingerprinting • VNTRs-variable number tandem repeats; composed of 8-80 bp repeat units (e.g., [GCGCAATG]n) which are tandemly repeated so that the overall length is 1-30 kb • STRs-short tandem repeats; composed of 2-7 bp repeat units (e.g., [AC]n) which are tandemly repeated so that the overall length is less than 1 kb • RFLPs-restriction fragment length polymorphisms • SNPs-single nucleotide polymorphisms • Mitochondrial DNA-maternal inheritance, tends to be more stable than nuclear DNA • Y chromosome DNA- passed from father to son

19. DNA fingerprinting: an example • D1S80, a VNTR located on human chromosome 1, contains a 16 bp repeat unit • The number of repeats varies from one individual to the next, and is known to range from 14-41

20. Some examples of DNA fingerprinting • Paternity cases • Crime scenes

23. Determining the probability of a match • Relies on statistics • Analysis depends upon your ethic background (i.e. African American, Caucasian, Hispanic Asian, etc.)

25. Technical Considerations • Preserve the integrity of DNA sample • Avoid DNA contamination & degradation • Avoid incomplete digestions if REs are used • Use standard hybridization conditions • Use standard PCR primers and procedures • Gel analysis is less reproducible than capillary electrophoresis of PCR products • Difficulties in interpreting bands on a gel or X-ray film

26. DNA databases • Already in place in the FBI for convicted felons (i.e., CODIS-COmbined DNA Index System, involves 13 STR loci) and the Dept. of Defense for armed service personnel and the Virginia saliva and blood bank of convicted felons • A national DNA database has been suggested. What do you think? • Could current or potential employers or insurance companies base decisions they make on this kind of data?

27. Fig. 9.20 Real Time PCR • A way to quantitate DNA in a PCR • Involves the use of SYBR green dye • SYBR green only binds to and fluoresces with dsDNA

28. Fig. 9.16 Bacterial biosensors • One example involves using Pseudomonas fluorescens (genetically engineered for bioluminescence) to monitor pollutants • If pollutants are present in a sample, then cell death occurs and “the light goes out” lux genes in the chromosomal DNA

29. Fig. 9.5 Bacterial biosensors (another example) • Green fluorescent protein (GFP) can be used a reporter gene under the control of some inducible promoter (e.g., one that responds to some environmental signal such as a toxin) • If the signal is present GFP will be produced

30. Molecular Diagnosis of Genetic Disease • Cystic fibrosis • Sickle-cell anemia • (see Fig. 9.28)

31. Genetic Testing for Traits, Diseases, and Ancestry (SNPs, PCR, DNA Sequencing) 23 and me https://www.23andme.com/ or https://www.youtube.com/watch?v=Naona1y_I2U Ancestry.com http://www.ancestry.com/ Sure Genomics http://www.suregenomics.com/ And many other companies http://isogg.org/wiki/List_of_DNA_testing_companies Ethical Implications: see https://www.youtube.com/watch?v=ICdWvlZFkdE