Cells

1. Methods in cell biology and functional genomics Individualized High throughput Cells DNA FACS Genomics Markers RNA Tissues Transcriptomics In situ hyb Protein Organs Proteomics Immuno techniques Metabolite Metabolomics Organisms Microscopy Structure Wild type Mutant

2. Applications Using Monoclonal and Polyclonal Antibodies • Western Blotting (WB) • Immunoprecipitation (IP) • Immunocytochemistry (ICC) • Immuno electron microscopy (IEM) • Immunofluorescence • Enzyme-Linked Immunosorbent Assay (ELISA) • Flow Cytometry (FC)

3. Antibody Production • Immune response when foreign molecule enters system. • Binds antigen with high specificity and affinity. • Same response can be induced on purpose for specific selection or detection of Your Favorite Antigen (YFA). • Can produce millions of antibodies that recognize YFA. Why Induce on Purpose?

4. Several line of defense offer protection from invaders Plasma Cell Phagocyte

5. Blood Cells (Part 1)

6. Blood Cells (Part 2)

7. Blood Cells (Part 3)

8. Third line of defense consists of a specific response from lymphocytes and antibodies of the immune system. • There are two main types of lymphocytes: B lymphocytes (B cells) and T lymphocytes (T cells) • Both are types of white blood cells produced in bone marrow. They circulate in blood and lymph, and are concentrated in spleen, lymph nodes, and other lymphatic tissues. • Lymphocytes respond to and recognize specific microbes and foreign molecules or antigens (antibody generator) • Antigens include molecules belonging to viruses, bacteria, fungi, protozoa, and parasitic worms, as well as molecules on the surface of pollen and transplanted tissue/organs. • Antibody proteins provide highly specific recognition of foreign invaders.

9. The immune system has two types of responses: the humoral immune response and the cell-mediated immune response.

10. Antigens interact with lymphocytes to initiate the immune response. • Bone marrow produces a large and diverse pool of B and T lymphocytes each with antigen receptor of unique specificity. • The specificity of antigen receptors is so enormous that there will be, at least, one B cell and T cell line capable of dealing with almost any antigen. • Binding of an antigen to the receptor triggers proliferation (clonal selection) of antibody producing effector B (plasma) and T cells, and long-lived memorycells ready to rapidly respond upon future antigen exposure.

11. The graph below shows the time required for antibody production after initial exposure to an antigen (e.g. flu shot). • Notice that upon second exposure (second peak of the blue line) to the same antigen the production of antibodies is both faster and dramatically larger (log scale). • The reason for the rapid and dramatic response upon second exposure to the same antigen is because of the presence of memory B and T cells produced during the first exposure. Second exposure to A and first exposure to B First exposure to A

12. Each B cell produces a unique antibody expressed on its surface. • Antibodies are proteins, immunoglobulins, of two “light” and two “heavy” polypeptides held together by disulfide bonds. • Each polypeptide has a “constant region” and a unique “variable region” composing the antigen binding site. • The range of antibody specificity is accomplished by rearrangements and mutation in genes coding for variable regions. • The “constant region” determines the type, location, and action of the antibody in the immune response. Variable Constant

20. Four types of non-covalent forces operates over a very short distance • ( generally 1 angstrom ) • - The interaction depends on a very close fit between the Ab & Ag.

21. Antibody affinity • is a quantitative measure of binding strength • combined strength of the noncovalent interactions • between a binding site on an Ab & monovalent Ag • Antibody avidity • Incorporates affinity of multiple binding sites • True strength of the Ab-Ag interaction within biological systems • The interaction at one site will increase the possibility • of reaction at a second site • High avidity can compensate for low affinity • ( secreted pentameric IgM has a higher avidity than IgG )

24. Polyclonal Antibody Production antigen boost for 4-8 weeks wait 2 weeks Y Y Y Y Y rabbit bled several times over several weeks and blood containing Ab is tested Y Y Y Y Y Y Y Y Y + Y Y Y Y Y Y Y Y Y Y Y Ab purified from blood

25. Monoclonal Antibody Production 1 2 3 Select for hybridomas. 4 5

26. Monoclonal Antibody Production Immunization with antigen A and a booster immunization three days before they are killed, in order to produce a large population of spleen cells secreting specific antibody. Spleen cells die after a few days in culture. Fusion with immortal myeloma cells to produce a hybridoma. The myeloma cells are sensitive to the hypoxanthine-aminopterin-thymidine (HAT) medium because they lack the enzyme hypoxanthine:guanine phosphoribosyl transferase (HGPRT). The HGPRT gene contributed by the spleen cell allows hybrid cells to survive in the HAT medium, and only hybrid cells can grow continuously in culture because of the malignant potential contributed by the myeloma cells. Individual hybridomas are then screened for antibody production. The cloned hybridoma cells are grown in bulk culture to produce large amounts of antibody.

27. HAT medium contains aminopterin, which blocks DNA de novo synthesis by blocking tetrahydrofolate production. If tetrahydrofolate is not produced, IMP, a precursor for GTP is not produced and therefore blocks DNA synthesis. Hypoxanthiine and Phosphoribosyl pyrophosphate are components of the HAT medium. HGPRT reacts hypoxanthine absorbed from the medium with PRPP, liberating pyrophosphate, to produce IMP by a salvage pathway. So, cells containing HGPRT can grow in the presence of medium containing aminopterin.

28. Monoclonal Specific target Single antibody recognizes single epitope of antigen. Polyclonal Specific target Several antibodies recognize several epitopes of antigen. Monoclonal v. Polyclonal Antibodies antibody antigen antigen epitope epitope

29. Monoclonal Typically produced in mice and rats Antibodies ultimately produced and recovered in cell culture Virtually unlimited resource Polyclonal Produced in larger animals such as rabbits, sheep, goats, donkeys Antibodies recovered from blood at a certain time-point Finite resource Monoclonal v. Polyclonal Antibodies

30. Monoclonal Very specific Can bind antigen within mix of related molecules Polyclonal Tolerant of small changes in antigen Can recognize native and denatured proteins More robust detection because multiple epitopes recognized Monoclonal v. Polyclonal Antibodies

31. Antibodies production Choice of antigen Whole protein peptide small molecule - need to be conjugated or coupled coupling is also done for non-immunogenic proteins coupling agents - BSA, PPD, ovalbumin, keyhole limpet hemacyanin (KLH) Use peptide, if: Protein is conserved Site-directed antibodies are needed Budget is not a problem Use protein, if: Budget is a problem Antibodies for native protein is required

32. Antibodies production Adjuvants non-specific stimulators of immune response Need to satisfy following two properties: prevent rapid catabolism of antigen -mineral oil or aluminium hydroxide precipitates (ii) substance to stimulate immune response by inducing lymphokines production and a local inflammatory response Heat killed bacteria or lipo poly saccharide (LPS) Freund’s adjuvants (FA), (FCA) (FIA)