Semantic resources project/Antibodies/Preliminary work/Methods

AlzForum Methods Glossary

Immunoprecipitation
Abbreviations: IP

Names: Immunoprecipitation

AlzForum definition: When an antibody has multiple binding sites, each specific to a separate epitope, an antibody, antigen chain may form which grows to be heavy enough to precipitate out of the solution. Applications of imunoprecipitation can be for immunodiffusion (ID) and for Immunoblotting (IB).

MeSH Term: Immunoprecipitation

OBI Term: http://purl.obolibrary.org/obo/OBI_0000690

See Also: Immunoprecipitation (Wikipedia)

** Protein complex immunoprecipitation
Abbreviations: Co-IP

Names: Protein complex immunoprecipitation

Definition: Immunoprecipitation of intact protein complexes is known as co-immunoprecipitation (Co-IP). Co-IP works by selecting an antibody that targets a known protein that is believed to be a member of a larger complex of proteins. By targeting this known member with an antibody it may become possible to pull the entire protein complex out of solution and thereby identify unknown members of the complex.Co-IP is a powerful technique that is used regularly by molecular biologists to analyze protein-protein interactions. (form Wikipedia)

MeSH Term: N.A.

OBI Term: N.A.

** Chromatin immunoprecipitation
Abbreviations: ChIP

Names: Chromatin immunoprecipitation

Definition: Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a particular protein of interest. This technique gives a picture of the protein-DNA interactions that occur inside the nucleus of living cells or tissues. The in vivo nature of this method is in contrast to other approaches traditionally employed to answer the same questions. (form Wikipedia)

MeSH Term: http://www.nlm.nih.gov/cgi/mesh/2009/MB_cgi?mode=&term=Chromatin+immunoprecipitation

OBI Term: N.A.

** Radio immunoprecipitation
Abbreviations: RIP

Names: Radio immunoprecipitation, Radioimmunoprecipitation Assay

Definition: Sensitive assay using radiolabeled antigens to detect specific antibodies in serum. The antigens are allowed to react with the serum and then precipitated using a special reagent such as Protein A sepharose beads. The bound radiolabeled immunoprecipitate is then commonly analyzed by gel electrophoresis (from AlzForum).

MeSH Terms: Farr Assay; Radioimmunoprecipitation Analysis (link)

OBI Term: N.A.

Immunodiffusion
Abbreviations: DID (Double immunodiffusion) or IDD (Immuno double diffusion) or ID (Ouchterlony, or Immunodiffusion)

Names: Double immunodiffusion, Immuno double diffusion, Ouchterlony (Ouchterlony double immuno diffusion), Immunodiffusion

AlzForum definition: A technique designed to establish the identity of unknown protein samples based on the interaction between antibodies and antigens in solution. Anti-serum, antigens, and/or an unkown substance are each placed into separate wells and allowed to diffuse radially outward through an agarose gel. As the expanding rings come in contact with each other, insoluble antigen/antibody complexes precipitate out of solution forming readily recognizable patterns.

MeSH Term: Immunodiffusion

OBI Term: N.A.

See Also: Immunodiffusion (Wikipedia), Ouchterlony (Wikipedia)

Alan edited definition
Notes: Wikipedia page is a bust. The names field in the alzforum name subclasses other than the last - they need separate definitions. I decided to search for the term in pubmed. Found the earliest reference (where it says page 1 of 2457 and has an input box, I put in 2457. The link to paper had a first page in lieu of abstract. I read the first paragraph and then paraphrased, adding the superclass assay to the def. The definition source is in obi specified format described here.

Definition "An assay in which an antigen and antibodies diffuse through semisolid matrixes and in which a visible precipitate forms indicating that antibody and antigen bind."

Definition source: "PMID:13696667#Interpretation of immunodiffusion tests, AJ Crowle, Annual Review of Microbiology, Vol. 14: 161-176 (doi:10.1146/annurev.mi.14.100160.001113)"

Definition editor: Person:Alan Ruttenberg

Immunoblotting
Abbreviations: IB, IEB

Names: Immunoblotting, Immunoelectroblotting

Definition: A general term for Western blots, dot blots, slot blots, etc. After a gel separation the immobilized proteins are transferred to a filter paper or blotting paper via a sandwich involving the gel, nitrocelulose paper/blotting paper, and filter paper, either by electrophoresis under a low current for 20-30 minutes or by capillary blotting from wet to dry filter paper. The three popular blotting methods are Southern Blot, for DNA cut with restriction enzymes and probed with radioactive DNA, Northern Blot, for RNA probed with radioactive RNA or DNA, and Western Blot, for proteins (antigens) probed with proteins (antibodies). See Western blots (WB) (from AlzForum).

MeSH Terms: Dot Immunoblotting; Electroimmunoblotting; Immunoblotting, Dot; Immunoblotting, Reverse; Immunoelectroblotting; Reverse Immunoblotting (link)

OBI Term: http://purl.obolibrary.org/obo/OBI_0000690

** Western blotting
Abbreviations: WP

Names: Western blotting, Western blot

Definition: Western Blot The common means for probing proteins with radioactive or enzymatically-tagged antibodies after they have been spatialy separated and immobilized, typically on an agarose or poly-acrylamide gel (see IEP), and transfered to a filter paper or blotting paper through electrophoresis or capillary blotting. The antibody probe is typically enzyme-conjugated by cross-linking to the enzyme, and is added to the paper in buffer and incubated for several hours. Extra probe is washed away, and the filter paper is then soaked in a solution that is a substrate for the enzyme and results in an insoluble colored deposit (from AlzForum).

MeSH Terms: Blot, Western; Immunoblot, Western; Immunoblotting, Western; Western Blot; Western Blotting; Western Immunoblot; Western Immunoblotting (link)

OBI Term: N.A.

%% Uses: Gel electrophoresis (By far the most common type of gel electrophoresis employs SDS-PAGE)

%% Detects: Proteins

See Also: Western blot (Wikipedia)

Citation: Renart J, Reiser J, Stark GR (1979). "Transfer of proteins from gels to diazobenzyloxymethyl-paper and detection with antisera: a method for studying antibody specificity and antigen structure.". Proc Natl Acad Sci U S A. 76 (7): 3116–3120. doi:10.1073/pnas.76.7.3116. PMID 91164.

Citation: Towbin H, Staehelin T, Gordon J. (1979). "Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications.". Proc Natl Acad Sci U S A. 76 (9): 4350–4354. doi:10.1073/pnas.76.9.4350. PMID 388439

Alan edited definition
Notes: I edited the wikipedia first paragraph, slightly changing the wording to give it an explicit genus, and with other minor style changes.

Definition: A western blot is an assay whose objective is to detect a target type of protein in a given sample of tissue homogenate or extract. In it, gel electrophoresis is used to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are detected using antibodies specific to the target protein

Definition source: WEB:http://en.wikipedia.org/wiki/Western_blot@2009/10/04

Definition editor: Person:Alan Ruttenberg

Example of usage: PMID:388439#Towbin H, Staehelin T, Gordon J. (1979). "Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications.". Proc Natl Acad Sci U S A. 76 (9): 4350–4354. doi:10.1073/pnas.76.9.4350.

Example of usage: PMID:91164#Renart J, Reiser J, Stark GR (1979). "Transfer of proteins from gels to diazobenzyloxymethyl-paper and detection with antisera: a method for studying antibody specificity and antigen structure.". Proc Natl Acad Sci U S A. 76 (7): 3116–3120. doi:10.1073/pnas.76.7.3116

Electrophoresis
Abbreviations: EP

Names: Electrophoresis

Definition: EP is used to separate a complex mixture of proteins with respect to the presence or other characteristics of one or more proteins to which they bond. The separation is through migration of the charged molecules across a support medium and in response to an electric field. The medium is typically a gel but may be paper, potato starch, cellulose acetate, agarose or polyacrylamide gel; the last two gels are the most commonly used media. Agarose is usually made into dilute gels for separating large macromolecules, proteins and protein complexes. Polyacrylamide gels (see PAGE) are used at higher concentrations, to separate most proteins and small oligonucleotides. Proteins of known molecular weight are often included in the initial mixture, to serve as calibrating markers (from AlzForum). .

MeSH Terms: Electrophoresis; Isotachophoresis (link)

OBI Term: http://purl.obolibrary.org/obo/OBI_0600053

See Also: Electrophoresis (Wikipedia), Colorful Electrophoresis (University of Utah)

** Gel electrophoresis
Abbreviations: N.A.

Names: Gel electrophoresis

Definition: Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or protein molecules using an electric current applied to a gel matrix (from Wikipedia).

MeSH Terms: N.A.

OBI Term: N.A.

%% Detects: Proteins (Proteins are usually analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), by native gel electrophoresis, by quantitative preparative native continuous polyacrylamide gel electrophoresis (QPNC-PAGE), or by 2-D electrophoresis), DNA, RNA (Gel electrophoresis of large DNA or RNA is usually done by agarose gel electrophoresis)

See Also: Gel electrophoresis (Wikipedia), agarose gel electrophoresis (Wikipedia), 2-D electrophoresis (Wikipedia), QPNC-PAGE (Wikipedia), SDS-PAGE (Wikipedia)

Immunofluorescence
Abbreviations: IF

Names: Immunofluorescence

Definition: The use of a fluorescene conjugated antibody or secondary antibody to visualize an antigen when viewed under a microscope or flow cytometer. For fluorescent microscopy, the specimen is fixed to a slide and then the flourescent labelled antibody (primary or secondary) is added and the mixture is incubated, rinsed and examined with a fluorescent microscope using filters appropriate for excitation and emission of the particular fluorochrome, can also be used with confocal microscopy (see CM). For FAC, single cell suspensions are fixed in solution and then a fluorescent-labeled antibody is added. The mixture is inserted through a flow cell and each cell scatters some of the light, and labeled cells emit fluorescent light excited by the laser beam. Results are recorded as peaks and scatter lines corresponding to wavelenth (see FAC) (from AlzForum).

MeSH Terms: Coon's Technic; Coon's Technique; Fluorescent Antibody Technic; Fluorescent Antinuclear Antibody Test; Fluorescent Protein Tracing; Immunofluorescence; Immunofluorescence Technic; Immunofluorescence Technique (link)

OBI Term: N.A.

See Also: Immunofluorescence (Wikipedia)

Immunohistochemistry
Abbreviations: IHC, IH

IHC(F), IH(F) 	Immunohistochemistry, Frozen sections - IHC(P), IH(P) 	Immunohistochemistry, Paraffin sections

Names: Immunohistochemistry

Definition: IHC is the process of staining tissues with antibodies and developing the result with histologic labels such as enzymes or fluorochromes. The tissues are rapidly frozen or fixed and embedded [paraffin (P)], then sectioned, stained and examined under a light or fluorescent microscope. The antibodies are labeled with enzymes or fluorescent tags, either by directly conjugating the antibody or by using tagged secondary antibodies. The enzymes labeled specimens are developed with a dye. It is possible to develop the specimens with more than one antibody by using different colored dyes or different fluorochromes having different wavelengths. See Immunofluorescence (IF) (from AlzForum).

MeSH Terms: Immunocytochemistry; Immunogold Technics; Immunogold Techniques Entry Term; Entry Term	Immunogold-Silver Techniques; Immunohistocytochemistry; Immunolabeling Technics; Immunolabeling Techniques (link)

OBI Term: N.A.

See Also: Immunohistochemistry (Wikipedia)

Citation: Sternberger LA, Hardy PH Jr, Cuculis JJ, Meyer HG. (1970). "The unlabeled antibody enzyme method of immunohistochemistry: preparation and properties of soluble antigen-antibody complex (horseradish peroxidase-antihorseradish peroxidase) and its use in identification of spirochetes". J Histochem Cytochem. 1970 May;18(5):315-33. PMID: 4192899.

Immunocytochemistry
Abbreviations: IC

Names: Immunocytochemistry

Definition: The use of antibodies to detect proteins within cells. Often the antibodies are bound with electron-opaque markers, so as to visualize the proteins under an electron microscope. Typically the cells are embedded or frozen, then sectioned and labelled with antibodies and markers (from AlzForum).

MeSH Terms: Immunocytochemistry; Immunogold Technics; Immunogold Techniques Entry Term; Entry Term	Immunogold-Silver Techniques; Immunohistocytochemistry; Immunolabeling Technics; Immunolabeling Techniques (link)

OBI Term: N.A.

See Also: Immunocytochemistry (Wikipedia)

Note: Immunocytochemistry differs from immunohistochemistry in that the former is performed on samples of intact cells that have had most, if not all, of their surrounding extracellular matrix removed. This includes cells grown within a culture, deposited from suspension, or taken from a smear. In contrast, immunohistochemical samples are sections of tissue (biology), where each cell is surrounded by tissue architecture and other cells normally

Enzyme-linked Immuno Sorbant Assay
Abbreviations: ELISA

Names: Enzyme-linked Immuno Sorbant Assay

Definition: ELISA typically involves a two-stage incubated immuno reaction. First the target antigen binds with a solid phase antibody. Non-bound materials are washed away and an enzyme-labeled antibody, called a conjugate, binds to form a 'sandwich' complex. Finally the antigen-antibody is introduced to a substrate where a chromogen is used to give a color change indicating the presence of the antibody (from AlzForum).

MeSH Terms: ELISA (link)

OBI Term: http://purl.obolibrary.org/obo/OBI_0000661

See Also: ELISA (Wikipedia)

Citation: Engvall E, Perlman P (1971). "Enzyme-linked immunosorbent assay (ELISA). Quantitative assay of immunoglobulin G". Immunochemistry 8 (9): 871–4. doi:10.1016/0019-2791(71)90454-X. PMID 5135623.

Citation: Van Weemen BK, Schuurs AH (1971). "Immunoassay using antigen-enzyme conjugates". FEBS Letters 15 (3): 232–6. doi:10.1016/0014-5793(71)80319-8. PMID 11945853. .

Radio Immunoassay
Abbreviations: RIA

Names: Radio Immunoassay, Radioimmunoassay

Definition: In this highly sensitive test a radioactive isotope is bound to the antigen and the amount of antigen is quantified by a gamma-ray counter. The antigen is initially bound to the walls of a test tube or microplate, serum is added which binds to the antigen and the bound antibody is detected by adding a radiolabeled ligand. The addition of various concentrations of unlabeled ligand and the measurement of the various ratios of bound labeled to free labeled ligand produces a calibration curve for determining the ligand concentration. (from AlzForum).

MeSH Terms: Radioimmunoassay (link)

OBI Term: N.A.

See Also: Radioimmunoassay (Wikipedia)

Citation: Yalow RS, Berson SA. Immunoassay of endogenous plasma insulin in man. J Clin Invest 1960;39:1157-75. PMID 13846364