Instruct: Given a question, retrieve passages that answer the question.
Query: What are antigens?
In immunology, antigens (Ag) are structures (aka substances) specifically bound by antibodies (Ab) or a cell surface version of Ab ~ B cell antigen receptor (BCR). The term antigen originally described a structural molecule that binds specifically to an antibody only in the form of native antigen. It was expanded later to refer to any molecule or a linear molecular fragment after processing the native antigen that can be recognized by T-cell receptor (TCR). BCR and TCR are both highly variable antigen receptors diversified by somatic V(D)J recombination. Both T cells and B cells are cellular components of adaptive immunity. [1] The Ag abbreviation stands for an anti</b>body gen</b>erator. [2]
Immunoassays rely on the ability of an antibody to recognize and bind a specific macromolecule in what might be a complex mixture of macromolecules. In immunology the particular macromolecule bound by an antibody is referred to as an antigen and the area on an antigen to which the antibody binds is called an epitope.
According to the National Cancer Institute, a tumor antigen vaccine is a "vaccine made of cancer cells, parts of cancer cells, or pure tumor antigens (substances isolated from tumor cells)". A tumor antigen vaccine may stimulate the body's immune system to find and kill cancer cells. As such, tumor antigen vaccines are a type of cancer immunotherapy.
Tumor antigen vaccines work the same way that viral vaccines work, by training the immune system to attack cells that contain the antigens in the vaccine. The difference is that the antigens for viral vaccines are derived from viruses or cells infected with virus, while the antigens for tumor antigen vaccines are derived from cancer cells. Since tumor antigens are antigens found in cancer cells but not normal cells, vaccinations containing tumor antigens should train the immune system to target cancer cells not healthy cells. Cancer-specific tumor antigens include peptides from proteins that are not typically found in normal cells but are activated in cancer cells or peptides containing cancer-specific mutations. Antigen-presenting cells (APCs) such as dendritic cells take up antigens from the vaccine, process them into epitopes, and present the epitopes to T-cells via Major Histocompatibility Complex proteins. If T-cells recognize the epitope as foreign, the adaptive immune system is activated and target cells that express the antigens.
Precipitation occurs with most antigens because the antigen is multivalent (i.e. has several antigenic determinants per molecule to which antibodies can bind). Antibodies have at least two antigen binding sites (and in the case of Immunoglobulin M there is a multimeric complex with up to 10 antigen binding sites), thus large aggregates or gel-like lattices of antigen and antibody are formed. Experimentally, an increasing amount of antigen is added to a constant amount of antibody in solution. Initially at low antigen concentration, all of the antibody is contained in the precipitate. This is called the antibody-excess zone (i.e. prozone phenomenon). As more antigen is added, the amount of protein precipitated increases until the antigen/antibody molecules are at an optimal ratio. This is known as the zone of equivalence or equivalence point. When the amount of antigen in solution exceeds the amount of antibody, the amount of precipitation will decrease. This is known as the antigen excess zone.
The name 'HLA-DP' originally describes a transplantation antigen of MHC class II category of the major histocompatibility complex of humans, however this antigen is an artifact of the era of organ transplantation. HLA DP functions as a cell surface receptor for foreign or self antigens. The immune system surveys antigens for foreign pathogens when presented by MHC receptors (like HLA-DP). The MHC Class II antigens are found on antigen presenting cells (APC)(macrophages, dendritic cells, and B-lymphocytes). Normally, these APC 'present' class II receptor/antigens to a great many T-cells, each with unique T-cell receptor (TCR) variants. A few TCR variants that recognize these DQ/antigen complexes are on CD4 positive T-cells. These T-cells, called T-helper (T) cells, can promote the amplification of B-cells that recognize a different portion of the same antigen. Alternatively, macrophages and other cytotoxic lymphocytes consume or destroy cells by apoptotic signaling and present self-antigens. Self antigens, in the right context, form a suppressor T-cell population that protects self tissues from immune attack or autoimmunity.
In the late 1960s, scientist began reacting sera from patients with rejecting transplants to donor or 'third party' tissues. Their sera (the liquid part of the blood when blood clots) was sensitized to the cells from donors - it was "alloreactive". By testing different anti-sera from recipients they were able to uncover some with unique reactivities. As a result, scientists were able to identify a few antigens. At first the first antigens were called the Hu-1 antigens and tentatively tagged as gene products of the Human equivalent of the mouse histocompatibility locus (H2). In 1968, it was discovered that matching these antigens between kidney donor and recipient improved the likelihood of kidney survival in the recipient. The antigen list still exists, although it has been reorganized to fit what we have since learned about genetics, refined, and greatly expanded.
Tumor antigens are those antigens that are presented by MHC class I or MHC class II molecules on the surface of tumor cells. Antigens found only on such cells are called tumor-specific antigens (TSAs) and generally result from a tumor-specific mutation. More common are antigens that are presented by tumor cells and normal cells, called tumor-associated antigens (TAAs). Cytotoxic T lymphocytes that recognize these antigens may be able to destroy tumor cells.[15]
HLA-DQ (DQ) is encoded on the HLA region of chromosome 6p21.3, in what was classically known as the "D" antigen region. This region encoded the subunits for DP,-Q and -R which are the major MHC class II antigens in humans. Each of these proteins have slightly different functions and are regulated in slightly different ways.
Agglutination, using blood agglutinins known as hemagglutinins, is used diagnostically to identify blood types of human beings based on the reaction between the erythrocyte (Red blood cell) antigens and agglutinins . Human erythrocytes have only two types of antigens (Antigen A and B) expressed in different combinations to give either erythrocytes that express only antigen A, antigen B, antigen A and B together or no antigen at all. When erythrocytes are exposed to hemagglutinins (anti-A and Anti-B antibodies), those expressing antigen A or B coagulate upon contacting anti-A and anti-B hemagglutinins respectively. Erythrocytes expressing both antigens coagulate upon contacting either anti-A or anti-B hemagglutinins while those not expressing any antigen do not coagulate upon contact with any hemagglutinin. This technique serves as a quick and effective method for identifying the blood type of a person and it is essential when blood transfusion has to be performed quickly to replenish lost blood.
The H gene of the ABO system encodes a fucosyltransferase that adds fucose to type 2 precursor substances on the surface of RBCs to make H antigen. The h gene is an amorph. If no further modifications are made to the H antigen, the person is type O. When the A gene product acts on the H antigen and adds an N-acetylgalactosamine, the A antigen results and the person is type A. When the B gene product acts on the H antigen to add a galactose, the B antigen results and the person is type B.
Immunodominance is the immunological phenomenon in which immune responses are mounted against only a few of the antigenic peptides out of the many produced. That is, despite multiple allelic variations of MHC molecules and multiple peptides presented on antigen presenting cells, the immune response is skewed to only specific combinations of the two. Immunodominance is evident for both antibody-mediated immunity and cell-mediated immunity. Epitopes that are not targeted or targeted to a lower degree during an immune response are known as subdominant epitopes. The impact of immunodominance is immunodomination, where immunodominant epitopes will curtail immune responses against non-dominant epitopes.
Antigen-presenting cells such as dendritic cells, can have up to six different types of MHC molecules for antigen presentation. There is a potential for generation of hundreds to thousands of different peptides from the proteins of pathogens. Yet, the effector cell population that is reactive against the pathogen is dominated by cells that recognize only a certain class of MHC bound to only certain pathogen-derived peptides presented by that MHC class.
Antigens from a particular pathogen can be of variable immunogenicity, with the antigen that stimulates the strongest response being the immunodominant one. The different levels of immunogenicity amongst antigens forms what is known as dominance hierarchy.
"'Antigen processing" or cytosolic' pathway is an immunological process that prepares antigens for presentation to special cells of the immune system called T lymphocytes. It is considered to be a stage of antigen presentation pathways. This process involves two distinct pathways for processing of antigens from an organism's own (self) proteins or intracellular pathogens (e.g. viruses), or from phagocytosed pathogens (e.g. bacteria); subsequent presentation of these antigens on class I or class II major histocompatibility complex (MHC) molecules is dependent on which pathway is used. Both MHC class I and II are required to bind antigen before they are stably expressed on a cell surface. MHC I antigen presentation typically (considering cross-presentation) involves the endogenous pathway of antigen processing, and MHC II antigen presentation involves the exogenous pathway of antigen processing. Cross-presentation involves parts of the exogenous and the endogenous pathways but ultimately involves the latter portion of the endogenous pathway (e.g. proteolysis of antigens for binding to MHC I molecules).
Initially, genetic mapping of the mouse class I antigens suggested the existence of multiple class I loci in the "H2" complex. Soon, however, inconsistencies in the assignment of certain antigens to loci signaled that something was amiss with the "H2" maps, as they were then drawn. Klein and Donald C. Shreffler solved the problem by demonstrating that a given antigen could be present on molecules controlled by different loci. Taking this finding into account, they were able to reduce the number of the class I loci to two, "H2K" and "H2D". This "two-locus model" played a n important part in subsequent interpretations of the "Mhc". The model was also consistent with the results of earlier Klein's PhD work, in which he discovered that immune selection for a loss of certain H2 antigens on somatic cells was accompanied by the loss of some but not other unselected antigens. In this respect, the antigens fell into two groups as if carried by two different molecules. The discovery of the class II genes had been fitted into the model by the demonstration that they mapped between the "H2K" and the "H2D". Shreffler also demonstrated the existence of another locus mapping between the two class I loci. It coded for what he called the "serum serological" or Ss protein, present in a soluble form in the blood fluid phase, in contrast to the class I and class II antigens, which were expressed on cell surfaces. At that stage, the "H2" complex could be divided into four regions: class I ("H2K")...Class II ("Ir-1")..."Ss"...Class I ("H2D").
The specificity of the H antigen is determined by the sequence of oligosaccharides. More specifically, the minimum requirement for H antigenicity is the terminal disaccharide Fucose-Galactose, where the fucose has an alpha(1-2)linkage. This antigen is produced by a specific fucosyl transferase that catalyzes the final step in the synthesis of the molecule. Depending upon a person's ABO blood type, the H antigen is converted into either the A antigen, B antigen, or both. If a person has group O blood, the H antigen remains unmodified. Therefore, the H antigen is present more in blood type O and less in blood type AB.
The underlying tumor causes circulating and tissue-bound antibodies to direct themselves against antigens in the plakin family, which are involved in the intracellular attachment structures in various levels of the skin/respiratory tract/membranes (keeping skin tissue together throughout the body). The number of target antigens varies on a case by case basis. The variability is likely what accounts for the different presentations of PNP. Through immunoprecipitation, target antigens have been found to include desmoglein-3, desmoglein-1, envoplakin, periplakin, desmoplakin 1, desmoplakin 2, and bullous pemphigoid antigen I.
Lymphocytes are one of the five kinds of white blood cells or leukocytes, circulating in the blood. 
Although mature lymphocytes all look pretty much alike, they are extraordinarily diverse in their functions. The most abundant lymphocytes are:
B lymphocytes (often simply called B cells) and
T lymphocytes (likewise called T cells).
B cells are produced in the bone marrow.
The precursors of T cells are also produced in the bone marrow but leave the bone marrow and mature in the thymus (which accounts for their designation).
Link to drawing showing the organs of the immune system. 
Each B cell and T cell is specific for a particular antigen. What this means is that each is able to bind to a particular molecular structure.
The specificity of binding resides in a receptor for antigen:
the B cell receptor (BCR) for antigen and
the T cell receptor (TCR) respectively.
Both BCRs and TCRs share these properties:
They are integral membrane proteins.
They are present in thousands of identical copies exposed at the cell surface.
They are made before the cell ever encounters an antigen.
They are encoded by genes assembled by the recombination of segments of DNA.
How antigen receptor diversity is generated.
They have a unique binding site.
This site binds to a portion of the antigen called an antigenic determinant or epitope.
The binding, like that between an enzyme and its substrate depends on complementarity of the surface of the receptor and the surface of the epitope.
The binding occurs by non-covalent forces (again, like an enzyme binding to its substrate).
Successful binding of the antigen receptor to the epitope, if accompanied by additional signals, results in:
stimulation of the cell to leave G0 and enter the cell cycle.
Repeated mitosis leads to the development of a clone of cells bearing the same antigen receptor; that is, a clone of cells of the identical specificity.
BCRs and TCRs differ in:
their structure;
the genes that encode them;
the type of epitope to which they bind.
B Cells
Goulmy did groundbreaking research on the role of antigens in organ and stem cell transplantation. She is the pioneer of the so-called Minor Transplantation Antigens in men. Minor antigens can induce strong immune reactions. She discovered the H-Y minor antigen encoded by the Y-chromosome (1976) and the autosomally encoded HA-1 antigen (1983). She then described the polymorphism and the population frequencies of several autosomal minor antigens. Crucial was her work on the differential expression of minor antigens showing either overall expression on all body cells, such as the male specific H-Y antigens, or restricted expression on solely blood and blood cancer cells, such as HA-1. Goulmy was the first to describe the chemical structure of the human minor antigens (1995). In 1996 she demonstrated the crucial role of minor antigens in the outcome of organ and stem cell transplantation. In 1997 she launched new concepts for immunotherapy of blood cancer applying the blood and cancer cell specific minor antigens, such as HA-1, for tumor specific treatment. The basis for the translation ‘from the lab to the clinic’ of these cancer and patient specific treatment was laid in her laboratory. Hereby minor antigens, such as HA-1, are used as ‘vaccin’ to boost the anti-blood cancer reaction in the patients' body.
The Kauffman–White classification scheme is the basis for naming the manifold serovars of "Salmonella". To date, more than 2600 different serotypes have been identified. A "Salmonella" serotype is determined by the unique combination of reactions of cell surface antigens. The "O" antigen is determined by the outermost portion of the Lipopolysaccharide (LPS) and the "H" antigen is based on the flagellar (protein) antigens. 
There are two species of "Salmonella": "Salmonella bongori" and "Salmonella enterica". "Salmonella enterica" can be subdivided into six subspecies.
The process to identify the serovar of the bacterium consists of finding the formula of cell antigens which represent the variations of the bacteria. First of all, the use of the agglutination method on slides is required in order to get the antigen formula. The agglutination between the antigen and the antibody is made with a specific antisera, which reacts with the antigen to produce a mass. The antigen O is tested with a bacterial suspension from an agar plate whereas the antigen H is tested with a bacterial suspension from a broth culture. The scheme is used to classify the serovar depending on its antigen formula obtained with the reaction of the agglutination.
The ABO blood group system involves two antigens and two antibodies found in human blood. The two antigens are antigen A and antigen B. The two antibodies are antibody A and antibody B. The antigens are present on the red blood cells and the antibodies in the serum. Regarding the antigen property of the blood all human beings can be classified into 4 groups, those with antigen A (group A), those with antigen B (group B), those with both antigen A and B (group AB) and those with neither antigen (group O). The antibodies present together with the antigens are found as follows:
In Cross-presentation, peptides derived from extracellular proteins are presented in the context of MHC class I. The cell starts off with the exogenous pathways but diverts the antigens (cytosolic diversion) to the endogenous pathway. This can allow the cell to skip the parts of the endogenous pathway that involve synthesis of antigens from the antigenic genes with cellular machinery upon infection, because the endogenous pathway can involve infection before being able to present antigens with MHC I, and cross-presentation saves them the effort needed for that and allows the professional antigen-presenting cells (dendritic cells) to process and present antigens without getting infected, which does not tend to happen to dendritic cells and is quite common scenario of antigen-processing using the endogenous pathway. Not all antigen-presenting cells utilize cross-presentation.
Antigens are "targeted" by antibodies. Each antibody is specifically produced by the immune system to match an antigen after cells in the immune system come into contact with it; this allows a precise identification or matching of the antigen and the initiation of a tailored response. The antibody is said to "match" the antigen in the sense that it can bind to it due to an adaptation in a region of the antibody; because of this, many different antibodies are produced, each able to bind a different antigen while sharing the same basic structure. In most cases, an adapted antibody can only react to and bind one specific antigen; in some instances, however, antibodies may cross-react and bind more than one antigen.
Chemically, heterophile antigens are composed of lipoprotein-polysaccharide complexes. There is a possibility of there being identical chemical groupings in the structure of mucopolysaccharids and lipids.
Example: Forssman antigen, cross reacting microbial antigen
so antibodies to these antigens produced by one species cross react with antigens of other species. It is widely present in some plants bacteria animal and birds. However it is not present in rabbit. Therefore antibodies are produced in rabbit serum by injecting the antigen (antiforssman antibodies).
Langerhans' cells are particular type of dendritic cells present in non lymphoid tissues together with interstitial cells.When these cells (in an immature state) come in contact with antigenic cells or disease causing viruses etc. these cells produce an inflammatory stimulus and start antigen processing and move toward lymph nodes where these APCs present antigen to mature T lymphocytes.
T-dependent antigen – Antigens that require the assistance of T cells to induce the formation of specific antibodies.
T-independent antigen – Antigens that stimulate B cells directly.
HLA Naming can be quite confusing at first. All alleles start with "HLA", signifying they are part of the human MHC genes. The next portion (HLA-A or HLA-B) identifies which gene the allele is a modification of. The first two numbers (HLA-A*02) signifies what antigen type that particular allele is, which typically signifies the serological antigen present. In other words, HLAs with the same antigen type (HLA-A*02:101 and HLA-A*02:102) will not react with each other in serological tests. The next set of digits (HLA-A*02:101) indicates what protein the allele codes for, and these are numbered sequentially in the order they are discovered. Any HLA that has a different number here produces a different protein (AKA has a nucleotide change that replaces an amino acid with another). The third set of numbers (HLA-A*02:101:01) indicates an allele variant that has a different DNA sequence but produces the same protein as the normal gene. The final set of numbers (HLA-A*02:101:01:01) is used to designate a single or multiple nucleotide polymorphism in a non-coding region of the gene. The final aspect of HLA naming is a letter (HLA-A*02:101:01:01L). There are six letters, each with a different meaning.
Heterophile antigens are antigens of similar nature, if not identical, that are present in different tissues in different biological species, classes or kingdoms. Usually different species have different antigen sets but the hetereophile antigen is shared by different species. Other heterophile antigens are responsible for some diagnostic serological tests such as: