Instruct: Given a question, retrieve relevant documents that answer the question.
Query: What are antigens?
Antigenic variation refers to the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters its surface proteins in order to avoid a host immune response. It is related to phase variation. Immune evasion is particularly important for organisms that target long-lived hosts, repeatedly infect a single host and are easily transmittable. Antigenic variation not only enables immune evasion by the pathogen, but also allows the microbes to cause re-infection, as their antigens are no longer recognized by the host's immune system. When an organism is exposed to a particular antigen (i.e. a protein on the surface of a bacterium) an immune response is stimulated and antibodies are generated to target that specific antigen. The immune system will then "remember" that particular antigen, and defenses aimed at that antigen become part of the immune system’s acquired immune response. If the same pathogen tries to re-infect the same host the antibodies will act rapidly to target the pathogen for destruction. However, if the pathogen can alter its surface antigens, it can evade the host's acquired immune system. This will allow the pathogen to re-infect the host while the immune system generates new antibodies to target the newly identified antigen. Antigenic variation can occur by altering a variety of surface molecules including proteins and carbohydrates. There are many molecular mechanisms behind antigenic variation, including gene conversion, site-specific DNA inversions, hypermutation, as well as recombination of sequence cassettes. In all cases, antigenic variation and phase variation result in a heterogenic phenotype of a clonal population. Individual cells either express the phase-variable protein(s) or express one of multiple antigenic forms of the protein. This form of regulation has been identified mainly, but not exclusively, for a wide variety of surface structures in pathogens and is implicated as a virulence strategy.
Initial studies of mutants revealed that residues on the back side of the central alpha helix were required for super antigenic activity. Changing the histidine at position 135 to alanine caused TSST-1 to be neither lethal or superantigenic. Changes in residues that were in close proximity to H135A, also had the effect of diminishing the lethality and superantigenic quality of these mutants. Although most of these mutants did not result in loss of antigenicity of TSST-1. Tests done using mutagenic TSST-1 toxins indicated that the lethal and superantigenic properties are separable. When Lys-132 in TSST-O was changed to a Glu, the resulting mutant became completely lethal but non superantigenic. The same results, lethal but not superantigenic, were found for TSST-1 Gly16Val. Residues Gly16, Glu132,and Gln 136, located on the back of the back-side groove of the putative TCR binding region of TSST-1, it has been proposed that they are also a part of a second functionally lethal site in the TSST-1.
Luc Antoine Montagnier (; born 18 August 1932) is a French virologist and joint recipient with and of the 2008 Nobel Prize in Physiology or Medicine for his discovery of the human immunodeficiency virus (HIV). A long-time researcher at the Pasteur Institute in Paris, he currently works as a full-time professor at Shanghai Jiao Tong University in China.
This was the first evidence that blood variation exists in humans – it was believed that all humans have similar blood. The next year, in 1901, he made a definitive observation that blood serum of an individual would agglutinate with only those of certain individuals. Based on this he classified human bloods into three groups, namely group A, group B, and group C. He defined that group A blood agglutinates with group B, but never with its own type. Similarly, group B blood agglutinates with group A. Group C blood is different in that it agglutinates with both A and B. This was the discovery of blood groups for which Landsteiner was awarded the Nobel Prize in Physiology or Medicine in 1930. In his paper, he called the specific blood group interactions as isoagglutination, and also introduced the concept of agglutinins (antibodies), which is the actual basis of antigen-antibody reaction in ABO system. He asserted:
Thus, he discovered two antigens (agglutinogens A and B) and two antibodies (agglutinins - anti-A and anti-B). His third group (C) indicated absence of both A and B antigens, but contains anti-A and anti-B. The following year, his students Adriano Sturli and Alfred von Decastello discovered the fourth type (but not naming it, and simply referred to it as "no particular type”).
Transplant rejection occurs when transplanted tissue is rejected by the recipient's immune system, which destroys the transplanted tissue. Transplant rejection can be lessened by determining the molecular similitude between donor and recipient and by use of immunosuppressant drugs after transplant.
The first Diego antigen, Di, was discovered in 1953, when a child in Venezuela died of hemolytic disease three days after birth. Rh and ABO blood type mismatches were soon ruled out, and investigators began searching for a rare blood factor. Red blood cells from the father reacted strongly to blood serum from the mother. Rare blood types known at the time were eliminated, and the new type was classified as a "private" or "family" blood type. The investigators, with the agreement of the father, named the new type after his surname, "Diego". In 1955 investigators found that the Diego family included ancestry from Indigenous peoples of the Americas, and that the Diego factor (Di) was not restricted to the Diego family, but occurred in several populations in Venezuela and elsewhere in South America. Investigators suspected that the Diego factor might be a Mongoloid trait, and tested groups of Native Americans in the United States and people of Chinese and Japanese ancestry, and found Di in those groups. Anti-Di was found in 1967, establishing the Diego group as a two-antigen system. In 1993 the Diego pair of antigens was found to result from a single point mutation (nucleotide 2561) on what is now called the SLC4A1 gene on chromosome 17.
While kidneys can routinely be obtained from human donors, most organs are in short supply leading to consideration of xenotransplants from other species. Pigs are especially likely sources for xenotransplants, chosen for the anatomical and physiological characteristics they share with humans. However, the sugar galactose-alpha-1,3-galactose (αGal) has been implicated as a major factor in hyperacute rejection in xenotransplantation. Unlike virtually all other mammals, humans and other primates do not make αGal, and in fact recognize it as an antigen. During transplantation, xenoreactive natural antibodies recognize αGal on the graft endothelium as an antigen, and the resulting complement-mediated immune response leads to a rejection of the transplant.
The first practical use of blood typing in transfusion was by an American physician Reuben Ottenberg in 1907. And the large-scale application started during the First World War (1914-1915) when citric acid was developed as blood clot prevention. Felix Bernstein demonstrated the correct blood group inheritance pattern of multiple alleles at one locus in 1924. Watkins and Morgan, in England, discovered that the ABO epitopes were conferred by sugars, to be specific, N-acetylgalactosamine for the A-type and galactose for the B-type. After much published literature claiming that the ABH substances were all attached to glycosphingolipids, Finne "et al". (1978) found that the human erythrocyte glycoproteins contain polylactosamine chains that contains ABH substances attached and represent the majority of the antigens. The main glycoproteins carrying the ABH antigens were identified to be the Band 3 and Band 4.5 proteins and glycophorin. Later, Yamamoto's group showed the precise glycosyl transferase set that confers the A, B and O epitopes.
Veterinarians also administer transfusions to other animals. Various species require different levels of testing to ensure a compatible match. For example, cats have 3 known blood types, cattle have 11, dogs have 12, pigs 16 and horses have 34. However, in many species (especially horses and dogs), cross matching is not required before the "first" transfusion, as antibodies against non-self cell surface antigens are not expressed constitutively – i.e. the animal has to be sensitized before it will mount an immune response against the transfused blood.
A supercolony occurs when many ant colonies over a large area unite. They still continue to recognize genetic differences in order to mate, but the different colonies within the super colony avoid aggression. Until 2000, the largest known ant supercolony was on the Ishikari coast of Hokkaidō, Japan. The colony was estimated to contain 306 million worker ants and one million queen ants living in 45,000 nests interconnected by underground passages over an area of . In 2000, an enormous supercolony of Argentine ants was found in Southern Europe (report published in 2002). Of 33 ant populations tested along the stretch along the Mediterranean and Atlantic coasts in Southern Europe, 30 belonged to one supercolony with estimated millions of nests and billions of workers, interspersed with three populations of another supercolony. The researchers claim that this case of unicoloniality cannot be explained by loss of their genetic diversity due to the genetic bottleneck of the imported ants. In 2009, it was demonstrated that the largest Japanese, Californian and European Argentine ant supercolonies were in fact part of a single global "megacolony". This intercontinental megacolony represents the most populous recorded animal society on earth, other than humans. Although a good story, this has proven to be incorrect and no ant colony could reach such an enormous size without the 1 million queen ants collapsing their tiny ant economy due to fighting for the power of the ultimate queen.
A metabolite is the intermediate end product of metabolism. The term "metabolite" is usually restricted to small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones). A primary metabolite is directly involved in normal "growth", development, and reproduction. Ethylene is an example of a primary metabolite produced in large-scale by industrial microbiology. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include antibiotics and pigments such as resins and terpenes etc. Some antibiotics use primary metabolites as precursors, such as actinomycin which is created from the primary metabolite, tryptophan. Some sugars are metabolites, such as fructose or glucose, which are both present in the metabolic pathways.
Amino acids are organic compounds containing amine (-NH) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.
Metabolites are the intermediates and products of metabolism. Within the context of metabolomics, a metabolite is usually defined as any molecule less than 1 kDa in size. However, there are exceptions to this depending on the sample and detection method. For example, macromolecules such as lipoproteins and albumin are reliably detected in NMR-based metabolomics studies of blood plasma. In plant-based metabolomics, it is common to refer to "primary" and "secondary" metabolites. A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function. Examples include antibiotics and pigments. By contrast, in human-based metabolomics, it is more common to describe metabolites as being either endogenous (produced by the host organism) or exogenous. Metabolites of foreign substances such as drugs are termed xenometabolites.
One example of glycoproteins found in the body is mucins, which are secreted in the mucus of the respiratory and digestive tracts. The sugars when attached to mucins give them considerable water-holding capacity and also make them resistant to proteolysis by digestive enzymes.
A typical fire ant colony produces large mounds in open areas, and feeds mostly on young plants and seeds. Fire ants often attack small animals and can kill them. Unlike many other ants, which bite and then spray acid on the wound, fire ants bite only to get a grip and then sting (from the abdomen) and inject a toxic alkaloid venom called solenopsin, a compound from the class of piperidines. For humans, this is a painful sting, a sensation similar to what one feels when burned by fire (hence the name), and the after effects of the sting can be deadly to sensitive people. Fire ants are more aggressive than most native species, so have pushed many species away from their local habitat. One such species that "Solenopsis" ants parasitically take advantage of are bees, such as "Euglossa imperialis", a nonsocial orchid bee species, from which the ants would enter the cells from below the nest and rob the cell's contents. These ants are renowned for their ability to survive extreme conditions. They do not hibernate, but can survive cold conditions, although this is costly to fire ant populations as observed during several winters in Tennessee, where 80 to 90% of colonies died due to several consecutive days of extremely low temperatures.
The Antarctical realm is one of eight terrestrial biogeographic realms. The ecosystem includes Antarctica and several island groups in the southern Atlantic and Indian Oceans. The continent of Antarctica is so cold and dry that it has supported only 2 vascular plants for millions of years, and its flora presently consists of around 250 lichens, 100 mosses, 25-30 liverworts, and around 700 terrestrial and aquatic algal species, which live on the areas of exposed rock and soil around the shore of the continent. Antarctica's two flowering plant species, the Antarctic hair grass ("Deschampsia antarctica") and Antarctic pearlwort ("Colobanthus quitensis"), are found on the northern and western parts of the Antarctic Peninsula. Antarctica is also home to a diversity of animal life, including penguins, seals, and whales.
Toxin-antitoxin systems are typically classified according to how the antitoxin neutralises the toxin. In a type I toxin-antitoxin system, the translation of messenger RNA (mRNA) that encodes the toxin is inhibited by the binding of a small non-coding RNA antitoxin that binds the toxin mRNA. The toxic protein in a type II system is inhibited post-translationally by the binding of an antitoxin protein. Type III toxin-antitoxin systems consist of a small RNA that binds directly to the toxin protein and inhibits its activity. There are also types IV-VI, which are less common. Toxin-antitoxin genes are often inherited through horizontal gene transfer and are associated with pathogenic bacteria, having been found on plasmids conferring antibiotic resistance and virulence.
There are eight major recognized blood groups in horses. Seven of them, A, C, D, K, P, Q, and U, are internationally recognized, with an eighth, T, which is primarily used in research. Each blood group has at least two allelic factors (for example, the A blood group has a, b, c, d, e, f, and g), which can be combined in all combinations (Aa, Afg, Abedg, etc.), to make many different alleles. This means that horses can have around 400,000 allelic combinations, allowing blood testing to be used as an accurate method of identifying a horse or determining parentage. Unlike humans, horses do not naturally produce antibodies against red blood cell antigens that they do not possess; this only occurs if they are somehow exposed to a different blood type, such as through blood transfusion of transplacental hemorrhage during parturition.
These ants are very common in Europe and live in meadows and gardens. They live on a diet of honeydew excreted by aphids and feed on many types of insect and other invertebrates. They will attack any creature that disturbs their nest, but are not as aggressive as the red imported fire ant. They also consume pollen, a phenomenon rarely documented in ants of the temperate zone.
The discovery of the MHC and role of histocompatibility in transplantation was a combined effort of many scientists in the 20th century. A genetic basis for transplantation rejection was proposed in a 1914 Nature paper by C.C. Little and Ernest Tyyzer, which showed that tumors transplanted between genetically identical mice grew normally, but tumors transplanted between non-identical mice were rejected and failed to grow. The role of the immune system in transplant reject was proposed by Peter Medawar, whose skin graft transplants in world war two victims showed that skin transplants between individuals had much higher rejection rates then self-transplants within an individual, and that suppressing the immune system delayed skin transplant rejection. Medawar shared the 1960 Nobel Prize in part for this work.
Dinomyrmex is a monotypic genus of ant containing the species Dinomyrmex gigas or giant forest ant. "D. gigas" is a large species of ant, native to Southeast Asian forests. It is one of the largest ants in existence, measuring in at for normal workers, and for the soldiers. Honeydew makes up 90% of their diet, but they will also consume insects and bird droppings. The ant is an effective forager, utilizing both efficient communication and recruitment. A handful of these ants may meet at night to engage in what has been observed to be ritual battle. These fights can continue for several months.
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
Antibodies are a key component of the adaptive immune response, playing a central role in both recognizing foreign antigens and stimulating an immune response. Antibodies are Y-shaped proteins produced by some B cells and are composed of two regions: an antigen-binding fragment (Fab), which binds to antigens, and a Fragment crystallizable (Fc) region, which interacts with so-called Fc receptors that are expressed on the surface of different immune cell types including macrophages, neutrophils and NK cells. Many immunotherapeutic regimens involve antibodies. Monoclonal antibody technology engineers and generates antibodies against specific antigens, such as those present on tumor surfaces. These antibodies that are specific to the antigens of the tumor, can then be injected into a tumor
Antigenicity is the capacity of a chemical structure (either an antigen or hapten) to bind specifically with a group of certain products that have adaptive immunity: T cell receptors or antibodies (a.k.a. B cell receptors). Antigenicity was more commonly used in the past to refer to what is now known as immunogenicity, and the two are still often used interchangeably. However, strictly speaking, immunogenicity refers to the ability of an antigen to induce an adaptive immune response. Thus an antigen might bind specifically to a T or B cell receptor, but not induce an adaptive immune response. If the antigen does induce a response, it is an 'immunogenic antigen', which is referred to as an immunogen.
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