glossary of terms

AGROBACTERIUM TUMEFACIENS: a soil pathogen that is a very popular tool in biotechnology, used to transform plants with a foreign gene. This bacterium originally infects a plant with its own DNA to cause a crown gall or a tumour, but in the lab, is modified so that the tumour-inducing bacterial DNA is replaced with a transgene of interest. See entry for transgenic, and the Methodology section.

ADAPTIVE IMMUNITY: one of the two branches of the body's immune response, the other being innate immunity. Adaptive immunity is not present at birth, and is developed through exposure to pathogens and foreign antigens. Key players in this response are the B cells and T cells of the immune system. Key characteristics of adaptive immunity is that it only kicks in the second time an antigen is presented, and is much more rapid and effective the second time around.

ANTIBODY: also known as immunoglobulin. A soluble Y-shaped molecule secreted by B cells of the immune system, sometimes known as a B cell receptor (BCR) when presented on the surface of the B cells. Contain two light and two heavy chains that are held together by disulfide bonds. The variable region at the ends of the antibody are unique to each and responsible for antigen recognition. The constant region of the antibody is used to classify it into one of the five immunoglobulin isotypes (IgA, IgD, IgE, IgG, and IgM).

ANTIGEN: molecule that is recognized by the immune system; can be of immune or non-immune origin.

ANTIGEN PRESENTING CELL (APC): cell that displays foreign antigen complexed with MHC on its surface. Often involved in the body's immune response against invading pathogens, such as viruses, in which foreign peptides are chopped up and displayed on infected cells' surface to signal their infected state. These cells will be targeted by the immune system for killing, while the antigen displayed is used to produce antibodies.


AUTOANTIBODIES: antibodies generated by the body's immune system against components of the body, such as cell surface receptors. Production of these types of antibodies is associated with the development of autoimmune diseases (see below).

AUTOIMMUNITY: broadly speaking, when the immune system is unable to differentiate between foreign antigen and self-antigen, and mount attacks upon self-antigen. Since self-antigen is always present, this often leads to chronic disease, such as Type I diabetes, arthritis, and various forms of lupus.

B CELLS: a class of lymphocyte, B cells mature in the bone marrow, unlike thymocytes. They are involved in humoral immunity, as opposed to cell-mediated immunity. These cells are responsible for the production of antibodies that recognise exogenous antigens. B cells, once activated (by T cell help), are also known as plasma effector cells and can function as professional antigen presenting cells (APC).

BONE MARROW: soft, highly vascularized connective tissue enclosed within the harder outer shell of the bones of the body. There are two types of bone marrow: yellow (fatty) marrow, and red (blood cell related) marrow. Yellow marrow consists mostly of fat cells and is found in the center of the long bones of the body, such as those in the leg. In contrast, red marrow is only found in certain flat bones of the body, such as the shoulder blades, and is involved in blood cell generation (hematopoeisis). These cells include white blood cells (leukocytes) and red blood cells (erythrocytes). Red marrow is also the site of B cell maturation. Here, immature B cells expressing immunoglobulins on their surface are "processed" in a mechanism similar to that of T cell selection in the thymus: B cells expressing antibodies that do not respond to antigens are destroyed, as are antibodies that respond to self-antigens, which prevents autoimmune diseases.

β(beta)-PANCREATIC CELLS: a cell population found in the renal glands (kidney) in the region of the islets of Langerhan. It produces insulin in response to high sugar levels.

CARTILAGE: a type of connective tissue that acts as to absorb contact and reduce wearing of the bone. It has a dense matrix which is created by the chondrocytes, the cell population that exists in the cartilage.

cDNA: DNA of a gene, with all introns and regulatory sequences removed. Often used in the expression of recombinant proteins, to avoid the mRNA splicing and translation problems inherent in having introns present in a gene.

CONSTANT REGION: region on the heavy chain of antibodies that are conserved (same) between different antibodies. There are five variants of the constant region, which are used to classify antibodies into their different families.

COMPLEMENT CASCADE: precise sequence of protein activation in the blood, designed to kill infectious pathogens. Complement cascade is usually elicited during an immune response by the recognition of antigens by the immune system. Complement is part of both adaptive immunity and innate immunity.

CHEMOKINES: a subset of cytokines, standing for chemotactic cytokines. They are produced by various cells (at sites of inflammation), that are thought to provide directional cues for the movement of white blood cells, and that include some playing a role in HIV infection because the cell surface receptors to which they bind are also used by specific strains of HIV for entry into cells

COLONY-STIMULATING FACTORS (CSF): a subset of cytokines; for example granulocyte colony-stimulating factor (G-CSF) or granulocyte-macrophage colony-stimulating factor (GM-CSF). These cytokines trigger the growth of certain types of hematopoietic cells, hence the name (i.e. they will stimulate the growth of colonies of cells in vitro). In vivo, they encourage the differentiation of progenitor cells towards certain lineages. G-CSF only encourage commitment to the granulocyte lineage, whereas GM-CSF is responsible for commitment to both the granulocyte and macrophage lineages.

CYTOKINES: soluble proteins secreted by cells of the immune system (usually cells of a hematopoietic lineage), important in the regulation of both the innate and adaptive branches of immune response. Their secretion and production are triggered by hematopoietic cell activation and also as the result of an external physiological insult, such as an infection or a wound. Cytokines are characterised often by biological redundancy; that is, more than one cytokine may effect the same end result. They often act in a very broad-spectrum manner, influencing many aspects of the immune response, such as fighting infection, cell differentiation, inflammation, and tissue repair. Cytokines act by binding to their specific cognate receptor on the surfaces of various cells, and triggering downstream signalling cascades.

CYTOTOXIC T CELLS: these T cells recognise other infected cells of the body and destroy them. They are usually positive for the co-receptor CD8 and so are sometimes known as CD8+ T cells though this association may not always hold true. However, it is always true that CD8+ T cells are MHC class I restricted.

EPISOMAL DNA: DNA possessed by an organism, but not on its chromosomes. This extra DNA is usually present in the form of a small plasmid, or circular strand of DNA.

FIBROBLAST: a cell population that has the ability to create many different types of fibres in connective tissue. They can also differentiate in to specific types of connective tissue cells.

FUSION INHIBITOR: prevents HIV cells from binding to the CD4+T Lymphocytes.

GENE GUN TRANSFER: also known as particle bombardment. This method of transformation coats a microscopic gold particle with DNA and then fires the particle into the nucleus of a cell, hopefully so that the DNA will be integrated into the organism's genomic DNA. See the Methodology section of the site for more.

GLUCAGON: a molecule that is used in the regulation of blood glucose levels. High levels of blood glucose, lead to decreased levels of glucagon. It is secreted by the a pancreatic cells.

GLYCOPROTEIN: this is a large macromolecule comprised of complex sugars and proteins. It can be used for structural integrity, or simply for cell recognition.

HIGHLY ACTIVE ANTIRETROVIRAL THERAPY (HAART): a type of drug regime for tackling HIV. Although it does not completely deplete HIV from the body, it does restore CD4+T lymphocytes to a normal functional level.

HELPER T CELLS: these T cells recognise antigen by professional antigen presenting cells (APC) and in response secrete cytokines to activate immune response in general and also help activate other specific immunological cells. They are usually positive for the co-receptor CD4 and so are sometimes known as CD4+ T cells, but this association is not always true. However, CD4+ T cells are always MHC class II restricted. These T cells are the targets of HIV.

HUMAN LYMPHOCYTE ANTIGENS (HLA): a series of genes found in the MHC.

HUMAN IMMUNODEFICIENCY VIRUS (HIV): a retrovirus that attacks the CD4+ T lymphocytes in the body. This results in decreased immune function. It is transmitted through bodily fluids, such as blood, semen, vaginal fluid and breast milk.

HYPOGLYCEMIA: below normal blood glucose levels.

ISLET CELL CYTOPLASMIC ANTIBODIES (ICCA): antibodies found on the interior of the α and β pancreatic cells, which are found in the Islet of Langerhan.

IMMUNOGLOBULIN: see entry for antibody.

IMMUNOTHERAPY: very generally, the treatment of disease states by manipulating or using the components of the natural immune system.

INNATE IMMUNITY: one of the two branches of the body's immune response, the other being adaptive immunity. Innate immunity is not specific to any type of infection or antigen, and thus is present as soon as one is born to act as a general security system. This is the body's first line of defense, since the adaptive immune response may take much longer to mount. This includes the body's skin or other barriers; macrophages and other phagocytic cells, which do not require prior antigen interaction in order to recognise a foreign molecule and engulf it; and other cells.

INSULIN: a hormone that regulates blood glucose levels and is secreted by the β-pancreatic cells.

INSULIN DEPENDENT DIABETES MELLITUS (IDDM): Type 1 Diabetes in which the patient has an autoimmune response to their β-pancreatic cells, no longer produce insulin, and can no longer regulate their blood sugar levels.

INTERFERON (IFN): a subset of cytokines. There are three families of interferon: α, β, and γ. IFN-α and -β are known as Type I interferons, whereas IFN-γ is known as Type II. These cytokines have a huge range of activity and sometimes the different subfamilies counteract each other. They are involved in cell differentiation, cell proliferation and activation, protection from viruses, etc. They can be secreted by different cells. Interferons are clinically important, foremost in research for the treatment of multiple diseases.

INTERLEUKINS (IL): a subset of cytokines. These cytokines were originally discovered to be secreted by leukocytes, but the term is obsolete now since later it was discovered that other cells secreted them, too. Examples include IL-1, IL-2, IL-4 and IL-10, but there are many more that are produced.

ISLET CELL CYTOPLASMIC ANTIBODIES: antibodies found on the interior of the a and pancreatic cells, which are found in the Islet of Langerhan.

KETONE: a chemical compound that contains a carbonyl group attached to two carbon groups.

KETOACIDOSIS: relates to an increased acid level of the blood.

LEUKOCYTES: also known as white blood cells, this class of hematopoietic cells can be broken down into several other ones including lymphocytes, granulocytes, and monocytes (the latter two also falling into the inclusive nomenclature of myeloid cells). Granulocytes include neutrophils, basophils, and eosinophils, whereas monocytes are also known as macrophages, the most famous example of the phagocytic cell.

LIPOPROTEIN: same as a glycoprotein, only a lipid is attached to the protein molecule in stead.

LYMPHOCYTES: a lineage of hematopoietic cell, also a subset of white blood cells. There are two general classes of lymphocytes: T and B cells. T cells are involved in cell-mediated immunity and B cells are involved in humoral immunity (i.e. antibody production). See their respective entries for more information. This class also includes natural killer (NK) cells but these are not touched upon in our topic.

MAJOR HISTOCOMPATIBILITY COMPLEX (MHC): these molecules encoded by several different genetic loci are the basis of the HLA "blood type" system in addition to the usual A/B/O blood types. These molecules are on the surfaces of cells, and are "docking" sites for antigen to be presented to T cell receptors. Whereas B cells recognise antigens simply via antibodies, T cells only recognise antigen when it is presented to them chopped up into peptide fragments and in the context of MHC. There are two types of MHC, both critical to the immune system:

MHC CLASS I: this class is present on the surfaces of virtually all ennucleated cells of the body. Cells will make them and constantly present both foreign and self-antigens with them. Only CD8+ T cells will recognise MHC class I. If these T cells detect foreign antigen (presented during an infection, for example), they will destroy the cell with the MHC so that the infection goes no further.

MHC CLASS II: this class is only present on the surfaces of a small subset of cells called professional antigen presenting cells (APC). APCs include activated B cells, dendritic cells, sometimes macrophages, etc. These cells will constantly present antigen in the context of MHC class II, which is recognised by CD4+ T cells. If the antigen is foreign, the CD4+ T cell will react by giving the APC "help" to eliminate the infection, and will also trigger a wider immune response, such as complement cascade or cytokines.

MONOCYTES/MACROPHAGES: a phagocytic white blood cell/leukocyte. Monocytes are not terminally differentiated yet, and have also not migrated to their proper tissues. After these lineage commitment events, they are known as macrophages. Essentially, the two are the same. Macrophages are the classic phagocytic blood cell of the body, and usually act as part of the innate immunity to engulf and destroy pathogens.

NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITORS (NRTIs): this inhibits the activity of Reverse Transcriptase.

PANNUS: a sheet of inflammatory granulation tissue that spreads from the synovial membrane and invades the joint in rheumatoid arthritis ultimately leading to fibrous ankylosis .

PROMOTER: a regulatory sequence of DNA preceding (upstream or 5' of) the coding sequence that will usually recruits many transcription factors. The presence of a promoter allows the DNA's transcription to be tightly controlled, upregulated, or downregulated. For example, the cauliflower mosaic virus 35S promoter allows following DNA sequences to have high amounts of constitutive expression.

PROTEASE INHIBITOR: a molecule that inhibits the function of protein degradation molecules.

POLYADENYLATION SIGNAL: at the termination of a coding sequence for a protein (downstream or 3' of the coding DNA), eukaryotic DNA will usually have a polyadenylation signal that allows the transcribed mRNA to have a "tail" of adenine nucleotide repeats. This "polyA tail" confers stability to the mRNA entity, crucial during transport and translation.

rRNA: short for ribosomal RNA; any one of several large RNA molecules that are structural and functional components of ribosomes, which are responsible for translating mRNA codes copied from cellular genes into protein. The ribosome is unique in that it contains both RNA and protein, since most structures in the cell that have enzymatic function are protein-based only.

REGULATORY T CELLS: these T cells are CD4+ and CD25+ and are involved in immune system homeostasis.

REVERSE TRANSCRIPTION: the conversion of RNA to DNA by the use of Reverse transcriptase.

SELECTABLE MARKER: a foreign piece of DNA (usually secondary to another gene of interest on the same vector) that will allow the transformed organism to grow under selective conditions that would usually kill the organism or inhibit its growth. Popular selectable markers include resistance to antibiotics, such as kanamycin. An organism that has this resistance gene will grow in kanamycin, thus easily demonstrating to the scientist or researcher that the organism has indeed successfully taken up the foreign DNA.

SELF-ANTIGENS: molecules that are present on the surface of cells in the body. B cells that recognize these self-antigens are usually destroyed during development to prevent immune responses against oneself, which occurs in autoimmune diseases.

SYNOVIAL MEMBRANE: membrane comprised of synoviocytes that lines the non-articulating surfaces of joints. Normally only about 1 or 2 cell layers thick, it is very delicate. It contains a matrix of hyaluron which provides a small portion of structural integrity.

T CELLS: a class of lymphocyte, T stands for thymus since although T cells are produced initially by the bone marrow like all blood cells, they migrate to the thymus for maturation. T cells are a large part of the immune response, involved in antigen recognition and cell-mediated immunity. There are different types of T cells: cytotoxic T cells, helper T cells, and regulatory T cells.

TRANSFORMATION: the process of changing the genetic material of an organism by adding a foreign transgene to it. Transformation can include both genomic integration of foreign DNA or addition of episomal (i.e. plasmid) DNA.

TRANSGENIC: an organism that has been modified through molecular biology techniques to contain a gene or genes from another organism. This foreign gene is known as a transgene.

THYMUS: small immune-related organ in the throat in which immature T cells undergo both positive and negative selection. In negative selection, T cells that do not react to antigens presented by MHC complexes are destroyed since they are incapable of eliciting an immune response in the future. In contrast, T cells that react to self-antigens presented by MHC complexes are also destroyed to avoid autoimmune diseases; this is called positive selection. B cells undergo similar processes of selection in the bone marrow.

TUMOUR-NECROSIS FACTOR (TNF): primarily this term is used to refer to TNF-α, a cytokine of utmost importance in inflammation, which includes pain, swelling, and redness. Unusually high amounts of TNF-α is characteristic of certain inflammatory autoimmune diseases like arthritis. Treatments of such diseases involves monoclonal antibodies against TNF-α, or other methods of downregulating TNF-α concentration.

VARIABLE REGION: region at the "tips" of antibodies that are unique to each antibody and responsible for antigen recognition.




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