Alanine transaminase - Alanine transaminase is a transaminase enzyme. It is also called serum glutamate pyruvate transaminase (SGPT). It is commonly measured clinically as a part of a diagnostic liver function test, to determine liver health.

Albumin - One of the liver function tests. Albumin is the most abundant plasma protein in humans and is essential to the proper distribution of body fluids. It is made specifically by the liver; levels are decreased in chronic liver disease, such as cirrhosis.

Alkaline Phosphatase - An enzyme responsible for removing phosphate groups from many types of molecules, including nucleotides, proteins, and alkaloids. It is present in all tissues throughout the entire body, but is particularly concentrated in liver, bile duct, kidney, bone, and the placenta. One of the liver function tests, elevated Alkaline Phosphatase indicates the presence of biliary problems.

Allele - Usually alleles are sequences that code for a gene, but sometimes the term is used to refer to a non-gene sequence. An individual's genotype for that gene is the set of alleles it happens to possess. example is the gene for blossom colour in many species of flower — a single gene controls the colour of the petals, but there may be several different versions (or alleles) of the gene. One version might result in red petals, while another might result in white petals. The resulting colour of an individual flower will depend on which two alleles it possesses for the gene and how the two interact.

ALT - Alanine transaminase.

AMA - Anti-mitochondrial antibody.

Amino acids - A molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids, a class of amino acids sharing the same basic formula. Amino acids are found in all forms of life.

Anion - Negatively charged ions

Antibody - Also known as immunoglobulin; proteins that are found in blood or other bodily fluids used by the immune system to identify and neutralize foreign objects, such as bacteria and viruses. Antibodies are produced by a kind of white blood cell called a B cell. Antibodies come in different varieties known as isotypes or classes.

Antigen - Also known as immunogen. A molecule that sometimes stimulates an immune response. The word originated from the notion that they can stimulate antibody generation.

Anti-mitochondrial antibody - Antibodies (immunoglobulins) formed against mitochondria. The presence of AMAs is indicative of Primary Biliary Cirrhosis, present in about 95% of all cases.

Apoptosis - A form of programmed cell death in multicellular organisms. Contrast with necrosis, a form of traumatic cell death resulting from acute cellular injury. Apoptosis, in general, confers advantages during an organism's life cycle.

Ascites - Fluid retention in the abdominal cavity most commonly due to cirrhosis and severe liver disease.

Aspartate transaminase - Aspartate transaminase (AST) also called serum glutamic oxaloacetic transaminase (SGOT). One of the liver function tests, its ratio with respect to ALT is sometimes used to determine the cause of liver damage.

AST - See Aspartate transaminase.

Autoimmunity - The failure of an organism to recognize its own constituent parts (down to the sub-molecular levels) as "self", which results in an immune response against its own cells and tissues. Any disease that results from such an aberrant immune response is termed an autoimmune disease.

B cell - B cells are lymphocytes that play a large role in the humoral immune response as opposed to the cell-mediated immune response that is governed by T cells. B cells produce antibodies against antigens and are produced in bone-marrow.

BEC - Biliary epithelial cell. See cholangiocyte.

Betaretrovirus - Retrovirus of type B or type C. Example: Mouse Mammary Tumor Virus

Bile - A bitter, yellow or green alkaline fluid secreted by hepatocytes in the liver. It is stored in the gallbladder between meals and upon eating is discharged into the duodenum where it excretes waste and aids the process of digestion of lipids.

Bile acid - Steroid acids found predominantly in the bile of mammals. In humans taurocholic acid, and glycocholic acid (derivatives of cholic acid) represent approximately eighty percent of all bile acids. The two major bile acids are cholic acid, and chenodeoxycholic acid. Bile acids are produced in the liver by the oxidation of cholesterol, conjugated (with either the amino acid taurine or glycine, or a sulfate, or a glucuronide) and are stored in the gallbladder. They serve multiple functions, which include: elimination of cholesterol from the body, driving the flow of bile to eliminate catabolites from the liver, serving to emulsify lipids and fat soluble vitamins in the intestine, and (likely) to aid reducing the bacteria flora found in the small intestine and biliary tract. Bile acids are potentially toxic to cells and their levels are tightly regulated. They function directly as signaling molecules in the liver and the intestines by activating a nuclear hormone receptor known as FXR. This results in inhibition of bile acid synthesis in the liver when bile acid levels are too high. Emerging evidence associates FXR activation with alterations in triglyceride metabolism, glucose metabolism and liver growth.

Bile duct - Any of a number of long tube-like structures that carry bile in the liver.

Bile salt - Also known as "bile acid".

Biliary - Pertaining to bile ducts.

Biliary epithelial cell - Also known as a "cholangiocyte".

Bilirubin - A yellow breakdown blood product processed by the liver into bile, its levels are elevated in certain diseases. It is responsible for the yellow color of bruises and the brown color of feces. One of the liver function tests, measurements of total bilirubin and direct bilirubin are compared to pinpoint the source of the problem when a patient is jaundiced.

Biogeography - The study of the distribution of biodiversity over space and time. It aims to reveal where organisms live, at what abundance, and why.

Cell-mediated immunity - An immune response that involves the activation of macrophages, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen and does not involve antibodies.

Chemokine - A family of small cytokines, or proteins secreted by cells. Some chemokines are considered pro-inflammatory and can be induced during an immune response to promote cells of the immune system to a site of infection.

Cholangiocyte - Cholangiocytes are the epithelial cells of the bile duct. These cells modify bile by water reabsorption and through secretion under the influence of the hormones secretin and somatostatin.

Cholestasis - Congestion of the bile ducts; a condition where bile cannot flow from the liver to the duodenum.

Cirrhosis - A consequence of chronic liver disease characterized by replacement of liver tissue by fibrotic scar tissue

Cytokines - A group of proteins and peptides used in organisms as signaling compounds. These chemical signals are similar to hormones and neurotransmitters and are used to allow one cell to communicate with another.

Cytotoxic - Toxic to cells; cytotoxic agents include chemical substances and immune cells (white blood cells/leukocytes).

Deoxyribonucleic acid - A nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

DNA - Deoxyribonucleic acid

Ductopenia - Bile duct loss.

Duodenum - The first of the three sections of the small intestine, the duodenum is a hollow jointed tube about 25-30 cm long connecting the stomach to the jejunum. The duodenum is largely responsible for the breakdown of food in the small intestine.

Encephalopathy - A potentially reversible neuropsychiatic abnormality in the setting of liver failure.

Enzyme - A protein that initiates/accelerates a chemical reaction.

Epidemiology - The study of factors affecting the health and illness of populations, serving as the foundation and logic of interventions made in the interest of public health and preventive medicine. Considered a cornerstone methodology of public health research, it is highly regarded in evidence-based medicine for identifying risk factors for disease and determining optimal treatment approaches to clinical practice.

Epithelial - Pertaining to any tissue that lines the cavities and surfaces of structures throughout the body, composed of layers of cells.

Epitope - The unique part of an antigen recognized by an antibody (B cell or T cell).

Etiology - The cause of disease.

Eukaryote - An organism whose cells are organized into complex structures by internal membranes and a cytoskeleton.

Farnesoid X receptor - A nuclear hormone receptor with activity similar to that seen in other steroid receptors such as estrogen or progesterone. Chenodeoxycholic acid and other bile acids are the natural ligand for FXR. One of the primary functions of FXR activation is the suppression of cholesterol 7 alpha-hydroxylase (CYP7A1), the rate-limiting enzyme in bile acid synthesis from cholesterol.

Fibrosis - The formation or development of excess fibrous connective tissue in an organ or tissue as a reparative or reactive process

FXR - Farnesoid X receptor

Gallbladder - A pear-shaped organ that stores about 50 ml of bile (or "gall") until the body needs it for digestion.

Gamma glutamyl transpeptidase - Gamma glutamyl transferase (GGT or GGTP, or Gamma-GT), a liver enzyme involved in the transfer of amino acids across the cellular membrane. One of the liver function tests, it is not always part of the routine set and sometimes must be specifically ordered. It is a more sensitive indicator of cholestatic damage.

Genetics - The science of heredity and variation in living organisms.

Genome - The genome of an organism is a complete DNA sequence of one set of chromosomes.

Genotype - The genetic constitution of an individual; i.e., the specific allelic makeup of an individual, usually with reference to a specific characteristic under consideration; the inherited instructions an organisim carries, which may or may not be expressed.

GGT - Gamma glutamyl transpeptidase

Hepatocyte - The cells that make up 70-80% of the liver. Hepatocytes are involved in protein synthesis, protein storage and transformation of carbohydrates, synthesis of cholesterol, bile salts and phospholipids, and detoxification, modification and excretion of substances. Hepatocytes also initiates the formation and secretion of bile.

Histology - The study of tissue sectioned as a thin slice. It can be described as microscopic anatomy.

Hormone - A chemical messenger that carries a signal from one cell (or group of cells) to another via the blood. Hormones regulate the function of their target cells, i.e., cells that express a receptor for the hormone. Hormone effects include but are not limited to: induction or suppression of apoptosis (programmed cell death), activation or inhibition of the immune system and regulation of metabolism.

Humoral immunity - The aspect of immunity mediated by secreted antibodies produced by B cells.

Hypercholesterolemia - High blood cholesterol; the presence of high levels of cholesterol in the blood, not a disease but a metabolic derangement that can be secondary to many diseases.

Ileum - The final section of the small intestine, its primary function is the absorption of Vitamin B12, bile salts, and any products not absorbed in the jejunum. The surface of the ileum contains large numbers of capillaries which take the amino acids and glucose produced by digestion to the hepatic portal vein and the liver.

Immunoglobulin - See antibody; proteins that are found in blood or other bodily fluids of vertebrates, and are used by the immune system to identify and neutralize foreign objects, such as bacteria and viruses. Antibodies are produced by a kind of white blood cell called a B cell. Antibodies can come in different varieties known as isotypes or classes.

in vitro - From Latin: "within the glass", refers to the technique of performing a given experiment in a controlled environment outside of a living organism; for example, in a test tube.

in vivo - From Latin: "within the living", means that which takes place inside an organism.

INR - International Normalized Ratio

Interferon - (INFs) Interferons are cytokines, natural proteins produced by the cells of the immune system in response to foreign agents such as viruses, bacteria, parasites and tumor cells. Interferons assist the immune response by inhibiting viral replication within other cells of the body.

Interleuken - (ILs) A group of cytokines produced by a wide variety of bodily cells. The function of the immune system depends in a large part on interleukins.

International Normalized Ratio - Measures the speed of coagulation, comparing it to normal. If the INR is increased, it means it is taking longer than usual for blood to clot. The INR will only be increased if the liver is so damaged that synthesis of vitamin K-dependent coagulation factors has been impaired: it is not a sensitive measure of liver function.

Isotype - Antibody classes and subclasses: IgA 1, 2; IgD; IgE; IgG 1, 2, 3, 4; IgM

Jaundice - Yellowish discoloration of the skin, conjunctiva (a clear covering over the sclera, or whites of the eyes) and mucous membranes caused by hyperbilirubinemia (increased levels of bilirubin in red blooded animals).

Jejunum - The central section of the small intestine, between the duodenum and the ileum. It contains the majority of the area of the small intestine responsible for nutrient absorbtion.

LFTs - Liver Function Tests

Ligand - From Latin: "to bind". An extracellular substance that binds to receptors; a molecule that is able to bind to and form a complex with a biomolecule to serve a biological purpose.

Lipid - Any fat-soluble (lipophilic), naturally-occurring molecule. Examples of lipids are fats, oils, waxes, cholesterol, steroids, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, etc.

Liver - An organ present in vertebrates and some other animals. It plays a major role in metabolism and has a number of functions in the body, including glycogen storage, decomposition of red blood cells, plasma protein synthesis, and detoxification. This organ also is the largest gland in the human body.

Liver Function Tests - A group of blood tests designed to provide information about a patient's liver. Some tests are associated with functionality (eg. Albumin); some with cellular integrity (eg. transaminase,) and some with conditions linked to the biliary tract (eg. alkaline phosphatase).

Lymphocyte - A type of white blood cell. There are two categories of lymphocytes: large, granular lymphocytes called "natural killer cells" and small lymphocytes - B and T cells.

Major histocompatibility complex - The most gene-dense region of the mammalian genome, it plays an important role in the immune system, autoimmunity, and reproductive success.

MHC - Major histocompatibility complex

Mitochondria - A mitochondrion (plural mitochondria) is a membrane-enclosed organelle (sub-unit) found in most eukaryotic (complex) cells.

MMTV - Mouse Mammary Tumor Virus

Molecular epidemiology - A branch of public health that deals with the contribution of potential genetic and environmental risk factors identified at the molecular level, to the etiology, distribution and control of the disease in groups of relatives and populations. Molecular epidemiology improves our understanding of the pathogenesis of disease by identifying specific pathways, molecules and genes that influence the risk of developing disease.

Morphology - The outward appearance (shape, structure, colour, pattern) of an organism and its component parts.

Mouse mammary tumor virus - Mouse mammary tumor virus is a milk-transmitted betaretrovirus like the Human T-lymphotropic (HTL) viruses, HIV and Bovine leukemia virus (BLV).

Organelle - In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is separately enclosed within its own lipid membrane. Mitochondria are a type of organelle.

Osteopenia - Osteopenia is a decrease in bone mineral density that can be a precursor condition to osteoporosis. However, not every person diagnosed with osteopenia will develop osteoporosis.

Osteoporosis - Osteoporosis is a disease of bone leading to an increased risk of fracture. In osteoporosis the bone mineral density (BMD) is reduced, bone microarchitecture is disrupted, and the amount and variety of non-collagenous proteins in bone is altered.

Overlap syndrome - An autoimmune disease in which the patient presents with symptoms of two or more diseases.

Pathogenesis - The mechanism by which a certain etiological factor causes disease (pathos = disease, genesis = development). The term can also be used to describe the development of the disease

Pathophysiology - The study of the disturbance of normal mechanical, physical, and biochemical functions, either caused by a disease, or resulting from a disease or abnormal syndrome or condition that may not qualify to be called a disease.

PBC - Primary biliary cirrhosis

PCR - Polymerase chain reaction, a laboratoray technique for amplifying a single or few copies of a piece of DNA across several orders of magnitude, generating millions or more copies of the DNA piece.

PDC-E2 - Pyruvate dehydrogenase E2 complex

Peptide - A subunit of a protein; a short polymer formed from the linking, in a defined order, of á-amino acids. Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and proteins are long.

Phenotype - Any observed quality of an organism (morphology, development, or behavior) as opposed to its genotype (inherited instructions it carries, regardless of expression). This genotype-phenotype distinction makes clear the difference between an organism's heredity and what that heredity produces. It is a generally accepted theory that inherited genotype, transmitted epigenetic factors, and non-hereditary environmental variation contribute to the phenotype of an individual.

Phospholipids - A class of lipids, and a major component of all biological membranes, along with glycolipids, cholesterol and proteins.

Physiology - The study of the mechanical, physical, and biochemical functions of living organisms.

Primary Biliary Cirrhosis - An autoimmune disease of the liver marked by the slow progressive destruction of the small bile ducts within the liver.

Protein - Large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code.

Prothrombin Time - A blood test used to determine the clotting tendency of blood, in the measure of warfarin dosage, liver damage and vitamin K status.

Pruritus - Itch; defined as an unpleasant sensation that evokes the desire or reflex to scratch. Itch has many similarities to pain and both are unpleasant sensory experiences but their behavioral response patterns are different.

PT - Prothrombin Time

Receptor - A protein on the cell membrane, within the cytoplasm or cell nucleus that binds to a specific molecule (a ligand), such as a neurotransmitter, hormone, or other substance, and initiates the cellular response to the ligand.

Retrovirus - Any virus belonging to the viral family Retroviridae. Retroviruses insert their own viral genome in the host genome.

Ribonucleic acid - RNA is very similar to DNA, but differs in a few important structural details: in the cell RNA is usually single stranded, while DNA is usually double stranded.

Ribosome - A complex of RNA and protein found in all cells. The function of ribosomes is the assembly of proteins, in a process called "translation".

RNA - Ribonucleic acid

RT-PCR - Reverse transcription polymerase chain reaction, a laboratory technique for amplifying a defined piece of a ribonucleic acid (RNA) molecule.

Secretin - A hormone that regulates the pH of the duodenum by controlling gastric acid secretion and buffering bile acid with bicarbonate.

Serology - The scientific study of blood serum. In practice, the term usually refers to the diagnostic identification of antibodies in the serum.

Somatostatin - Also known as growth hormone inhibiting hormone (GHIH), somatostatin is an inhibitory hormone with actions in various parts of the body, including the GI system.

T cell - T cells belong to a group of white blood cells known as lymphocytes, and play a central role in cell-mediated immunity. The thymus is the principal organ in the T cell's development.

T cell receptor - a molecule found on the surface of T lymphocytes (or T cells) that is generally responsible for recognizing antigens bound to major histocompatibility complex (MHC) molecules.

T lymphocyte - Also known as "T cell".

TCR - T cell receptor.

Thymus - An organ located in the upper portion of the chest cavity just behind the sternum key to the maturation of T cells.

TLR - Toll-like receptor

TNF - Tumor necrosis factor. A group of cytokines which can cause apoptosis. An abnormal production of TNF plays a fundamental role in several human diseases, especially in autoimmune diseases.

TNF-α - A specific tumor necrosis factor cytokine involved in systemic inflammation.

TNFR - Tumor necrosis factor receptor, a receptor which binds tumor necrosis factors (TNF).

Toll-like receptor - A class of single membrane-spanning receptors that activate immune cell responses.

Transcriptome - The set of all messenger RNA (mRNA) molecules, or "transcripts", produced in one or a population of cells.

UDCA - Also known as ursodeoxycholic acid.

Ursodeoxycholic acid - One of the secondary bile acids, which are metabolic byproducts of intestinal bacteria. Bile acids formed by synthesis in the liver are termed "primary" bile acids, and those made by bacteria are termed "secondary" bile acids.

Ursodiol - Synthetic ursodeoxycholic acid.

Varices - Dilated submucosal veins in the esophagus, stomach, or intestines which can be a life-threatening cause of hemorrhage. Varices are most often a consequence of portal hypertension, such as may be seen in late stage liver disease.

Xenobiotic - A chemical which is found in an organism but which is not normally produced or expected to be present in it.