Glossary of terms
ATP – adenosine triphosphate is the small molecule used in cells as the primary source of readily available energy.
Basophilic or haematoxophilic– structures that stain with the basic dye haematoxylin, one of the components of the standard haematoxylin and eosin (H&E) method (see Appendix 2). Acidic molecules such as DNA and RNA take up this dye, thus acquiring a blue colour.
Complement cascade – a group of enzymes found in inactive form in the blood. Binding of immune complexes or certain bacterial products activates the first enzyme, which is then able to activate larger amounts of the second that in turn switches on larger amounts of the third and so on. This cascade can very quickly produce large quantities of effector molecules that fight infection and promote inflammation.
Coronal planes – imaginary vertical planes at right angles to the median/sagittal plane (see below).
Cytokines – proteins or peptides released by cells that convey signals to nearby cells.
Distal – anatomical term meaning further from the centre or the root of a limb (e.g. the ankle is distal to the knee).
DNA – deoxyribonucleic acid is the chemical structure that holds the genetic code, which contains the blueprint for every protein produced by an individual. DNA is found in the nucleus where it forms the chromosomes (see Ch. 2).
Electron-dense – tissue stained for electron microscopy with heavy metals impedes the passage of electrons to a greater or lesser degree depending on the amount of heavy metal bound. Structures that take up large amounts of heavy metal stains are called electron-dense and appear dark grey to black.
Electron-lucent – tissue stained for electron microscopy with heavy metals impedes the passage of electrons to a greater or lesser degree depending on the amount of heavy metal bound. Those structures that bind little heavy metal and allow the passage of the electron beam are said to be electron-lucent and appear white to pale grey.
EM – two-dimensional electron micrograph views of objects, acquired by passing the electron beam through a thin section of the specimen (see Appendix 1). Almost all of the electron micrographs in this book are transmission electron micrographs and are referred to as ‘EMs’. Other authors sometimes use the abbreviation TEM, although by convention the abbreviation EM is assumed to be a transmission EM.
SEM – scanning electron micrographs are three-dimensional views of the surface of objects. SEMs in this book are identified in figure captions as ‘SEM’ (see Appendix 1 for further details).
Eosinophilic or acidophilic– these structures stain with the acidic dye eosin, the other component of the standard haematoxylin and eosin (H&E) method. Most cytoplasmic structures are basic and therefore acidophilic to some extent, so that in most tissues the cell cytoplasm stains with eosin and appears pinkish-red.
ER – endoplasmic reticulum is a membrane-bound cytoplasmic compartment where certain chemical reactions take place sequestered from the rest of the cytoplasm. There are two types—rough and smooth.
rER – rough endoplasmic reticulum is studded with ribosomes and is the site of synthesis and processing of proteins for export.
sER – smooth endoplasmic reticulum is a major site of lipid synthesis.
In vitro – an experiment taking place outside of a living body (e.g. in a tissue culture dish).
In vivo – occurring in a living body, used in experimental situations to describe events taking place in real life.
Protein superfamilies – proteins can be grouped into superfamilies by similarities in structure and function. An example is the immunoglobulin superfamily that has a range of functions in antigen recognition and cell-cell interactions.
Proximal – closer to the centre or the root of a limb (e.g., the elbow is proximal to the wrist).
RNA – ribonucleic acid is a chemical structure that exists in three forms: messenger RNA, transfer RNA and ribosomal RNA (see below).
mRNA – messenger RNA is a chemical copy of the sequence of bases in DNA and acts as a template for the synthesis of proteins (see Ch. 1).
rRNA – ribosomal RNA is the type of RNA that makes up the physical structure of the ribosome, the site of protein synthesis. Ribosomal RNA controls the docking of tRNA in the correct order as defined by mRNA to produce the correct sequence of amino acids in a particular polypeptide chain.
tRNA – transfer RNA interacts with mRNA during protein synthesis to assemble the amino acids in the correct order to create a particular protein.
Sagittal or median plane – an imaginary vertical plane through the body, dividing it into right and left halves. Additional paramedian or parasagittal planes are parallel to the sagittal plane.
Section or tissue section – a very thin slice of tissue that is prepared in one of a number of ways for staining and microscopic examination:
Frozen section – this type of section is used for urgent diagnosis intra-operatively. The tissue is snap frozen, sections cut and stained and a diagnosis given within a sort space of time (15–30 minutes). The disadvantage of this method is that tissue preservation is not nearly so good as with routine paraffin sections, and so diagnosis is more difficult. Frozen sections are also used for immunofluorescence microscopy, certain stains to detect lipids in tissue and for enzyme histochemistry.
Paraffin sections – most of the photomicrographs in this book are of paraffin sections. The fixed tissues are dehydrated and infiltrated by hot liquid paraffin wax and cooled until the wax is solid (at room temperature). The wax provides support for the tissue and allows sections as thin as 1–2 µm to be cut. The wax is dissolved away by an organic solvent, and the tissue slice is rehydrated before stains are applied. This procedure requires hours to carry out, and most routine tissue sections are processed overnight.
Resin sections – in some circumstances, paraffin wax offers inadequate support for tissue sectioning, and resins are used as the embedding medium. Two main types are used. Acrylic resins are harder than paraffin wax and offer greater support when cutting hard tissues such as fingernail and undecalcified bone. A wide range of stains can be applied. Epoxy resins are even harder and are particularly used in electron microscopy. Using special glass ‘knives’, very thin sections can be cut and stained with Toluidine blue (see Appendix 2, ‘Notes on stains’) for very high-resolution light microscopy, and even thinner sections (ultrathin sections) stained for transmission electron microscopy.