Inclusion bodies
Inclusion bodies are nuclear or cytoplasmic aggregates of stainable substances, usually proteins. They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell and usually consist of viral capsid proteins.

# Composition
Protein inclusion bodies are classically thought to contain misfolded protein.  However, this has recently been contested, as green fluorescent protein will sometimes fluoresce in inclusions bodies, which indicates some semblance of the native structure and researchers have recover folded protein from inclusion bodies .  

# Mechanism of formation
When genes from one organism are expressed in another the resulting protein sometimes forms inclusion bodies. This is often true when large evolutionary distances are crossed:  a cDNA isolated from Eukarya for example, and expressed as a recombinant gene in a prokaryote risks the formation of the inactive aggregates of protein known as inclusion bodies. While the cDNA may properly code for a translatable mRNA, the protein that results will emerge in a foreign microenvironment. This often has fatal effects, especially if the intent of cloning is to produce a biologically active protein. For example, eukaryotic systems for carbohydrate modification and membrane transport are not found in prokaryotes.  The internal microenvironment of a prokaryotic cell (pH, osmolality) may differ from that of the original source of the gene. Mechanisms for folding a protein may also be absent, and hydrophobic residues that normally would remain buried may be exposed and available for interaction with similar exposed sites on other ectopic proteins. Processing systems for the cleavage and removal of internal peptides would also be absent in bacteria.  The initial attempts to clone insulin in a bacterium suffered all of these deficits. In addition, the fine controls that may keep the concentration of a protein low will also be missing in a prokaryotic cell, and overexpression can result in filling a cell with ectopic protein that, even if it were properly folded, would precipitate by saturating its environment.

# Viral inclusion bodies
Examples of viral inclusion bodies include Negri bodies (which are inclusion bodies of Rabies virus in neurons) and intranuclear inclusion bodies seen in Varicella-Zoster virus infection.

# Inclusion bodies in Erythrocytes
Normally a red blood cell does not contain inclusions in the cytoplasm. However, it maybe seen because of certain hematologic disorders.
There are three kinds of erythrocyte inclusions:
- Developmental Organelles
Howell-Jolly Bodies: small, round fragments of the nucleus resulting from karyorrhexis or nuclear disintegration of the late reticulocyte and stain reddish-blue with Wright stain.
Basophilic Stipplings - this stipplings is either fine or coarse, deep blue to purple staining inclusion that appears in erythrocytes on a dried Wright stain.
Pappenheimer Bodies - are siderotic granules which are small, irregular, dark-staining granules that appear near the periphery of a young erythrocyte in a Wright stain.
Polychromatophilic red cells - young red cells that no longer have nucleus but still contain some RNA.
Cabot Rings - ring-like structure and may appear in erythrocytes in megaloblastic anemia or in severe anemias, lead poisoning, and in dyserythropoiesis, in which erythrocytes are destroyed before being released from the bone marrow.
- Howell-Jolly Bodies: small, round fragments of the nucleus resulting from karyorrhexis or nuclear disintegration of the late reticulocyte and stain reddish-blue with Wright stain.
- Basophilic Stipplings - this stipplings is either fine or coarse, deep blue to purple staining inclusion that appears in erythrocytes on a dried Wright stain.
- Pappenheimer Bodies - are siderotic granules which are small, irregular, dark-staining granules that appear near the periphery of a young erythrocyte in a Wright stain.
- Polychromatophilic red cells - young red cells that no longer have nucleus but still contain some RNA.
- Cabot Rings - ring-like structure and may appear in erythrocytes in megaloblastic anemia or in severe anemias, lead poisoning, and in dyserythropoiesis, in which erythrocytes are destroyed before being released from the bone marrow.
- Abnormal Hemoglobin Precipitation
Heinz Bodies - round bodies, refractile inclusions not visible on a Wright stain film. It is best identified by supravital staining with basic dyes.
Hemoglobin H Inclusions - alpha thalassemia, greenish-blue inclusion bodies appear in many erythrocytes after four drops of blood is incubated with 0.5mL of Brilliant cresyl blue for 20 minutes at 37C.
- Heinz Bodies - round bodies, refractile inclusions not visible on a Wright stain film. It is best identified by supravital staining with basic dyes.
- Hemoglobin H Inclusions - alpha thalassemia, greenish-blue inclusion bodies appear in many erythrocytes after four drops of blood is incubated with 0.5mL of Brilliant cresyl blue for 20 minutes at 37C.
- Protozoan Inclusion
Malaria
Babesia
- Malaria
- Babesia