Chapter: Immunology

illustration of red blood cell and lymphocyte nucleus with DAPI stanining

DAPI stands for 4′,6-diamidino-2-phenylindole and it is a fluorescent stain that binds to DNA in the nucleus. It is a stain used very often in fluorescence microscopy, when excited with ultraviolet light DAPI emits a blue light. This makes the stain very popular in fluorescence microscopy making the nuclei visible in a blue colour. As an example in the picture below there are various cells which you can distinguish by the blue nuclei and the cytoskeleton stained with another dye that emits a green  light. The picture was taken from thermofisher.

Mouse Anti Beta-Tubulin Monoclonal Antibody Nuclei (blue)

Plasma cell; B cell; shooting antibodies with a sling

Plasma cells, are a specialized type of B cells that produce large volumes of antibodies. This B cell here is using those antibodies to neutralize an invading flu virus that has entered the body.

Adoptive cell transfer of CD45.2 T lymphocytes to new host CD45.1 mouse host

Adoptive cell transfer refers to the transfer of cells into an organism, which could be a patient or in the case of this cartoon, a mouse. This is a very common technique used in immunology research to understand how the cells behave.

Adoptive Cell Transfer in Immunology Research

Typically, the cells that are being transfer have a different marker than the cells in the host. After being transferred to the new hosts, this marker allows the cells to be distinguished from the host cells. In this cartoon here the marker is CD45.1 and the marker of the host cells is CD45.2. Depending on the application, cells can also be labeled with a dye before being transferred so you can trace them back. An example of such a dye, that is also used to trace cell proliferation, is Carboxyfluorescein succinimidyl ester (CFSE).

If you are curious on some of the applications adoptive cell transfers in immunology research read this article Utilization of CD45.1 as a Marker of Donor Leukocytes in Recipient CD45.2 Mice in a Bone-Marrow Transfer Chimeric Experiment by Biocompare.

Adoptive Cell Transfer for Treating Disease

More recently, adoptive cell transfers have also been used to treat disease in humans. As an example, cells are taken out of a patient, the cells are then ‘re-educated’ and transferred back into the same patient. These now ‘educated’ or ‘activated’ cells can go ahead and perform their function to cure disease. You can read more about how this is applied to treat cancer in the article Adoptive cell transfer as personalized immunotherapy for human cancer published by Science Magazine.



cartoon of monocyte-dericed dendritic cell

This monocyte turned into a dendritic cell (DC) and doesn’t even know how it happened!
Many researchers isolate monocytes and then derive them into DCs to do studies on these cells. It is a common method followed by people studying DCs that need to generate some cells for their experiments.

In case you are interested in generating monocyte-derived dendritic cells (Mo-DCs) from human cells, below are some protocols you can follow.



Cartoon of Dendritic Cell Presenting Antigen on MHC to T Cell

The dendritic cell (DC) is presenting an antigen to a T cell but the T cell doesn’t recognize it. This is making the DC kind of sad.

In this case the DC is presenting the antigen on an MHC-I molecule and it is showing to a CD8 T cells. However, the T cell will recognize and respond to the antigen, only when if it is a specific antigen and it is bound to a particular MHC molecule. This process is called MHC restriction.

To learn more about antigen presentation and MHC restriction check out these links:

  • Video: MHC Class I Processing
  • Video: MHC Class II Processing
  • Poster: Nature Immunology Antigen Processing
  • Funny Comic by Pedromics: Presentation of the Antigen
  • Immunobiology Book: The major histocompatibility complex and its functions
  • Figure 5.16 T-cell recognition of antigens is MHC restricted

    The antigen-specific T-cell receptor (TCR) recognizes a complex of antigenic peptide and MHC. One consequence of this is that a T cell specific for peptide x and a particular MHC allele, MHCa (left panel), will not recognize the complex of peptide x with a different MHC allele, MHCb (center panel), or the complex of peptide y with MHCa (right panel). The co-recognition of peptide and MHC molecule is known as MHC restriction because the MHC molecule is said to restrict the ability of the T cell to recognize antigen. This restriction may either result from direct contact between MHC molecule and T-cell receptor or be an indirect effect of MHC polymorphism on the peptides that bind or on their bound conformation.

Cartoon of Dendritic Cell and Lymphocyte in the intestine

A big challenge of the immune system in the intestine is being able to distinguish between harmful pathogens and at the same time be tolerant towards harmless antigens derived from food and commensal bacteria (good bacteria). Mechanisms to maintain tolerance are therefore necessary to avoid unwanted immune responses that may lead to inflammatory bowel diseases (IBD) like Crohn’s disease or ulcerative colitis. The dendritic cells (DCs) found in the intestine are crucial to maintaining this equilibrium. DCs are constantly sampling antigens, such as food antigens. One way these cells sample antigens directly from the intestinal lumen is by inserting their dendritic processes between the epithelial cells layer [1].


The T cells found in the epithelium located between intestinal epithelial cells are called intraepithelial lymphocytes (IELs) and are thought to contribute to intestinal homeostasis by regulating the turnover of IECs and secreting hormones for epithelial repair [2].


Below are some resources in case you are interested in learning more about the immune system in the intestine.



1. Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nat Immunol. 2001 Apr;2(4):361-7
2. Intestinal T cells: facing the mucosal immune dilemma with synergy and diversity. Semin Immunol. 2009 Jun;21(3):130-8



Cartoon of infected cell shedding virus

A virus is a small infectious agent that needs other cells to replicate. The virus gets its genetic material inside the cell and the cell then uses its machinery to read the genetic code and create virus proteins that will form new viral particles.
The cartoon is showing a cell that has been infected and is now producing virus that are being released.

Neutrophil, a leukocyte phagocytoses bacteria

Neutrophil are the most abundant type of white blood cells and are part of the granulocyte family or the polymorphonuclear cells family.  They get the name ‘polymorphonuclear cells’ because of the varying shapes of the nucleus, which is usually lobed into three segments.

Neutrophils are the first cells to get to the site of infection, they are professional phagocytes and ferocious eaters that rapidly engulf invaders.

Here is a video you can watch of a neutrophil chasing a bacteria.


The lab of Dr. Paul Kubes from Calgary University does research on neutrophils. He and his team have published some pretty neat videos of neutrophils moving around tissue. The technique he uses to generate these videos is called intravital microscopy.

In the video below the neutrophils are seen in green migrating through blood vessels (blue) towards an area of tissue damage in the liver (red).

For those who want a more in-depth overview of neutrophils and the latest and most up to date findings here are some resources.

Leukocyte extravasation cartoon cell migration biology

Leukocyte extravasation is the movement of leukocytes out of the circulatory system and towards the site of tissue damage or infection. This process is regulated by a concerted action between endothelial cells and leukocytes, whereby endothelial cells activate leukocytes and direct them to extravasation sites, and leukocytes in turn instruct endothelial cells to open a path for transmigration.

To learn more about leukocyte extravasation and some of the mechanisms involved in this process check out these resources:

Below is a figure from the Nature Immunolog review, that I mentioned above, with an illustration of the steps involved in leukocyte extravasation.

The multistep cascade of leukocyte extravasation. A range of cell adhesion receptors on endothelial cells (as shown at the bottom of the panel) mediates the capture, rolling, arrest and crawling of leukocytes on the luminal endothelial cell surface.




Immunobiology, 5th edition The Immune System in Health and Disease

How leukocytes cross the vascular endothelium Nature Reviews Immunology