Download PDF How the brain works

By Dr Ava Easton, Encephalitis Society

In order to understand the effects of encephalitis on the brain, it can be helpful to understand how the brain works.

The brain

The brain is an amazing organ: it controls everything you think, feel and do. The brain is made up of billions of nerve cells (neurons). A neuron has a cell body containing a nucleus and an axon which carries the impulse away from the cell body. Each neuron makes thousands connections to other neurons. This ‘neural network’ is similar to the way roads connect to make road networks. 

At birth all the neurons you will ever have are present but there are very few connections.   During early development, the neurons form trillions of connections. These connections are fine-tuned by the neurons' electrical activity: useful connections are maintained or added, while others often disappear. Axons that become regularly used, are gradually covered by a protective coating (the myelin sheath). A good analogy is the covering of a main road with tarmac allowing traffic to flow more freely. Neurons communicate with one another via specialised chemicals called neurotransmitters, of which there are several. Neurons transmit electrical and chemical signals, and this transmission of signals between neurons is how the brain functions.

The brain and infection

The brain is protected by a blood-brain barrier which prevents any large molecules passing from the blood into the brain. The blood-brain barrier acts very effectively to protect the brain from many common infections. Thus, infections of the brain are very rare.

The outcome of any infection is dependent upon the ability of the infection to cause disease and the response of the immune system. The immune response protects organisms against injury and infection by delivering white blood cells to sites of injury to kill potential pathogens and promote tissue repair. However, the powerful inflammatory response also has the capacity to cause damage to normal tissue. Unfortunately the immune response to an infection of the brain can contribute more to the disease process than the infection itself.

The brain and encephalitis

In infectious encephalitis, viruses entering neurons utilise components of the cell in order to replicate (make copies of themselves). This uses up energy stores and oxygen, damaging the cell. In post-infectious / autoimmune encephalitis it is the immune system that causes damage to neurons or other brain cells. In both types of encephalitis, by-products of the immune system’s actions (fluid, white blood cells, the contents of dead nerve cells and disabled viruses) can significantly alter the fluid surrounding neurons and affect their functioning.  For instance, the characteristics of the cell membrane may be altered, disturbing the electrical properties of the neuron. Swelling resulting from additional fluid entering the brain can interfere with blood supply causing anoxic (lack of oxygen) damage.

The extra unwanted fluids build up rapidly, and glial cells (cells that support neurons)  try to absorb the unwanted chemicals and fluids in order to protect neurons from harm, and in the process they swell up too. Glial cells act as sponges and scavengers of toxic by-products, caused by the inflammation but when they become overloaded, they die and then re-release the toxic chemicals back into the fluid, where they kill additional neurons. The extremely high levels of these substances are sufficient to kill vulnerable and weakened neurons by damaging their membranes or by exciting them to a point where they “burn out” and die.

At the site of inflammation and in nearby tissue, there is biological chaos, as the brain tries to adjust and fight the consequences of the damage. The dying cells give off chemicals that activate macrophages (white blood cells), which move from the bloodstream into the injury area, to absorb and eliminate debris. Glial cells and their helpers, which have gathered at the site to clean it up, now begin to form the scar tissue that will remain a part of the brain's new architecture. Sometimes, the glial barriers prevent healthy, remaining neurons from restoring axonal connections. In other cases, nerve terminals cannot pass the scar, and abnormal activity is then generated that can lead to epileptic seizures.


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Page created: August 2002/ Last update: February 2016/ Review date: February 2019

Disclaimer: We try to ensure that the information is easy to understand, accurate and up-to-date as possible. If you would like more information on the source material the author used to write this document please contact the Encephalitis Society. None of the authors of the above document has declared any conflict of interest which may arise from being named as an author of this document.