Hartmut Wekerle was appointed Director and Scientific Member of the Max Planck Institute of Neurobiology in 1988. Until his retirement in 2012, he headed the Department of Neuroimmunology. In 2012, Hartmut Wekerle was awarded a Hertie Senior Professorship, with which he led an Extended Emeritus Group until 2018.

Hartmut Wekerle investigated the development of autoimmune diseases in the central nervous system (CNS), especially in multiple sclerosis (MS). A focus was on the study of autoimmune lymphocytes - how they are activated in the peripheral immune system, how they find their way into the isolated nervous system and how they finally destroy the brain and spinal cord tissue. With his work, Hartmut Wekerle was able to identify brain reactive autoimmune T lymphocytes in the immune system and, using new imaging approaches, to detail their migration into the brain. More recently, he identified the commensal bacterial gut flora as a factor triggering brain autoimmune disease.

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