Amygdala is a almond-shaped structure in the human (and animal) brain, whose primary function is to regulate emotions. For example, the amygdala becomes active when we are experiencing pleasure, fear, hate, and so on. In humans, it is also the seat of biases (racial, cultural), as the amygdala conditions our brain to distrust anything that is out of the ordinary. This conditioning made sense in ancient days, when humans used to live in small tribal communities with homogenous cultural and racial structures. Now scientists from UCLA have found that negative feelings about black people may be subconsciously learned by both white and black Americans! The research is among the first to test the brain physiology of racial biases in both black and white subjects.

Amygdala (Courtesy: University of Virginia)It seems that both whites and blacks demonstrate an increased activity in their amygdala, when presented with images of black faces. Our amygdala also fires up when we see unknown faces, so both whites and blacks were first shown the pictures in another context. So next time when they see the pictures, they should recognize them, but this did not stop the amygdala from firing up when confronted with black faces! This suggests that both whites and blacks feel threatened (typical amygdala behavior) by black faces. According to the researchers, this suggests pervasive cultural cues, to associate black people with fear.
However, the study is not conclusive. A lot of other factors (past experiences, social and cultural differences, etc.) do color the responses. More study needs to be done with larger populations, and with perhaps isolated populations of Africans in Africa to set up a benchmark against which such comparisons can be made. Another interesting avenue would be to test if the response is towards the color of the skin only; for example, by using say black and white cats (instead of humans) to test the corresponding amygdala behavior (if any).
Scientists have only just started looking at the physiological changes that are brought about in the brain due to social and cultural conditionings. More interesting studies are definitely in the pipeline :).