Hi John,

From our experience, different profiles from BDNF and CORT could be observed following acute or chronic stress. But in our case, we used strong stressors (restraint and particularly immobilization: IS). Other stress paradigms don't gave similar results. The choice of the paradigm is crucial. Further, the chronicity period is also important. 

When IS is applied during 1 h, we have a down regulation of some exons of BDNF (Charrier et al., Brain Res.2006) concomitant to a big rise in CORT levels. This rise has not been abolished nor decreased dramatically. They decrease significantly but still remain at high levels compared to controls. But, BDNF levels in hypothalamus and brainstem  seem to show similar levels during the chronic stress period configuring probably an adaptability situation (Chigr et al., Neuroscience. 2009).

See also:

- Rapid induction of BDNF expression in the hippocampus during immobilization stress challenge in adult rats. Marmigère F, Givalois L, Rage F, Arancibia S, Tapia-Arancibia L. Hippocampus. 2003;13(5):646-55..

- Immobilization stress rapidly modulates BDNF mRNA expression in the hypothalamus of adult male rats.Rage F, Givalois L, Marmigère F, Tapia-Arancibia L, Arancibia S. Neuroscience. 2002;112(2):309-18.

-Immobilization stress rapidly and differentially modulates BDNF and TrkB mRNA expression in the pituitary gland of adult male rats.Givalois L, Marmigère F, Rage F, Ixart G, Arancibia S, Tapia-Arancibia L. Neuroendocrinology 2001 Sep;74(3):148-59.