Sean Maguire edited Methods.md  over 9 years ago

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## Tissue processing  The brains were randomly split into two groups of four. One group was sectioned at 16uM while the other was sectioned at 30uM. Slides were kept at -20 during the sectioning process and heated only breifly to thaw mount each section before being returned to -20. All brains were sectioned in four series: three of the four were used for COX histochemistry at varying incubation times (30, 60, 90 min) and the fourth series of each individual was used for a Nissl stain. Slides were processed in two batches and slides were removed from the batch in turn at each time point. Each time point included 1-2 slides of homogenized cichlid brains sectioned at 10, 20, 30, 40, 50 and 60uM as an internal standard curve. In addition three slides of mouse brain sectioned at 40uM (donated to this study by the Crews lab) were included as positive control and processed at the 60 min time point in the first batch.  ## COX histochemistry  The first three series of each individual brain was stained for COX activity using a previously described protocol (Gonzalez-Lima and Jones). For the incubation time points, the entire slide rack was removed from the incubation solution,the slides for that time point were removed as quickly as possible and the slide rack was returned to the incubation solution. The following solutions were used: 1) fixation solution of 0.5% gluteraldehyde in 10% sucrose; 2) phosphate buffer (0.1 M, pH 7.6); 3) preincubation solution of 0.05 M Tris buffer (pH 7.6), 0.0275% cobalt chloride, 10% sucrose, and .5% dimethylsulfoxide (DMSO); 4) incubation solution of 0.05% diaminobenzidine (DAB), 0.0075% cytochrome c, 5% sucrose, 0.002% catalase, 0.25% DMSO (v/v), and phosphate buffer. Sections were kept frozen on the slides and solutions were kept at 4 degrees until the start of the procedure so that the sections would warm gradually as they moved through the baths. The sequence of baths was: 1) light fixation in gluteraldhyde solution for 5 min.; min;  2) rinse in phosphate buffer with 10% sucrose, 3 changes for 5 min each; 3) preincubation in cobalt chloride Tris-buffer for 10 min; 4) rinse in phosphate buffer; 5) incubation in DAB solution (oxygenated for 5 min before) at 37°C in a dark oven for 30-90 min; 6) post-fixation with 4% buffered formaldehyde in 10% sucrose for 30 min; 7) ethanol baths of 30, 50, 70, 95 (2 changes), and 100% (2 changes) for 5 min each; 8) xylene,  3 changesof xylene  for 5 min each; 9) cover-slipped with Permount. ## Nissl  The Nissl stain was done using a modified version of the Hofmann lab in-house protocol. Briefly, slides were processed through the following series of baths: 1) fixation in chilled 4% paraformaldhyde for 10 min; 2) rinsed in chilled phosphate buffered saline saline,  3 changes for 5 min each; 3) rinsed in room temperature deionized water; 4) stained with 1% cresyl violet for 3 min; 5) rinsed again in deionized water; 6) ethanol baths of 70% for 30 seconds, 95% for 2 min and 100% 100%,  2 changes for 2 min each; 7) xylenes xylenes,  2 changes for 5 min each; 8) cover-slipped with Permount. ## Quantification