The levels of cyclophilin, rhodopsin, bFGF, glial fibrillary acidic protein (GFAP), CNTF, and brain-derived neurotrophic factor (BDNF) mRNAs present in the retinas 6 and 48 hours after IPC were determined with a semiquantitative reverse transcription-polymerase chain reaction technique (RT-PCR), as described previously.
20 Briefly, total RNA was isolated, and first strand cDNA synthesis performed on 2 μg DNase-treated RNA. The individual cDNA species were amplified in a 10-μL reaction, containing the 2-μL cDNA aliquot, PCR buffer (10 mM Tris-HCl [pH 8.3] and 50 mM KCl), 4 mM MgCl
2, 200 μM of each dNTP, 4 ng/μL of both the sense and antisense primers, and 2.5 U
Taq polymerase. Reactions were initiated by incubating at 94°C for 10 minutes and PCRs (94°C for 15 seconds; 52°C, 55°C, or 56°C for 30 seconds; 72°C for 30 seconds) performed for a suitable number of cycles followed by a final extension at 72°C for 3 minutes. Interexperimental variations were avoided by performing all amplifications in a single run. The oligonucleotides primer pairs and their annealing temperatures are shown in
Table 1 . The PCR products of all primer pairs yielded single bands corresponding to the expected molecular weights, which are also shown in
Table 1 . PCR reaction products were separated on 1.5% agarose gels using ethidium bromide for visualization. The relative abundance of each PCR product was determined by digital analysis of gel photographs on computer (Labworks software; Ultra-violet Products, Cambridge, UK). For semiquantitative analysis, the ratio of the densitometric readings between the preconditioned and sham-treated eyes was calculated and was then compared to an internal standard mRNA ratio (cyclophilin), which was assumed to be unaffected by the IPC.