Mammalian hibernation is a complex phenotype involving metabolic rate reduction, bradycardia, profound hypothermia, and a reliance on stored fat that allows the animal to survive for months without food in a state of suspended animation. To determine the genes responsible for this phenotype in the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) we used the Roche 454 platform to sequence mRNA isolated at six points throughout the year from three key tissues: heart, skeletal muscle, and white adipose tissue (WAT). Deep sequencing generated approximately 3.7 million cDNA reads from 18 samples (6 time points ×3 tissues) with a mean read length of 335 bases. Of these, 3,125,337 reads were assembled into 140,703 contigs. Approximately 90% of all sequences were matched to proteins in the human UniProt database. The total number of distinct human proteins matched by ground squirrel transcripts was 13,637 for heart, 12,496 for skeletal muscle, and 14,351 for WAT. Extensive mitochondrial RNA sequences enabled a novel approach of using the transcriptome to construct the complete mitochondrial genome for I. tridecemlineatus. Seasonal and activity-specific changes in mRNA levels that met our stringent false discovery rate cutoff (1.0×10−11) were used to identify patterns of gene expression involving various aspects of the hibernation phenotype. Among these patterns are differentially expressed genes encoding heart proteins AT1A1, NAC1 and RYR2 controlling ion transport required for contraction and relaxation at low body temperatures. Abundant RNAs in skeletal muscle coding ubiquitin pathway proteins ASB2, UBC and DDB1 peak in October, suggesting an increase in muscle proteolysis. Finally, genes in WAT that encode proteins involved in lipogenesis (ACOD, FABP4) are highly expressed in August, but gradually decline in expression during the seasonal transition to lipolysis.

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Rats were conditioned to fear a tone paired with shock to the feet. Retention tests 4 days later showed that consolidation had occurred. Other animals were not tested for retention at 4 days, but the tone was presented in order to reactivate their memories of the conditioning. An amnesia gradient was generated by low-intensity electrical stimulation of the amygdaloid complex at different intervals after the tone, but stimulation was without effect either when given to rats not previously conditioned or when given to conditioned rats without preceding memory reactivation. Thus, stimulation of the amygdaloid complex can can affect memory retrieval. Moreover, the data call into question the assumption that an amnesia gradient indicates that the memory consolidation process has been modified.

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Three experiments were designed to investigate some effects of low-level stimulation of the amygdaloid complex (AMYG) and the mesencephalic reticular formation (MRF). Experiment 1 used a tilt box to test for motivational and/or reinforcement effects and failed to demonstrate these effects with stimulation of either structure. Experiment 2 used a one-trial fearconditioning task and revealed that stimulation of the AMYG disrupted retention when given immediately after training or, under some conditions, 4 days after training. In the same task, Experiment 3 showed that stimulation of the MRF enhanced retention when given immediately after training or, under some conditions, 4 days after training. These data indicate that under these conditions, modification of retention by low-level stimulation of specific brain structures is independent of the age of the memory. Some implications of this result are discussed.