Nestlet “treatment” of isolation reared rats.

<p>Twice weekly cages are changed and replaced with a new Nestlet (A), the Nestlet is shredded by the rat prior to forming the nest (B), and then the rat spends time resting in the formed nest (C).</p

Entrez Gene ID Numbers and Primer Sequences of Genes Used for Quantitative Polymerase Chain Reaction Experiments

<p>Entrez Gene ID Numbers and Primer Sequences of Genes Used for Quantitative Polymerase Chain Reaction Experiments</p

Degree of impaired burn healing rats in each condition.

<p>For each rat, the number of pixels comprising the width of the maximum gap of unhealed tissue was normalized to the width of its back. The average normalized pixels of unhealed tissue were significantly greater for the isolation-reared rats (middle column) compared with both the group-reared rats (first column) and the isolation reared rats treated with Nestlets (third column). Average±S.E.M., *p<.05, ** <i>P</i><0.01.</p

Gene expression changes in the hippocampus by condition.

<p>Rats treated with Nestlets had significantly higher gene expression compared to isolation reared rats without Nestlets for cfos and junb (compare columns 3 and 4 for these genes). Gene expression of rats treated with Nestlets returned to that of group reared rats for these genes (compare columns 1 and 4 for cfos and junb). Group reared rats treated with Nestlets showed an increase in these genes above the expression level for group reared rats not treated with Nestlets (compare columns 1 and 2) even though there was no additional benefit to their wound healing (since wound healing was maximal for the group reared rats without the Nestlets). Average±SEM, *p<0.05, **p<.01, ***p<.001.</p

Effect of Nestlet treatment on open field test behavior.

<p>Ambulatory time was significantly lower for isolation reared rats treated with Nestlets (column 4) compared to untreated isolation reared rats (column 3) and not different from group reared rats (column 1) or group reared rats treated with Nestlets (column 2). Average±SEM.,*<i>P</i><0.05, ** <i>P</i><0.01, ***<i>P</i><0.001.</p

Example of healing in rats in the different conditions examined

<p>(A). 92% of group reared rats healed well (n = 12, column 1, 2B, and top row 2C), 12% of isolation reared rats healed well (n = 8, middle column 2B, and middle row 2C), and 64% of isolation reared rats treated with Nestlets healed well (n = 11 see third column 2B, and bottom row 2C).* <i>P</i><0.05, ** <i>P</i><0.01, *** <i>P</i><0.001.</p

Time series analysis of Nest Building and Oxytocin effect on wound healing.

<p>Panel A shows an example of wound healing over six weeks from weaning (PN20 to PN62) in the four conditions examined. Panel B shows that group reared rats had significantly better healing compared to isolation reared rats by 21 days post burn injury, while Nestlet and oxytocin treated rats showed similar healing to group reared rats by 28 days post burn injury. The difference between Nestlet treated, oxytocin treated, and group reared rats compared to isolation reared rats continued until 42 days post burn injury. Average±S.E.M., *p<.05, ** p<0.01, ***p<0.001.</p

Rapidly expanding sequence diversity during HIV-1 infection.

<p>Heat maps illustrate sites exhibiting amino acid sequence diversity at days 0, 3, 59, 165, 476 and 1543 post-presentation. Plotted is the percentage of amino acid diversity at each position with respect to the dominant baseline (day 0) amino acid residue. All 3174 amino acids of HIV-1 are represented, with the first amino acid of Gag located in the top left corner of the grid and the last amino acid of Nef located in the bottom right corner. Completely conserved residues are <i>dark blue</i>, low-level variant residues (<10% divergent from baseline) are <i>light blue</i>, moderately variable residues (10–50%) in <i>orange</i>, and highly variant residues (>50%) in <i>red</i>. (<b>A</b>) 0 days p.p., (<b>B</b>) 3 days p.p., (<b>C</b>) 59 days p.p., (<b>D</b>) 165 days p.p., (<b>E</b>) 476 days p.p., (<b>F</b>) 1543 days p.p..</p

Limited evolution in the HIV-1 proteome prior to establishment of viral set point.

<p>Sequence diversity is plotted for all evolving codons in each HIV-1 protein as the percent of sequences with an amino acid residue different from the dominant baseline residue. Colored lines denote individual evolving amino acid residues within each protein. The time of infection prior to the establishment of viral set point (day 165) is highlighted in <i>grey</i>.</p

Cellular immune responses drive early low-frequency quasispecies diversity.

<p>(<b>A</b>) For each protein, the average frequency of non-dominant baseline residues of positions within the 19 described CD8 epitopes restricted by subject 9213's HLA alleles (<i>left</i>) and outside of the 19 described epitopes (<i>right</i>) is plotted for each time point sequenced. <i>Colored lines</i> denote the proteins for which diversity was substantially higher inside of CD8 epitopes versus outside CD8 epitopes. (<b>B</b>) To determine rates of viral escape for each epitope escape mutations were defined as any amino acid substitution within the epitope. <i>Symbols</i> denote the cumulative observed frequency of all escape mutations, and lines depict the best fit by non-linear regression of the observed frequency data to the CTL escape model of Asquith et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002529#ppat.1002529-Asquith1" target="_blank">[65]</a>. <i>Open symbols</i> and dashed lines denote epitopes for which evolution was consistent with reversion. <i>Black symbols</i> and <i>dotted lines</i> denote epitopes for which there was no evidence of escape. CD8 responses against each epitope are shown in parentheses in the legend and were measured by IFN-gamma Elispot assay (Spot Forming Cells/Mill PBMC (SFC)). (<b>C</b>) Frequency of wild-type (<i>black</i>) and variant (<i>red</i>) haplotypes of the Vif B38-WI9 epitope and flanking regions over time. Shown at the top is the clade B consensus sequence for reference. (<b>D</b>) Frequency of wild-type (<i>black</i>) and variant (<i>red</i>) haplotypes of the Nef A24-RW8 B38-WI9 epitope and flanking regions over time. <i>Blue</i> residues highlight differences between the day 0 transmitted sequence and HIV-1B consensus sequence.</p