Results: 5

1.
Fig. 2.

Fig. 2. From: Convergent recombination shapes the clonotypic landscape of the na?ve T-cell repertoire.

Prevalence of unique TCRβ clonotypes in sampled naïve CD8+ T-cell repertoires. The distributions of unique TCRβ amino acid (a.a.) sequences (A–C) and nucleotide (n.t.) sequences (D–F) are shown across samples of the depicted naïve CD8+ T-cell repertoires for mouse 1 (A and D), mouse 2 (B and E), and mouse 3 (C and F).

Máire F. Quigley, et al. Proc Natl Acad Sci U S A. 2010 November 9;107(45):19414-19419.
2.
Fig. 5.

Fig. 5. From: Convergent recombination shapes the clonotypic landscape of the na?ve T-cell repertoire.

The relationship between TRBV1/TRBJ2-1 naïve CD8+ T-cell clonotype frequency and sharing between mice. Each pie chart represents all TCRβ amino acid sequences detected in a given number of aliquots in one mouse. The size of each pie slice indicates the proportion of those TCRβ sequences present in the other mouse; colors indicate the number of aliquots in which each sequence was detected in the other mouse, as depicted in the key.

Máire F. Quigley, et al. Proc Natl Acad Sci U S A. 2010 November 9;107(45):19414-19419.
3.
Fig. 4.

Fig. 4. From: Convergent recombination shapes the clonotypic landscape of the na?ve T-cell repertoire.

Representation of convergent recombination in the TRBV1/TRBJ2-1 naïve CD8+ T-cell repertoire. Convergent recombination is illustrated for the amino acid sequence CTCSAGNYAEQFF, which was detected in seven aliquots in mouse 1 and in six aliquots in mouse 2. (A) This TCRβ clonotype was encoded by a total of eight different nucleotide sequences across both repertoires. One possible alignment with TRBV1 (blue), TRBD1/TRBD2 (pink), and TRBJ2-1 (green) genes involving the minimal number of nucleotide additions (black) is shown. (B) At a second level of convergent recombination, multiple recombination mechanisms with similarly low numbers of nucleotide additions can produce the same nucleotide sequence. This is shown for one of the nucleotide sequences (red box) encoding CTCSAGNYAEQFF. (C) The mouse TRB gene sequences used.

Máire F. Quigley, et al. Proc Natl Acad Sci U S A. 2010 November 9;107(45):19414-19419.
4.
Fig. 3.

Fig. 3. From: Convergent recombination shapes the clonotypic landscape of the na?ve T-cell repertoire.

Features of the observed TRBV1/TRBJ2-1 naïve CD8+ T-cell repertoire in mouse 1. (A and B) Relationship between the minimum number of nucleotide additions and the number of aliquots in which a TCRβ amino acid (a.a.) sequence (A) or nucleotide (n.t.) sequence (B) was detected. (C) Relationship between the number of nucleotide sequences observed to encode each unique amino acid sequence and the number of aliquots in which a TCRβ amino acid sequence was detected. (D) The production of 2 × 107 in-frame TCRβ sequences was simulated; the number of times that each amino acid sequence was generated in silico is plotted against the number of aliquots in which the same sequence was observed in vivo. Each circle represents an observed TCRβ sequence. The opacity of the circles indicates the density of the points plotted, and the red lines indicate the median values. Correlations are based on Spearman's rank correlation test.

Máire F. Quigley, et al. Proc Natl Acad Sci U S A. 2010 November 9;107(45):19414-19419.
5.
Fig. 1.

Fig. 1. From: Convergent recombination shapes the clonotypic landscape of the na?ve T-cell repertoire.

Naïve CD8+ T-cell repertoire sampling strategy. (A) Representative gating scheme for flow cytometric sorting of TRBV1+ naïve CD8+ T cells from mouse spleen. (Upper) Bivariate plots delineating the sequential selection of singlet, live CD3+CD4CD8+ lymphocytes. (Lower) Bivariate plots showing the phenotypic markers used to define naïve CD8+ T cells within this population before sorting based on TCRVβ1 expression. A corresponding approach was adopted for the isolation of splenic TRBV16+ naïve CD8+ T cells from mouse 3. (B) Schematic representation of sample partitioning. In this cartoon, a mouse spleen contains 100 TCRVβ-defined naïve CD8+ T-cell clonotypes. White dots represent single copies of unique clonotypes; colored dots represent multiple copies of the same clonotype. The TCRVβ-defined naïve CD8+ T cells are sorted randomly into 10 collection tubes; accordingly, the number of aliquots in which any given clonotype is detected provides a measure of its original clonal frequency in the spleen.

Máire F. Quigley, et al. Proc Natl Acad Sci U S A. 2010 November 9;107(45):19414-19419.

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