Journal: Physiological Genomics

Article Title: Superoxide scavenging and Akt inhibition in myocardium ameliorate pressure overload-induced NF-?B activation and cardiac hypertrophy

doi: 10.1152/physiolgenomics.00202.2009

Figure Lengend Snippet: TAB-induced NF-κB activation is attenuated by AdCu/ZnSOD and AdDNAkt. Representative images at day 5 (A) and summary data (B) show the effects of AdLacZ, AdCu/ZnSOD, or AdDNAkt on NF-κB-driven luciferase activity (photon emission) over time in TAB mice compared with sham-operated mice. NF-κB activation was measured by in vivo bioluminescent imaging using Xenogen IVIS-200. In the pseudocolored scale, areas of high photon emission are displayed as red and areas of low photon emission are displayed as blue. Data are means ± SE (n = 4/group) expressed relative to sham-operated mice. *P < 0.05 vs. sham surgery; †P < 0.05 vs. TAB-AdLacZ. DNAkt, dominant-negative form of Akt.

Article Snippet: EMSA was performed with 6 μg of nuclear protein incubated with a γ- 32 P-labeled NF-κB consensus oligonucleotide probe 5′-AGTTGAGGGGACTTTCCCAGGC-3′ (Promega, Madison, WI) as described earlier ( 52 ).

Techniques: Activation Assay, Luciferase, Activity Assay, In Vivo, Imaging, Dominant Negative Mutation

Journal: Genome Research

Article Title: The mutational spectrum of non-CpG DNA varies with CpG content

doi: 10.1101/gr.103283.109

Figure Lengend Snippet: Primate L1 families. A full-length generic primate L1 element is shown. The primate-specific L1Pa families examined here are placed on a simplified primate tree according to their average ages (see Methods). The columns give the KB of ORFII orthologs of the various families used for the various analyses in this paper (see Methods). M, P, and H indicate Macaca mulatta (macaque, Old World monkey), Pan troglodytes (chimpanzee), and Homo sapiens (human), respectively. The ages for the divergences of theses species were derived as described earlier (Walser et al. 2008). See Methods and Results, for details on the various steps outlined on the right side of the figure.

Article Snippet: Consensus sequences of L1 families These were derived as described earlier ( Walser et al. 2008 ) except we limited ourselves to the ∼3800 bp (depending on the family) ORF2 sequence because we could use the highly conserved amino acid sequence of the ORF2 protein as a guide for aligning the base sequences.

Techniques: Derivative Assay

Journal: Genome Research

Article Title: The mutational spectrum of non-CpG DNA varies with CpG content

doi: 10.1101/gr.103283.109

Figure Lengend Snippet: Mutational fate of each of the four bases for different L1 families. Panel A shows the distribution of A mutations to G, C, and T that occurred between the human and chimpanzee lineages for each L1Pa family. There are two x-axes on the bottom of panel A: the top one (boxed in gray) gives the total mutations (N × 103) that occurred and the bottom one (in bold) indicates the L1Pa family. For example, we found (Methods, Determination of the Mutational Spectrum) that 17,458 substitutions of A occurred between the chimpanzee and human L1Pa3 orthologs (rounded to 17.5 × 103 in Fig. 5): 8387 and 9071, respectively, for the human and chimpanzee orthologs. Of the total, 10,095 (0.58) were G transitions (green bar, left y-axis), 4595 (0.26) were C transversions (red bar, right y-axis), and 2768 (0.16) were T transversions (blue bar, right y-axis). Note that the left (transitions) and right (transversions) axes cover different ranges. The numbers of A mutations to G, and A transversions to C or T were about the same for chimpanzee and human (results not shown). For L1Pa4, 16,678 (16.7 × 103) A mutations occurred, again with about one-half occurring in chimpanzee and human, and again the numbers of G transitions and C or T transversions were about the same in chimpanzees and human. And so on for the rest of the families in panel A and for the mutations of G, C, and T presented in panels G, C, and T respectively. In each case the green bar (left axis) shows transitions and the red and blue bars (right axis) show transversions. The gray line is the total non-CpG divergence for each L1Pa family normalized to that of L1Pa3, set to 1.0. Families that differ in total non-CpG divergence generally differ in their proportions of transitions and transversions, especially in regard to mutations of A, G, and C (much less so for T). For example, chi-square comparisons in panel A showed that the proportion of transitions and transversions in L1Pa3 are significantly different from that of L1Pa4 (indicated by the asterisks between these families). Likewise the distribution of transitions and transversions in L1Pa4 is significantly different from that of L1Pa5, but this is not the case for proportions of transitions and transversion between L1Pa7 and L1Pa8.

Article Snippet: Consensus sequences of L1 families These were derived as described earlier ( Walser et al. 2008 ) except we limited ourselves to the ∼3800 bp (depending on the family) ORF2 sequence because we could use the highly conserved amino acid sequence of the ORF2 protein as a guide for aligning the base sequences.

Techniques: