Relative ΔPβ graphs of transmissions of Sc237 among various hamster species visually aid interpretation of the results.

<p><b>A</b>. ΔPβ graphs of PrPs of various hamster species relative to that of Syrian hamster for the transmission of Sc237 from Syrian to other hamster species. The reference species are the donors of the transmissions and the former species are the recipients. Sy, Syrian hamster. Ch, Chinese hamster. Am, Armenian hamster. Dj, Djungarian hamster. <b>B</b>. ΔPβ graphs for back-transmissions of Sc237 from different hamster species to Syrian hamsters, and for transmission between Armenian and Chinese hamsters. The upward arrow indicates the position of the Pβ trough at residue ~115.</p

Pβ graphs of PrP of representative species look very alike but with certain differences.

<p><b>A</b>. Schematic illustration of the secondary-structure components of prion protein (PrP) and post-translational modifications, including disulfide links (yellow line with "SS"), N-linked glycans (fork-like objects) and glycosylphosphatidylinositol anchor (GPI anchor). B1 and B2, the first and the second β-strands, respectively. H1, H2 and H3, the first, second and third α-helices, respectively. <b>B</b>. Pβ graphs of PrP from various species. The blue, red and green arrows indicate peaks centered at residues 110, 140 and 175, respectively. Syrian ham, Syrian hamster; BV(109M), bank vole with methionine at residue 109 (in bank-vole numbering); Sh(ARQ), sheep with the A136/R150/Q171 polymorphism. <b>C and D</b>. Pβ-graphs of Aβ42 and human α-synuclein, respectively.</p

Smaller discrepancies in Pc values in Pβ trough regions are advantageous for cross-seeding of amyloids.

<p><b>A</b>. Pβ graphs of Hu23–144 and the equivalent C-terminally-truncated mouse (Mo12–143) and Syrian hamster (Sy23–144) PrPs [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref015" target="_blank">15</a>]. Hu23–140 had the highest peak at residue ~140, while Sy23–144 had the lowest and Mo23–143 had an intermediate peak. Peak heights correlated with amyloid formation efficiency, with Hu23–144 being the most efficient, Sy23–144 being the least efficient and Mo23–143 being intermediate. <b>B</b>. Pc graphs of Hu23–144, Mo23–143 and Sy23–144. The Pc peak at residue ~135 was located in a Pβ-trough at a position between two Pβ-peaks (compare with <b>Fig 3A</b>). The Pc peak is highest in Hu(23–144), lowest in Sy(23–144) and intermediate in Mo(23–143). <b>C</b>. Pβ graphs of tau-derived amyloidogenic peptide, R3, and its substitution variants, R3-S316A and R3-S316P, whose serine residue at the codon 316 was replaced with alanine or proline, respectively [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref016" target="_blank">16</a>]. The two variants had Pβ peaks at different positions (red and blue arrows). The wide Pβ trough of R3-S316P might explain the inefficiency of fibril formation owing to the overly high freedom of motion in the loop/kink between the two strands. <b>D</b>. Pc graphs of R3, the two substitution variants, and C-terminally-truncated variants, ΔCR3SK, ΔCR3S and ΔCR3. ΔCR3S and ΔCR3SK have serine residues at codon 316, whereas ΔCR3 lacks this codon. The curves of ΔCR3S and ΔCR3SK were similar to those of R3-S316P, whereas the curve of ΔCR3 was closer to the wild-type R3. R3-S316A is rather far from R3-S316P.</p

Positions of the β-strands and flexibility of the loop/kink region may affect cross-seeding efficiencies.

<p><b>A</b>. Anti-prion effects of a polymorphism V127 may be attributable to alterations in Pβ and Pc. Comparison of Pβ graphs of human wild-type PrP (G127M129) with PrPs with the polymorphisms V127 (V127M129) or V129 (G127V129). The red and blue arrows indicate the crests of peaks of V127M129 and G127V129, respectively. Black arrows indicate differences in Pβ values of V127M129 from those of wild-type. <b>B</b>. Pc graphs of wild-type human PrP and PrPs with the polymorphisms V129 and V127. The gray curve represents the Pβ graph of wild-type human PrP. <b>C</b>. Schematic illustration of the possible effect of the loop/kink region on parallel in-register β-sheet formation. Differences in the properties of loop/kink regions, such as flexibility or length, would result in the inability of these peptides to form stable parallel-in-register β-sheets. <b>D</b>. Schematic illustrations of two types of β-loop-β motifs (β-arch) with either a rigid (upper panels, red arrows, thick lines) or a flexible (green arrows; thin lines) loop. The middle panels illustrate heterologous template-substrate conversion reactions: the left panel shows a reaction in which the template has rigid loop/kink regions and the substrate has a flexible loop, whereas the right panel shows the opposite case. The bottom panels illustrate homologous substrate-template conversion reactions.</p

Biological relevance of Pβ: heights of Pβ peaks correlate with dominant-negative inhibition of ΔPrP-series mutants.

<p><b>A</b>. (<b>Left panel</b>) Schematic illustration of mutant PrP with deletions in the region between H1 and H2 (ΔPrP-series); (<b>right panel</b>), graph showing the PrP^Sc levels of convertible PrP coexisting with the indicated non-convertible ΔPrP mutant on 22L-infected N2a cells (adapted from reference [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref013" target="_blank">13</a>]). The PrP^Sc levels of convertible PrP increased as the size of the deletion of the co-existing ΔPrP increased, indicating that the dominant-negative inhibitory effects of non-convertible ΔPrP on co-existing convertible PrP are decreased as the size of the deletion increased. MoPrP, wild-type mouse PrP. <b>B</b>. Pβ graphs of wild-type mouse PrP and ΔPrP mutants. The height of the peak around residue 160 gradually decreased as the size of the deletion increased (red arrow), but had little effect on the appearances of the rest of the Pβ graphs. <b>C</b>. Pβ graphs of wild-type mouse PrP and ΔPrP mutants, focusing on the region from residue 140 to residue 180, showing the reduction of the peak more clearly. <b>D</b>. Pβ graphs of wild-type mouse PrP and ΔPrP mutants, focusing on the region from residue 150 to 190, specifically on the peak around residue 175 (black arrow). The peak became narrower in Δ159–171 (red arrow) and finally disappeared in Δ159–175 (blue curve with open squares). <b>E</b>. Pβ graphs of C-terminally-truncated human PrP (Hu23–144) and a deletion variant of the truncated mutant Hu23–144+Δ, with an internal deletion of residues 113–120 (left-right arrow) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref014" target="_blank">14</a>]. The latter protein contained another large peak (arrow).</p

Relative ΔPβ graphs of interspecies transmissions visually aid interpretation and are suggestive of how changes of host ranges could occur.

<p><b>A</b>. Relative ΔPβ graphs of transmissions of C-BSE from cattle to sheep with the ARQ polymorphism [Sh(ARQ)-Bo] and from cattle to Tg mice expressing elk PrP (Elk-Bo), and transmission of ovine PrP-adapted C-BSE to Tg mice expressing elk PrP [Elk-Sh(ARQ)][<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref026" target="_blank">26</a>]. The latter species are donors and the former species are recipients of transmissions. The blue, red and green curves represent efficient, inefficient and improved transmissions, respectively. <b>B</b>. Relative ΔPβ graphs of transmissions of C-BSE from cattle to Tg mice expressing porcine PrP (Pig-Bo) and of ovine PrP-adapted C-BSE to Tg mice expressing porcine PrP [Pig-Sh(ARQ)]. The bottom brackets indicate regions flattened by passage through sheep [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref027" target="_blank">27</a>]. <b>C</b>. Relative ΔPβ graphs of transmissions of C-BSE from cattle to mouse (Mo-Bo) and Syrian hamster (Sy-Bo) and from mouse-adapted C-BSE to Syrian hamster (Sy-Mo) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref028" target="_blank">28</a>]. <b>D</b>. Relative ΔPβ graphs of transmissions of C-BSE from cattle to Tg mice expressing human PrP (Hu-Bo) and of ovine PrP-adapted C-BSE to human [Hu-Sh(ARQ)] [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref025" target="_blank">25</a>]. <b>E</b>. Relative ΔPβ graphs of transmissions of CWD from elk to ferret (Ferret-Elk) and to Syrian hamster (Sy-Elk) and from ferret-adapted CWD to Syrian hamster (Sy-Ferret). The large negative peak at around residue 175 disappeared after passage through ferret (arrow) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref029" target="_blank">29</a>]. <b>F</b>. Relative ΔPβ graphs of transmissions of CWD from elk to Tg mice expressing human PrP (Human-Elk) and to Tg mice expressing human PrP with elk residues in the region of residues 166–174 (RLHuman-Elk) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171974#pone.0171974.ref031" target="_blank">31</a>]. The arrow indicates the region in which the graph pattern was changed by substitutions.</p

Colony-forming assay.

<p>Bone marrow mononuclear cells were collected 2 days after the last radiation treatment. Freshly isolated bone marrow mononuclear cells were mixed in methylcellulose complete medium, and the colony formation was observed under microscopy at 9 days after incubation. <b>A</b>) Different types of colonies, including CFU-GEMM, CFU-M, CFU-GM, and BFU-E were clearly formed from the bone marrow cells. <b>B</b>) A significantly higher number of total colonies (>50 cells) was formed from the bone marrow cells of the mice that were given nicaraven than those that received placebo. The open circles represent the mean of data from a mouse with duplicate assay. The red lines indicate the median values of each group.</p

Susceptibility of influenza viruses to NUD-1 and neuraminidase inhibitors.

<p>Susceptibility of influenza viruses to NUD-1 and neuraminidase inhibitors.</p

The levels of 8-OHdG in the plasma and urine.

<p>The plasma 8-OHdG levels were very low and did not significantly differ between the two groups (<b>A</b>), but the levels of urinary 8-OHdG were significantly lower in the mice that received nicaraven than in those that received a placebo (<b>B</b>). The open circles represent the mean of data from a mouse with duplicate assay. The red lines indicate median values of each group.</p

DNA damage in bone marrow cells.

<p>Bone marrow cells from mice were seeded in 4-well culture slides and cultured for 7 days. The DNA damage in the cells was estimated by immunostaining with an anti-53BP1 antibody. <b>A</b>) Representative images show the formation of 53BP1 foci within the nuclei of some cells (arrowheads). <b>B</b>) Quantitative analysis shows that the percentages of cells with 53BP1 foci were significantly lower in the Nicaraven group than the Placebo group. The open circles represent data from each mouse and the red lines indicate median values of each group.</p