Top scoring parameters by correlation analysis.

<p>Top scoring parameters by correlation analysis.</p

HuPON1 variants analyzed in this study.

<p>± indicates standard deviation over three experiments. Please note that deviations do not include errors in protein measurement.</p

The transition state conformations for VX P(+) and VX P(−).

<p>The structures were generated with the QM/MM capabilities of the AMBER molecular dynamics suite <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020335#pone.0020335-Case1" target="_blank">[21]</a>.</p

The clustering method used to group conformations by reaction mechanism.

<p>The two main parameters, d_s and d_t are shown.</p

Scatter plot of experimental vs. predicted activity for the top-scoring set of variables (D269 mechanism, d_s = 2.00 Å, d_t = 2.25 Å, ITASSER/SMD structure, VX_ts(−) enantiomer, and Gasteiger charges).

<p>This dataset has a Pearson correlation of 0.767 (p<10⁻⁴)</p

Optimizing preparation and scanning of museum specimens.

<p>(A) Comparison of T1-weighted 3D FSPGR (fast-spoiled gradient-recalled echo) and (B) T2-weighted 3D FIESTA MRI pulse sequences acquired on the 3<i>T</i> scanner (slice matrix = 512×512×236, slice thickness = 900 µm, resolution = 683 µm³, averages = 2) in the smooth hammerhead, <i>Sphyrna lewini</i> (SIO 64-528, SL 104 cm). Additional parameters for the T1-weighted 3D Fast-Spoiled Gradient Echo (FSPGR) pulse sequence include, FA = 35°, TR = 9.86 ms, TE = 4.112 ms, and for the T2-weighted 3D FIESTA pulse sequence, FA = 40°, TR = 4.456 ms, TE = 2.1 ms. (C) The red bream, <i>Beryx decadactylus</i> (SIO 85-77; SL 289 mm), was initially imaged with a T1-weighted FSPGR pulse sequence on the 3<i>T</i> scanner prior to rehydration, and (D) re-imaged following rehydration resulting in an enhanced image quality. Scan parameters: FA = 30°, TR = 11.904 ms, TE = 3.932 ms, slice matrix = 512×512×236, slice thickness = 600 µm, resolution = 527 µm³, averages = 3. (E) The fantail filefish, <i>Pervagor spilosoma</i> (SIO 53-539; SL 74 mm) was initially imaged on the 7<i>T</i> scanner using a T1-weighted FLASH pulse sequence without exposure to contrast agent, ProHance. (F) It was subsequently reimaged following exposure to 2.5 mM ProHance, resulting in a significantly brighter MR signal and enhanced visual contrast among tissues. Scan parameters: FA = 15°, TR = 25.875 ms, TE = 12.853 ms, slice matrix = 350×1000×420, slice thickness = 100 µm, resolution = 100 µm³, averages = 8.</p

Genes linked to SigH binding sites that show SigH-dependent expression following heat stress.

<p>Genes linked to SigH binding sites that show SigH-dependent expression following heat stress.</p

Sequence analysis of experimentally confirmed SigH promoters.

<p>25 promoters experimentally identified in this research plus 7 previously identified promoters recognized by SigH were analyzed using the MEME analysis suite. <b>A</b>. LOGO showing consensus -10 and -35 promoter elements derived from these sequences. <b>B</b>. 25 promoter sequences that match the SigH consensus sequences. The position of the TSP and the ratio of heat stress-induced expression in wild type relative to expression in a Δ<i>sigH</i> strain are also shown. <b>C</b>. 7 promoter sequences that do not match the SigH consensus.</p

Common problems encountered when scanning museum fishes.

<p>Specimens were prepared for imaging and scanned as described in the Methods. Specific details for each species can be found in the DFL. (A) 3T horizontal image slice (937 µm³ resolution) of an oarfish, <i>Regalecus glesne</i> (SIO 96-82; SL 730 cm) demonstrating the effects of delaying soft tissue preservation. Arrows indicate tissues with significant decomposition. (B) 3T horizontal image slice (1.1 mm³ resolution) of a megamouth shark, <i>Megachasma pelagios</i> (SIO 07-53; standard length (SL) 215 cm) with significant tissue damage (arrows) from repeated freezing and thawing prior to fixation, resulting in poor tissue MRI signal and contrast. The asterisk indicates mechanical damage to the jaw. (C) 3T sagittal image slice (761 µm³ resolution) of a coelacanth, <i>Latimeria chalumnae</i> (SIO 75-347; SL 950 mm) demonstrating poor MRI results from being frozen and thawed prior to fixation and from extensive handling including dissection. (D) 7T sagittal slice (100 µm³ resolution) of a triplespot blenny, <i>Crossosalarias macrospilus</i> (SIO 02-3; SL 73 mm) exhibiting poor imaging results caused by exposure to alcohol without prior formalin fixation. (E) 3T sagittal slice (586 µm³ resolution) of a spiny dogfish, <i>Squalus acanthias</i> (SIO 08-138; SL 740 mm) showing the presence of inorganic particles in the inner ear causing a prominent magnetic susceptibility artefact. (F) 7T sagittal slice (100 µm³ resolution) of a California killifish, <i>Fundulus parvipinnis</i> (SIO 09-224; SL 68 mm) exhibiting a prominent magnetic susceptibility artefact caused by gases trapped in its gut. (G) 7T sagittal and horizontal slices (60 µm³ resolution) of a benttooth bristlemouth, <i>Cyclothone acclinidens</i> (SIO 07-166; SL 53 mm) exhibiting very poor image contrast caused by its extreme low body mass leading to an insufficient signal loading of the RF coil. (H) 7T sagittal and horizontal slices (100 µm³ resolution) of a glass catfish, <i>Kryptopterus bicirrhis</i> (SIO Uncat; SL 45 mm) showing problems with slice plane misalignment associated with scanning very flat or thin-bodied fishes. (I) 3T sagittal and horizontal slices (586 µm³ resolution) of a shortfin mako, <i>Isurus oxyrinchus</i> (SIO 55-85; SL 875 mm) showing slice plane misalignment problems associated with scanning large and/or elongate specimens requiring sequential repositioning of the coil to scan their full length. (I) 7T sagittal and horizontal slices (100 µm³ resolution) of a Pacific hagfish, <i>Eptatretus stoutii</i> (SIO 87-125; SL 145 mm) illustrating slice plane misalignment problems associated with scanning specimens preserved with body positions that cannot be straightened, preventing acquisition of bilaterally symmetrical slices in every plane.</p

Expression of <i>sigH</i> and <i>sigH</i>-FLAG in <i>M</i>. <i>tuberculosis</i>.

<p><b>A.</b><i>sigH</i>-FLAG expression was induced in <i>M</i>. <i>tuberculosis</i> H37Rv (wild type) containing a vector expressing <i>sigH</i>-FLAG under control of a TetR-regulated promoter. Samples were obtained at serial time points following addition of aTc to a final concentration of 200 ng/ml, protein was extracted and Western blotting was performed with an anti-FLAG antibody (Sigma-Aldrich). <b>B</b>. <i>M</i>. <i>tuberculosis</i> H37Rv (wild type) or the Δ<i>sigH</i> strain were exposed to 52°C for 15 minutes. The same strains containing a vector expressing <i>sigH</i>-FLAG under control of a TetR-regulated promoter were induced by addition aTc to a final concentration of of 200 ng/ml (aTc). RNA was extracted after 24h and qRT-PCR was performed and analyzed as described in the Materials and Methods. The higher level of induced <i>sigH</i> expression in wild type compared to the Δ<i>sigH</i> strain likely results from increased expression in wild type of the native copy of <i>sigH</i> from its SigH-regulated promoter following induction of the TetR-regulated copy of <i>sigH</i>.</p