Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter

Inaccuracies in ion detection and signal processing can undermine confidence in the molecular formula assignment of high-resolution mass spectrometry, which relies on precise matching of the mass-to-charge ratio (m/z). This study proposes a novel graph-based spectra calibration method, MSCMcalib, which implements coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect plot, facilitating the automatic calibration of detected lines, i.e., the calibration of uncalibrated peaks aligned with these lines. The “propagation” method is subsequently employed to accurately and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval undergoing a process of “scaling” calibration. The utilization of narrower partitions effectively mitigates divergence issues at both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is validated through the calibration of SRFA data with m/z error ranges spanning from −10 to −6 ppm, resulting in an additional assignment of 11%–30% more molecular formulas compared to the quadratic fitting calibration

Graph-Based Method for Calibration of High-Resolution Mass Spectra of Natural Organic Matter

Inaccuracies in ion detection and signal processing can undermine confidence in the molecular formula assignment of high-resolution mass spectrometry, which relies on precise matching of the mass-to-charge ratio (m/z). This study proposes a novel graph-based spectra calibration method, MSCMcalib, which implements coordinate transformation and pattern detection. MSCMcalib maps uncalibrated m/z data onto a modified 2D mass defect plot, facilitating the automatic calibration of detected lines, i.e., the calibration of uncalibrated peaks aligned with these lines. The “propagation” method is subsequently employed to accurately and automatically calibrate 605 m/z values across multiple lines, encompassing 98% of the m/z range. The calibrated m/z values divide the m/z range of the spectrum into multiple subintervals, with each subinterval undergoing a process of “scaling” calibration. The utilization of narrower partitions effectively mitigates divergence issues at both ends that arise from the polynomial fitting of errors against m/z. The effectiveness of MSCMcalib is validated through the calibration of SRFA data with m/z error ranges spanning from −10 to −6 ppm, resulting in an additional assignment of 11%–30% more molecular formulas compared to the quadratic fitting calibration

Chromosome G-banding karyotype showing a complex chromosome rearrangement of the proband and her mother.

<p>(A) Aberrant chromosomes 3 and 5 of the proband. (B) CCRs between chromosomes 3, 5, 8, 11 and 15 of the mother. (C). Normal karyotype of the father. Arrows point to derivative chromosomes.</p

Sequencing results of the CCRs of the mother.

<p>Partial karyotype and ideogram of the proband’s mother showed the exceptional CCRs between chromosomes 3, 5, 8, 11 and 15. Reversed arrow indicates chromosome inversion.</p

Illumina SNP array results for the distal 15q region.

<p>(A) Proband's mother had a 1.6 Mb microdeletion at the 15q21.3 region (chr15: 57413776–59084268) (Human GRCh37/hg19 Assembly). (B) The Proband had a 35.4 Mb microduplication at the 15q21.3-q26.2 region (chr15: 58914326–94371025) (Human GRCh37/hg19 Assembly).</p

Analysis of genes involved in the variation region on different chromosome.

<p>Analysis of genes involved in the variation region on different chromosome.</p

PCR confirmation of chromosome arrangements of the proband and her parents.

<p>(A) PCR results of chromosome rearrangements of Chr3-15, Chr5r-5, Chr5-5r, Chr15-15 and Chr5-11 of the proband and her mother. The normal father was regarded as a control. (B) The sequence results of the rearrangement chromosomes using the Sanger method. Each three lines represent one chromosome; the first line and the third line show the normal chromosome sequence; and the middle line demonstrates the rearrangement chromosome sequence, according to the specific regions of chromosome rearrangements shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154574#pone.0154574.g004" target="_blank">Fig 4</a>. Chr3-15: combination of region 1 of chromosome 3 and region 3 of chromosome 15; Chr5r-5: combination of region 2 and region 3 of chromosome 5; Chr5-5r: combination of region 1 and region 2 of chromosome 5; Chr15-15: combination of region 1 and region 4 of chromosome 15; Chr5-11: combination of region 5 of chromosome 11 and region 5 of chromosome 5. F: father, P: proband, M: mother. 5r: reversed region 2 of chromosome 5. Der: derivative sequence of rearrangement chromosome. The red nucleotides represent the specific sites of translocation breakpoints.</p

Representative images from FISH analysis of the proband’s mother.

<p>(A) FISH using the Telomere 3p probe (spectrum green) and the Telomere 3q probe (spectrum red) revealed a green and red signal on der(3), indicating that the bottom of der(3) was the region of the translocation chromosome. (B) FISH using the Telomere 5p probe (spectrum green) and the Telomere 5q probe (spectrum red) revealed the absence of the red signal and presence of the green signal on der(5), as well as the presence of the red signal on der(11), indicating that telomere 5q was translocated to chromosome 11. (C) FISH using the Telomere 8p probe (spectrum green) and the Telomere 8q probe (spectrum red) revealed the absence of the red signal and presence of the green signal on der(8), as well as the presence of the red signal on der(3), indicating a translocation of 8q to chromosome 3. (D) FISH using the Telomere 15q probe (spectrum red) showed the presence of the red signal on der(15), indicating subtelomeric 15q sequences were retained on der(15) with a subterminal deletion on der(15). (E) FISH using probe D5S23 (spectrum green) at 5p15 and the probe EGR1 (spectrum red) at 5q31 revealed the absence of the red signal and presence of the green signal on distal der(5)’ short arm, as well as the presence of the red signal on der(11), indicating an inversion on the distal short arm of der(5)’. (F) FISH using the probe ETO (spectrum green) at 8q22 and the probe AML1 (spectrum red) at 21q22 showed the presence of the red signal on der(8) and the presence of the green signal on 21, indicating a breakpoint on chromosomes 8q22; the 22q regions of 21 were normal.(G)The MLL probe SCN4B (spectrum green) and TREH (spectrum red) at 11q23 showed the presence of the green and red signal on der(5), indicating a reciprocal translocation between chromosomes 11q and 5q. (H) FISH using probe D15Z1 (spectrum aqua) at 15p11.2, SNRPN (spectrum red) at 15q12 and PML (spectrum green) at 15q24.1 showed the presence of the aqua and red signal on der(15), as well as the presence of the green signal on der(3), indicating a reciprocal translocation between chromosomes 15q and 3q. (I) Probes used with FISH for the detection of chromosome breakpoints as well as CCRs. Reversed arrow demonstrates an inversion region.</p

Pentafluorosulfanyl-Substituted Benzopyran Analogues As New Cyclooxygenase‑2 Inhibitors with Excellent Pharmacokinetics and Efficacy in Blocking Inflammation

In this report, we disclose the design and synthesis of a series of pentafluorosulfanyl (SF₅) benzopyran derivatives as novel COX-2 inhibitors with improved pharmacokinetic and pharmacodynamic properties. The pentafluorosulfanyl compounds showed both potency and selectivity for COX-2 and demonstrated efficacy in several murine models of inflammation and pain. More interestingly, one of the compounds, <i>R</i>,<i>S</i>-<b>3a</b>, revealed exceptional efficacy in the adjuvant induced arthritis (AIA) model, achieving an ED₅₀ as low as 0.094 mg/kg. In addition, the pharmacokinetics of compound <i>R</i>,<i>S</i>-<b>3a</b> in rat revealed a half-life in excess of 12 h and plasma drug concentrations well above its IC₉₀ for up to 40 h. When <i>R</i>,<i>S</i>-<b>3a</b> was dosed just two times a week in the AIA model, efficacy was still maintained. Overall, drug <i>R</i>,<i>S</i>-<b>3a</b> and other analogues are suitable candidates that merit further investigation for the treatment of inflammation and pain as well as other diseases where COX-2 and PGE₂ play a role in their etiology

Knockdown of Ascl2 leads to the inhibition of the tumorsphere formation.

<p>1000 cells of shRNA-Ascl2/HT-29, shRNA-Ctr/HT-29 and non-transfected HT-29 cells are plated for tumorsphere formation as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032170#s2" target="_blank">Materials and methods</a> and quantified at 100× and 400× magnifications (A). The number of tumorspheres from shRNA-Ascl2/HT-29 cells is significantly less than that from shRNA-Ctr/HT-29 and non-transfected HT-29 cells (*: p<0.05) (B). The number of cells per tumorsphere from shRNA-Ascl2/HT-29 cells is significantly less than that from shRNA-Ctr/HT-29 cells and non-transfected HT-29 cells (*: p<0.05) (C).</p