Measurement of the e+e-→D(*)+D(*)- cross sections

journal articl

キョウカ ガクシュウホウ ニヨル システム ドウテイ ゴサ オ コウリョシタ ヒセンケイ セイギョ シュホウ

奈良先端科学技術大学院大学修士(工学)master thesi

Surfactant-Enhanced Desorption and Biodegradation of Polycyclic Aromatic Hydrocarbons in Contaminated Soil

We evaluated two nonionic surfactants, one hydrophobic (Brij 30) and one hydrophilic (C12E8), for their ability to enhance the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil after it had been treated in an aerobic bioreactor. The effects of each surfactant were evaluated at doses corresponding to equilibrium aqueous-phase concentrations well above the surfactant’s critical micelle concentration (CMC), slightly above the CMC, and below the CMC. The concentrations of all 3- and 4-ring PAHs were significantly lower in the soil amended with Brij 30 at the two lower doses compared to controls, whereas removal of only the 3-ring PAHs was significantly enhanced at the highest Brij 30 dose. In contrast, C12E8 did not enhance PAH removal at any dose. In the absence of surfactant, 12E8 at the lowest dose actually decreased the desorption of all PAHs. These findings suggest that the effects of the two surfactants on PAH biodegradation could be explained by their effects on PAH bioavailability. Overall, this study demonstrates that the properties of the surfactant and its dose relative to the corresponding aqueous-phase concentration are important factors in designing systems for surfactant-enhanced bioremediation of PAH-contaminated soils in which PAH bioavailability is limited

Cluster map of CULT domain proteins.

<p>The main clusters are named as described in the text and the domain architecture of the proteins in the respective cluster is shown. For this map, we searched the nr database at NCBI with PSI-Blast, using the CULT domain of human cereblon as a query. After convergence, we extracted all proteins above the cutoff of E = 0.005 and clustered them in CLANS using their all-against-all pairwise similarities as measured by BLAST P-values. Clustering was done to equilibrium in 2D at a P-value cutoff of 1e-10 using default settings.</p

CULT domain sequence and structure.

<p>(<b>a</b>) Multiple alignment of CULT domains from representative members of the groups in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi-1004023-g002" target="_blank">Fig. 2</a>. The alignment is based on the results of the PSI-Blast search with the CULT domain of human cereblon (first sequence in the alignment). Invariant residues of the three core groups (cereblon, secreted eukaryotic, bacterial) are underscored in black, residues conserved in at least two thirds of the sequences in the alignment are highlighted in dark grey and residues in at least one third of the sequences in light grey. The three tryptophan residues forming the thalidomide-binding site are marked by arrowheads and the two cysteine motifs coordinating the Zn ion, as well as a highly conserved motif at the tip of the inserted β-hairpin, are written out. The secondary structure above the alignment (S = β-strand) is the experimentally determined structure of the CULT domain from MGR_0879 of <i>Magnetospirillum gryphiswaldense</i> (first bacterial sequence in the alignment; <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi.1004023-Hartmann1" target="_blank">[18]</a>). The β-strands of the two main β-sheets are numbered according to the consensus structure of the β-tent fold and colored by whether they belong to the N-terminal β-sheet (purple) or the C-terminal one (gold); β3 is shown in brackets as it has lost its β-strand character in the CULT domain. The two β-strands of the inserted hairpin (teal) are labeled βI1 and βI2. The sequences are: (cereblon) HS - <i>Homo sapiens</i> NP_057386.2, DR - <i>Danio rerio</i> NP_001003996.1, DM - <i>Drosophila mojavensis</i> XP_001999319.1, CE - <i>Caenorhabditis elegans</i> NP_502300.2, AT - <i>Arabidopsis thaliana</i> NP_850069.1, EH - <i>Entamoeba hystolitica</i> XP_657530.1; (secreted eukaryotic) DR - <i>Danio rerio</i> NP_001121712.1, CB - <i>Caenorhabditis brenneri</i> EGT59438.1, TA - <i>Trichoplax adhaerens</i> XP_002115135.1, NV - <i>Nasonia virtipennis</i> XP_003427162.1; (bacterial) MG - <i>Magnetospirillum gryphiswaldense</i> CAM74667.1, GP - gamma proteobacterium BDW918 WP_008249149.1, HO - <i>Haliangium ochraceum</i> WP_012831591.1, DT - <i>Desulfonatronospira thiodismutans</i> WP_008870657.1, LS - <i>Leptospira</i> sp. B5-022 WP_020769190.1; (oomycete) PI - <i>Phytophthora infestans</i> XP_002999235.1, AL - <i>Albugo laibachii</i> CCA16326.1; (kinetoplastid) LM - <i>Leishmania major</i> strain Friedlin XP_001681231.1, TC - <i>Trypanosoma cruzi</i> EKG02463.1; (other) BP - <i>Bathycoccus prasinos</i> XP_007508760.1. (<b>b</b>) Superimposition of bacterial and eukaryotic CULT domain structures from <i>M. gryphiswaldense</i> (red), <i>H. sapiens</i> (blue; PDB ID:4TZ4), <i>M. musculus</i> (orange; PDB ID: 4TZC), and <i>G. gallus</i> (green; PDB ID:4CI2). The r.m.s. deviations in Cα positions for the pairwise comparisons ranged between 0.4 and 0.9 Å and are listed in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi.1004023.s004" target="_blank">S1 Table</a>. (<b>c</b>) Superimposition of the thalidomide binding site for the structures in panel (b). The ligand and the residues of the aromatic cage are shown in stick representation and colored as in panel (b). Residue numbering is for the human protein.</p

Gallery of β-tent domain binding sites.

<p>The panels show the β-hairpin inserted between β2 and β3, and the C-terminal β-meander (β4–β7), colored as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi-1004023-g006" target="_blank">Fig. 6</a>. Residues involved in ligand binding are colored magenta and blue, and the ligands cyan. Yippee is the molecular model from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi.1004023.s001" target="_blank">Fig. S1</a> and the ligand-binding residues are predicted based on conservation and location in the fold. For GFA, only the residues involved in binding the glutatione cofactor are known (magenta). Six highly conserved histidine residues (blue) may participate in catalysis, but the exact location and geometry of the formaldehyde-binding site is unknown. For Rig-I, the residues involved in coordinating the RNA 3′ end are shown in magenta and the 5′ end in blue. Residue numbers are: Cereblon: P51, W79, W85, W99, Y101, Yippee: Y43, F45, W82, Y84, MsrB: W73, R97, H111, F113, GFA: C54, T57, L58, C56, R98 (magenta) and H32, H50, H52, H107, H117, H126 (blue), RIG-I: E573, H576, W604, K602 (magenta) and V632, L621, V595, I597, F601, W604 (blue).</p

Effects of Nonionic Surfactant Addition on Populations of Polycyclic Aromatic Hydrocarbon-Degrading Bacteria in a Bioreactor Treating Contaminated Soil

We studied the effects of two polyethoxylated nonionic surfactants, Brij 30 and C12E8, on populations of polycyclic aromatic hydrocarbon- (PAH-) degrading bacteria from a bioreactor treating PAH-contaminated soil. Each surfactant was evaluated at doses that corresponded to aqueous-phase concentrations both above and below the critical micelle concentration (CMC) after mixing with reactor slurry. Real-time quantitative PCR was used to quantify 16S rRNA (rRNA) gene sequences representing degraders of salicylate, naphthalene, phenanthrene, or pyrene previously identified in the bioreactor community by stable-isotope probing. Sequences representing two groups of organisms associated with degradation of naphthalene and/or salicylate in the bioreactor increased in abundance by more than an order of magnitude after incubation with either surfactant at each dose tested. In contrast, the abundance of a group of uncultivated pyrene-degrading bacteria, whose relative abundance in the soil without surfactant addition was up to 9% of the total 16S rRNA genes, decreased by an order of magnitude or more in the presence of each surfactant at each dose. These results indicate that surfactant addition can have substantial, differential effects on populations of organisms responsible for contaminant degradation within a microbial community

Structure gallery and evolutionary inference for proteins with a β-tent fold.

<p>Only the core fold is shown; in structures where additional parts of the polypeptide chain obscured the view on the core fold, these were omitted. The β-strands of the insertion between β2 and β3 of the N-terminal β-meander is colored orange. The top image shows a superposition of the two halves of the MsrB structure 3HCJ (r.m.s.d. of 1 Å over the Cα carbons of the 30 superimposable residues) and the central image shows 3HCJ itself, as the most symmetrical of the β-tent structures. The images around the circumference show the seven domains of known structure discussed in this article (see also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004023#pcbi.1004023.s002" target="_blank">Fig. S2</a>). Of these, DUF427 and TCTP systematically lack a zinc binding site, and MsrB homologs have occasionally lost it. In the other domains, the zinc binding site is essentially always present, although the cysteine pattern is slightly modified in GFA relative to all other domains, the first cysteine tandem being CxCxxx, rather than xxCxxC. The arrows in the figure show our inference for a possible evolutionary path. The fold could thus have originated by duplication of a four-stranded β-meander and subsequently diverged into the domains seen today. Where homologous relationships are supported by sequence similarity, the arrows are black; otherwise they are grey.</p

Table_1_DIRAS2 Is a Prognostic Biomarker and Linked With Immune Infiltrates in Melanoma.xlsx

BackgroundSkin cutaneous melanoma (SKCM) is a highly malignant skin tumor. DIRAS2 is considered to be a tumor suppressor gene; however, its function in SKCM has not been explored.MethodsThe Gene Expression Profiling Interactive Analysis (GEPIA) was implemented to investigate the expression of DIRAS2 in SKCM, and plot the survival curve to determine the effect of DIRAS2 on the survival rates of SKCM patients. Then, the correlation between DIRAS2 and tumor immune infiltration was also discussed, and the expression of DIRAS2 and immune infiltration level in SKCM immune cells was determined using TIMER. The top 100 genes most associated with DIRAS2 expression were used for functional enrichment analysis. In order to confirm the anti-cancer effects of DIRAS2 in SKCM in the data analysis, in vitro assays as well as in vivo studies of DIRAS2 on SKCM tumor cell proliferation, migration, invasion, and metastasis were conducted. Western blot and immunofluorescence assay were employed to study the relationship between DIRAS2 and Wnt/β-catenin signaling pathway in SKCM.ResultsDIRAS2 expression was shown to be significantly correlated with tumor grade using univariate logistic regression analysis. DIRAS2 was found to be an independent prognostic factor for SKCM in multivariate analysis. Of note, DIRAS2 expression levels were positively correlated with the infiltration levels of B cells, CD4+ T cells, and CD8+ T cells in SKCM. The infiltration of B cells, CD4+ T cells, and CD8+ T cells was positively correlated with the cumulative survival rate of SKCM patients. In vitro experiments suggested that proliferation, migration, invasion, and metastasis of SKCM tumor cells were distinctly enhanced after DIRAS2 knockdown. Furthermore, DIRAS2 depletion promoted melanoma growth and metastasis in vivo. As for the mechanism, silencing DIRAS2 can activate the signal transduction of the Wnt/β-catenin signaling pathway.ConclusionDIRAS2 functions as a tumor suppressor gene in cases of SKCM by inhibiting the Wnt/β-catenin signaling. It is also associated with immune infiltration in SKCM.</p

Sequence relationships between proteins of the β-tent fold.

<p>The map shows the probabilities obtained for HMM to HMM comparisons, as implemented in HHpred. Queries are in rows, targets in columns. The proteins are: cereblon - CULT domain of human cereblon; Yippee - <i>Drosophila melanogaster</i> yippee isoform A (AAF48266.1); Mis18 - <i>Schizosaccharomyces pombe</i> Mis18 (CAB72327.2), res. 1–125; RIG-I - PDB: 4A2V; MsrB - PDB: 3HCG; GFA - PDB: 1X6M; MSS4 - PDB: 2FU5; TCTP - PDB: 1YZ1; Duf 427 - PDB: 3DJM.</p