Journal: PLoS ONE

Article Title: Mechanisms of Peptide-Induced Pore Formation in Lipid Bilayers Investigated by Oriented 31 P Solid-State NMR Spectroscopy

doi: 10.1371/journal.pone.0047745

Figure Lengend Snippet: The resonance in the spectrum of alamethicin is substantially broadened due to mosaic spread and the heterogeneous nature of the peptide-lipid interactions of the peptide , . (c,d) 31 P spectra of (c) a sample of alamethicin in oriented DMPC lipids with a peptide:lipid ratio of 1∶25 and (d) the novidin sample in (b). (e,f) Models showing the most likely conformations of the peptides and lipids at high peptide:lipid ratio for (e) alamethicin and (f) novicidin in lipid bilayers.

Article Snippet: Alamethicin (sequence in one-letter code: Ac-UPUAU AQUVU GLUPV UUEQ-Phol, Ac: acetyl, U: α-amino isobutyric acid, Phol: Phenyl alaninol) was synthesized as previously reported and novicidin (sequence in one-letter code: KNLRR IIRKG IHIIK KYF) was kindly provided by Novozymes A/S (Bagsværd, Denmark).

Techniques:

Journal: PLoS ONE

Article Title: Mechanisms of Peptide-Induced Pore Formation in Lipid Bilayers Investigated by Oriented 31 P Solid-State NMR Spectroscopy

doi: 10.1371/journal.pone.0047745

Figure Lengend Snippet: Parameters used for simulation of the 31 P spectra for the alamethicin samples ( Fig. 4 ). a

Article Snippet: Alamethicin (sequence in one-letter code: Ac-UPUAU AQUVU GLUPV UUEQ-Phol, Ac: acetyl, U: α-amino isobutyric acid, Phol: Phenyl alaninol) was synthesized as previously reported and novicidin (sequence in one-letter code: KNLRR IIRKG IHIIK KYF) was kindly provided by Novozymes A/S (Bagsværd, Denmark).

Techniques:

Journal: PLoS ONE

Article Title: Mechanisms of Peptide-Induced Pore Formation in Lipid Bilayers Investigated by Oriented 31 P Solid-State NMR Spectroscopy

doi: 10.1371/journal.pone.0047745

Figure Lengend Snippet: The lipids are illustrated by circles with the radial line illustrating the orientation of the 31 P head group. (a) Pure bilayers display a single sharp resonance at around 30 ppm. (b) At low peptide concentrations, weak interactions between peptide and lipids induce a slight disorder causing the 31 P resonance to shift to lower values. (c) The peptide insertion involves lipids that change orientation with reduced diffusion as a consequence. This gives rise to a peak at approximately −15 ppm. (d and e) The last step in the method of action of the peptide is the penetration of the lipids and disruption of the bilayer. Alamethicin forms barrel-stave channels without significant perturbation of the lipid (d), while novicidin creates toroidal pores in the lipids (e).

Article Snippet: Alamethicin (sequence in one-letter code: Ac-UPUAU AQUVU GLUPV UUEQ-Phol, Ac: acetyl, U: α-amino isobutyric acid, Phol: Phenyl alaninol) was synthesized as previously reported and novicidin (sequence in one-letter code: KNLRR IIRKG IHIIK KYF) was kindly provided by Novozymes A/S (Bagsværd, Denmark).

Techniques: Diffusion-based Assay, Disruption

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: Studies on the prognostic significance of STAT1 and STAT3 in breast cancer

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques:

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: No appreciable expression was detected in the negative controls of ph-STAT1 A. and ph-STAT3 B . C-H. show the staining intensity of the STAT1 and STAT3 expression as low (C and D), moderate (E and F), and strong (G and H). Original magnification, 20×. Scale bars = 100 μm (A-F), 10 μm (G and H).

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques: Expressing, Staining

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: The relationship between ph-STAT1 and ph-STAT3 tumour cell expression and clinicopathological characteristics (n=384)

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques: Expressing

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: A. Total STAT1 tumour cell expression and B. Ph-STAT1 tumour cell expression. C. Total STAT3 tumour cell expression and D. Ph-STAT3 tumour cell expression.

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques: Expressing

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: The relationship between clinicopathological characteristics, ph-STAT1 and ph-STAT3 tumour cell expression and cancer specific survival in patients with invasive ductal breast cancer (n=384)

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques: Expressing

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: The relationship between clinicopathological characteristics, ph-STAT1 and ph-STAT3 tumour cell expression and cancer specific survival in patients with high grade necrosis (n=201)

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques: Expressing

Journal: Oncotarget

Article Title: The relationship between total and phosphorylated STAT1 and STAT3 tumour cell expression, components of tumour microenvironment and survival in patients with invasive ductal breast cancer

doi: 10.18632/oncotarget.12730

Figure Lengend Snippet: Luminal A (n=174, 45%) and luminal B (n=92, 24%) show significant association between high tumour cell expression of ph-STAT3 (n=109, 28%) and improved cancer specific survival. Manipulation is permitted.

Article Snippet: TMA sections were then incubated overnight at 4°C with the primary antibodies as following: total STAT1 (STAT1 (42H3) Rabbit monoclonal antibody, code 9175, Cell Signaling Technology, USA) at a concentration of 1:100; ph-STAT1 (Rabbit PAb to STAT1 phosphoY701, code ab30645, Abcam, Cambridge) at a concentration of 1:150; total STAT3 (STAT3 Rabbit Ab, code 9132L, Cell Signaling Technology, USA) at a concentration of 1:200; Ph-STAT3 (Y705) antibody (P-STAT3 (Y705) Rabbit Ab, code 9131L, Cell Signaling Technology, USA) at a concentration of 1:200.

Techniques: Expressing

Journal: Biotechnology for Biofuels

Article Title: Boosting LPMO-driven lignocellulose degradation by polyphenol oxidase-activated lignin building blocks

doi: 10.1186/s13068-017-0810-4

Figure Lengend Snippet: Genome analysis of Ascomycota and Basidiomycota. The protein sequence annotations of 336 Ascomycota and 208 Basidiomycota genomes were used for genome analysis. In total, a 277 Ascomycota and b 178 Basidiomycota comprise AA9 LPMOs encoding genes ( blue column ). Next to this occurrence of AA9 LPMOs encoding genes in Ascomycota and Basidiomycota, the co-occurrence of both Ab PPO-like and Mt PPO7-like, or either Ab PPO-like or Mt PPO7-like enzymes is indicated on the right of each column . The number of Ascomycota and Basidiomycota without co-occurrence of AA9 LPMOs encoding genes was 59 and 30, respectively ( red column ). In total, 50 Ascomycota and 17 Basidiomycota species were determined that do not carry any genes encoding AA9 LPMOs, Ab PPOs, and Mt PPO7s. c Total number of AA9 LPMOs, Ab PPOs, and Mt PPO7s encoding genes annotated in 336 Ascomycota and 208 Basidiomycota genomes. d Distribution of annotated AA9 LPMOs, Ab PPOs, and Mt PPO7s encoding genes within 336 Ascomycota and 208 Basidiomycota genomes. See “ ” for details

Article Snippet: The protein BLAST was performed separately using ten Mt PPO7 sequences [PDB id: 4j3p and closely related Mt PPO7s: Q2UNF9, Aspergillus oryzae (strain ATCC 42149); G2QC95, Myceliophthora thermophila (ATCC 42464); Q2H7I7, Chaetomium globosum (ATCC 6205); G0SFX8, Chaetomium thermophilum (DSM 1495); L7IAQ4, Magnaporthe oryzae (strain Y34); L7JMT9, Magnaporthe oryzae (strain P131); G4N2I5, Magnaporthe oryzae (strain 70-15); A0A084GCK1, Scedosporium apiospermum ; A0A0C4DYF2, Magnaporthiopsis poae (ATCC 64411); J3P591, Gaeumannomyces graminis var. tritici (strain R3-111a-1)], ten AA9 LPMO sequences (PDB id: 4d7u and closely related LPMOs: Q7SHI8, Neurospora crassa (strain ATCC 24698); G2QCJ3, Myceliophthora thermophila (strain ATCC 42464); F7W1P4, Sordaria macrospora (strain ATCC MYA-333); G2RB73, Thielavia terrestris (strain ATCC 38088); Q2H8N9, Chaetomium globosum (strain ATCC 6205); G0S408, Chaetomium thermophilum (strain DSM 1495); F8MLY8, N eurospora tetrasperma (strain FGSC 2508); T0L448, Colletotrichum gloeosporioides (strain Cg-14); A0A0H4K9X4 and A0A1C9CXI0, Myceliophthora thermophila C1); and four Ab PPOs ( Ab PPO1, Ab PPO2, Ab PPO3, and Ab PPO4 [ , ]) as query sequences.

Techniques: Sequencing

Journal: Biotechnology for Biofuels

Article Title: Boosting LPMO-driven lignocellulose degradation by polyphenol oxidase-activated lignin building blocks

doi: 10.1186/s13068-017-0810-4

Figure Lengend Snippet: Statistical genome analysis of Ascomycota and Basidiomycota. a Principal component analysis (PCA) of genes encoding AA9 LPMOs, Ab PPOs, and Mt PPO7s of 336 Ascomycota and 208 Basidiomycota genomes. The numbers which describe the presence of genes encoding AA9 LPMOs, Mt PPO7s, and Ab PPOs in each fungal species were used as variables and are presented as principal components of Ascomycota ( red dots ) and Basidiomycota ( blue dots ). The first two components of the PCA explained 69.8 and 19.6% variation in the data, respectively. Vectors ( red arrows ) with a similar orientation illustrate a high correlation between the gene families ( b ). The axis legends indicate the overall contribution of the three gene families encoding AA9 LPMOs, Ab PPOs, and Mt PPO7s. b Correlation between the three gene families encoding AA9 LPMOs, Ab PPOs, and Mt PPO7s of 336 Ascomycota ( upper triangle ) and 208 Basidiomycota ( lower triangle ). c Correlation between genes encoding AA9 LPMOs, Ab PPOs, and Mt PPO7s of 27 Ascomycota ( upper triangle ) and 23 Basidiomycota ( lower triangle ), which have at least ten annotated genes encoding cellulose-degrading enzymes per fungus. Species of both fungal classes are listed in Additional file : Table S2 and Additional file : Table S3. Numerical values of the correlations of b and c are presented in Additional file : Figure S6. See “ ” for details

Article Snippet: The protein BLAST was performed separately using ten Mt PPO7 sequences [PDB id: 4j3p and closely related Mt PPO7s: Q2UNF9, Aspergillus oryzae (strain ATCC 42149); G2QC95, Myceliophthora thermophila (ATCC 42464); Q2H7I7, Chaetomium globosum (ATCC 6205); G0SFX8, Chaetomium thermophilum (DSM 1495); L7IAQ4, Magnaporthe oryzae (strain Y34); L7JMT9, Magnaporthe oryzae (strain P131); G4N2I5, Magnaporthe oryzae (strain 70-15); A0A084GCK1, Scedosporium apiospermum ; A0A0C4DYF2, Magnaporthiopsis poae (ATCC 64411); J3P591, Gaeumannomyces graminis var. tritici (strain R3-111a-1)], ten AA9 LPMO sequences (PDB id: 4d7u and closely related LPMOs: Q7SHI8, Neurospora crassa (strain ATCC 24698); G2QCJ3, Myceliophthora thermophila (strain ATCC 42464); F7W1P4, Sordaria macrospora (strain ATCC MYA-333); G2RB73, Thielavia terrestris (strain ATCC 38088); Q2H8N9, Chaetomium globosum (strain ATCC 6205); G0S408, Chaetomium thermophilum (strain DSM 1495); F8MLY8, N eurospora tetrasperma (strain FGSC 2508); T0L448, Colletotrichum gloeosporioides (strain Cg-14); A0A0H4K9X4 and A0A1C9CXI0, Myceliophthora thermophila C1); and four Ab PPOs ( Ab PPO1, Ab PPO2, Ab PPO3, and Ab PPO4 [ , ]) as query sequences.

Techniques: