MOESM2 of Fate of p-hydroxycinnamates and structural characteristics of residual hemicelluloses and lignin during alkaline-sulfite chemithermomechanical pretreatment of sugarcane bagasse

Additional file 2: Table S1. Assignments of 1H/13C correlation signals in the 2D HSQC spectra from untreated and pretreated sugarcane (Saccharum spp.) bagasse in DMSO-d6

MOESM1 of Role of surface tryptophan for peroxidase oxidation of nonphenolic lignin

Additional file 1. Additional figures including VP cycle, and additional kinetic, Py-GC/MS, SEC and NMR results. Fig. S1. VP catalytic cycle and CI, CII and resting state electronic absorption spectra. Fig. S2. Kinetics of CI reduction by native, acetylated and permethylated softwood and hardwood lignosulfonates: Native VP vs W164S variant. Fig. S3. Lignosulfonate permethylation: Py-GC/MS of softwood lignosulfonate before and after 1 h methylation with methyl iodide. Fig. S4. SEC profiles of softwood and hardwood nonphenolic lignosulfonates treated for 24 h with native VP and its W164S variant and controls without enzyme. Fig. S5. HSQC NMR spectra of acetylated softwood and hardwood lignosulfonates treated for 24 h with native VP and its W164S variant, and control without enzyme. Fig. S6. Kinetics of reduction of LiP CII by native and permethylated softwood and hardwood lignosulfonates. Fig. S7. SEC profiles of softwood and hardwood lignosulfonates treated for 24 h with native LiP and controls without enzyme. Fig. S8. HSQC NMR spectra of native softwood and hardwood lignosulfonates treated for 3 and 24 h with LiP-H8, and the corresponding controls without enzyme. Fig. S9. Difference spectra of peroxidase-treated softwood lignosulfonates minus their controls. Fig. S10. Difference spectra of peroxidase-treated hardwood lignosulfonates minus their controls

Fibrosis grade at laparotomy weeks along the study protocol in CCl4-treated mice.

<p>(A) Example of histological changes in CCl4-treated mice along the 16 weeks of study. Hepatic sections stained with Masson Trichrome (original magnification ×10), showing light to strong blue staining, as a reflection of the collagen deposition at different stages of the liver disease: no histopathological changes (week 0); focal mild portal fibrosis with short fibrous septa (week 6); moderate collagen fibber deposition in portal areas with occasional portal bridging (week 10); marked fibrosis in the majority of portal spaces with frequent portal-portal and portal-central bridging and architectural distortion (regenerative nodules) (weeks 13 and 16). (B) Fibrosis grade according to Ishak Scale in treated animals (n = 6/week) at different study weeks are represented as mean ± standard deviation. (C) Relative gene expression levels of different profibrogenic genes at different study weeks. MMP-2: Matrix metalloproteinase 2; TGF-β. Tumour growth factor beta; ProCol-1: Procollagen alpha-1(1); TIMP-1: Tissue inhibitor of metalloproteinase 1. Mean values of CCl4-treated mice (n = 6/week) are represented.</p

Temporal evolution of <i>Clostridium</i> groups and <i>Enterobacteriaceae</i> counts and their ratio in control and CCl₄-treated mice.

<p>(A, B, C) Bacterial counts from samples of cecum content were measured by quantitative real-time PCR and represented as <i>Log</i> cell/g intestinal content. Values shown as mean ± standard deviation are represented for control (n = 4/week) and treated mice (n = 6/week) along the 16 weeks of study. (D) Differences in the <i>Enterobacteriaceae/Clostridia</i> ratio are represented as mean ± standard deviation for control (n = 4/week) and treated mice (n = 6/week) along the 16 weeks of study.</p

List of primer pairs used in the study.

<p>List of primer pairs used in the study.</p

Gut microbiota changes during the study protocol in control and CCl₄-treated mice.

<p> <i>Bacterial counts: Log cells/g intestinal content:</i></p><p>**<i> p<0.05 compared with weekly control mice</i>.</p

Characteristics of animals at laparotomies.

<p>*<i>p<0,05 compared with the weekly control group.</i></p

Bacterial DNA translocation at laparotomies in control and treated mice.

<p>*<i>p<0,05 compared with the weekly control group; MLNs: mesenteric lymph nodes</i>.</p

Temporal pattern of key events related with development of bacterial DNA translocation in CCl₄-treated mice.

<p>The lowest levels of cytokine production, PMN butyrate specific-receptor GPR43 and <i>Clostridium</i> clusters counts from samples of intestinal cecum content along with the highest degrees of liver fibrosis, gut dysbiosis and bacterial translocation observed in treated animals are chronologically represented during the 16 weeks of study protocol.</p

Additional file 1: of Host-pathogen interplay at primary infection sites in pigs challenged with Actinobacillus pleuropneumoniae

Information about IL8 primers and optimised qPCR assays. More details about the optimisation and validation of qPCR assays for target gene-specific primers in the pig are included. Particularly in the figure is shown that the suitability of the newly designed primers was verified in separate experiments by performing of a cDNA pool. In melt curve and amplification plots samples are shown in green while controls (no reverse transcription control (NRT) and no template control (NTC)) are shown in yellow and orange respectively. Additionally, an agarose gel electrophoresis of the PCR products of undiluted cDNA pool and controls was performed. (DOCX 349 kb