Experimental and Mechanistic Modeling of Fast Pyrolysis of Neat Glucose-Based Carbohydrates. 2. Validation and Evaluation of the Mechanistic Model

A computational framework based on continuous distribution kinetics was constructed to solve the mechanistic model that was developed for fast pyrolysis of glucose-based carbohydrates in the first part of this study [Zhou et al. <i>Ind. Eng. Chem. Res.</i> <b>2014</b>, 53. DOI 10.1021/ie502259w]. Comparing modeling results with experimental yields from fast pyrolysis over a wide range of reaction conditions validates the model. Agreement between model yields of final pyrolysis products with experimental data of fast pyrolysis of cellulose at temperatures ranging from 400 to 600 °C and maltohexaose, cellobiose, and glucose at 500 °C showed that the mechanistic model was robust and extendable. In comparison to our previous model [Vinu, R.; Broadbelt, L. J. <i>Energy Environ. Sci.</i> <b>2012</b>, 5, 9808–9826], the mechanistic model presented in this work incorporating new findings from experiments and theoretical calculations showed enhanced performance in capturing experimental yields of major products such as levoglucosan-pyranose, char, H₂O, CO₂, CO, and especially glycolaldehyde and 5-hydroxymethylfurfural. The model was also able to well match the yields of pyrolysis products that our previous model did not include, such as levoglucosan-furanose, methyl glyoxal, and minor products with yields of less than 1 wt % like levoglucosenone, acetone, dihydroxyacetone, and propenal. The mechanistic model showed its versatility in providing insights that were difficult to obtain from experiments, including a time scale of 4–5 s for complete thermoconversion of cellulose at 500 °C. Analysis of the contributions of competing reaction pathways showed that decomposition of cellulosic chains played a more important role in the formation of levoglucosan and glycolaldehyde than in that of other pyrolysis products

Systematic Analysis of the Lysine Acetylome in Candida albicans

Candida albicans (C. albicans) is a worldwide cause of fungal infectious diseases. As a general post-translational modification (PTM), lysine acetylation of proteins play an important regulatory role in almost every cell. In our research, we used a high-resolution proteomic technique (LC-MS/MS) to present the comprehensive analysis of the acetylome in C. albicans. In general, we detected 477 acetylated proteins among all 9038 proteins (5.28%) in C. albicans, which had 1073 specific acetylated sites. The bioinformatics analysis of the acetylome showed a significant role in the regulation of metabolism. To be more precise, proteins involved in carbon metabolism and biosynthesis were the underlying objectives of acetylation. Besides, through the study of the acetylome, we found a universal rule in acetylated motifs: the +4, +5, or +6 position, which is an alkaline residue with a long side chain (K or R), and the +1 or +2 position, which is a residue with a long side chain (Y, H, W, or F). To the best of our knowledge, all screening acetylated histone sites of this study have not been previously reported. Moreover, protein–protein interaction network (PPI) study demonstrated that a variety of connections in glycolysis/gluconeogenesis, oxidative phosphorylation, and the ribosome were modulated by acetylation and phosphorylation, but the phosphorylated proteins in oxidative phosphorylation PPI network were not abundant, which indicated that acetylation may have a more significant effect than phosphorylation on oxidative phosphorylation. This is the first study of the acetylome in human pathogenic fungi, providing an important starting point for the in-depth discovery of the functional analysis of acetylated proteins in such fungal pathogens

Table_1_miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8.DOCX

<p>Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.</p

Image_1_miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8.TIF

<p>Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.</p

Image_2_miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8.TIF

<p>Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.</p

Image_4_miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8.TIF

<p>Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.</p

Image_3_miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8.TIF

<p>Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.</p

Table_2_miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8.XLSX

<p>Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.</p

Experimental and Mechanistic Modeling of Fast Pyrolysis of Neat Glucose-Based Carbohydrates. 1. Experiments and Development of a Detailed Mechanistic Model

Fast pyrolysis of lignocellulosic biomass, utilizing moderate temperatures ranging from 400 to 600 °C, produces a primary liquid product (pyrolytic bio-oil), which is potentially compatible with existing petroleum-based infrastructure and can be catalytically upgraded to fuels and chemicals. In this work, experiments were conducted with a micropyrolyzer coupled to a gas chromatography–mass spectrometry/flame ionization detector system to investigate fast pyrolysis of neat cellulose and other glucose-based carbohydrates. A detailed mechanistic model building on our previous work was developed for fast pyrolysis of neat glucose-based carbohydrates by integrating updated findings obtained through experiments and theoretical calculations. The model described the decomposition of cellulosic polymer chains, reactions of intermediates, and formation of a range of low molecular weight compounds at the mechanistic level and specified each elementary reaction step in terms of Arrhenius parameters. The mechanistic model for fast pyrolysis of neat cellulose included 342 reactions of 103 species, which included 96 reactions of 67 species comprising the mechanistic model of neat glucose decomposition

Additional file 2 of Decreased CD44v3 expression impairs endometrial stromal cell proliferation and decidualization in women with recurrent implantation failure

Additional file2: Table SI Primers used in this study