Respiratory viral infections in exacerbation of chronic airway inflammatory diseases: novel mechanisms and insights from the upper airway epithelium.

Respiratory virus infection is one of the major sources of exacerbation of chronic airway inflammatory diseases. These exacerbations are associated with high morbidity and even mortality worldwide. The current understanding on viral-induced exacerbations is that viral infection increases airway inflammation which aggravates disease symptoms. Recent advances in in vitro air-liquid interface 3D cultures, organoid cultures and the use of novel human and animal challenge models have evoked new understandings as to the mechanisms of viral exacerbations. In this review, we will focus on recent novel findings that elucidate how respiratory viral infections alter the epithelial barrier in the airways, the upper airway microbial environment, epigenetic modifications including miRNA modulation, and other changes in immune responses throughout the upper and lower airways. First, we reviewed the prevalence of different respiratory viral infections in causing exacerbations in chronic airway inflammatory diseases. Subsequently we also summarized how recent models have expanded our appreciation of the mechanisms of viral-induced exacerbations. Further we highlighted the importance of the virome within the airway microbiome environment and its impact on subsequent bacterial infection. This review consolidates the understanding of viral induced exacerbation in chronic airway inflammatory diseases and indicates pathways that may be targeted for more effective management of chronic inflammatory diseases

An Overview of Biodiesel Production via Calcium Oxide Based Catalysts: Current State and Perspective

Biodiesel is a clean, renewable, liquid fuel that can be used in existing diesel engines without modification as pure or blend. Transesterification (the primary process for biodiesel generation) via heterogeneous catalysis using low-cost waste feedstocks for catalyst synthesis improves the economics of biodiesel production. Heterogeneous catalysts are preferred for the industrial generation of biodiesel due to their robustness and low costs due to the easy separation and relatively higher reusability. Calcium oxides found in abundance in nature, e.g., in seashells and eggshells, are promising candidates for the synthesis of heterogeneous catalysts. However, process improvements are required to design productive calcium oxide-based catalysts at an industrial scale. The current work presents an overview of the biodiesel production advancements using calcium oxide-based catalysts (e.g., pure, supported, and mixed with metal oxides). The review discusses different factors involved in the synthesis of calcium oxide-based catalysts, and the effect of reaction parameters on the biodiesel yield of calcium oxide-based catalysis are studied. Further, the common reactor designs used for the heterogeneous catalysis using calcium oxide-based catalysts are explained. Moreover, the catalytic activity mechanism, challenges and prospects of the application of calcium oxide-based catalysts in biodiesel generation are discussed. The study of calcium oxide-based catalyst should continue to be evaluated for the potential of their application in the commercial sector as they remain the pivotal goal of these studies

Cyclic Tetrapyrrolic Photosensitisers from the leaves of Phaeanthus ophthalmicus

<p>Abstract</p> <p>Background</p> <p>Twenty-seven extracts from 26 plants were identified as photo-cytotoxic in the course of our bioassay guided screening program for photosensitisers from 128 extracts prepared from 64 terrestrial plants in two different collection sites in Malaysia - Royal Belum Forest Reserve in the State of Perak and Gunung Nuang in the State of Selangor. One of the photo-cytotoxic extracts from the leaves of <it>Phaeanthus ophtalmicus </it>was further investigated.</p> <p>Results</p> <p>The ethanolic extract of the leaves from <it>Phaeanthus ophtalmicus </it>was able to reduce the <it>in vitro </it>viability of leukaemic HL60 cells to < 50% when exposed to 9.6 J/cm²of a broad spectrum light at a concentration of 20 μg/mL. Dereplication of the photo-cytotoxic fractions from <it>P. ophthalmicus </it>extracts based on TLC R_fvalues and HPLC co-injection of reference tetrapyrrolic compounds enabled quick identification of known photosensitisers, pheophorbide-<it>a</it>, pheophorbide-<it>a </it>methyl ester, 13²-hydroxypheophorbide-<it>a </it>methyl ester, pheophytin-<it>a </it>and 15¹-hydroxypurpurin 7-lactone dimethyl ester. In addition, compound <b>1 </b>which was not previously isolated as a natural product was also identified as 7-formyl-15¹-hydroxypurpurin-7-lactone methyl ester using standard spectroscopic techniques.</p> <p>Conclusions</p> <p>Our results suggest that the main photosensitisers in plants are based on the cyclic tetrapyrrole structure and photosensitisers with other structures, if present, are present in very minor amounts or are not as active as those with the cyclic tetrapyrrole structure.</p

The condition-dependent transcriptional landscape of Burkholderia pseudomallei

This is the final version of the article. Available from the publisher via the DOI in this record.Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes--Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes--quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an "accidental pathogen", where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts.This work was funded by a core grant provided by the Agency for Science, Technology and Research to the Genome Institute of Singapore, and funding from the Defence Medical and Environmental Research Institute, Singapore. This work was supported in part through NIAID contract HHSN266200400035C to BWS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Effect of additivized biodiesel blends on diesel engine performance, emission, tribological characteristics, and lubricant tribology

© 2020 by the authors. This research work focuses on investigating the lubricity and analyzing the engine characteristics of diesel-biodiesel blends with fuel additives (titanium dioxide (TiO2) and dimethyl carbonate (DMC)) and their effect on the tribological properties of a mineral lubricant. A blend of palm-sesame oil was used to produce biodiesel using ultrasound-assisted transesterification. B30 (30% biodiesel + 70% diesel) fuel was selected as the base fuel. The additives used in the current study to prepare ternary fuel blends were TiO2 and DMC. B30 + TiO2 showed a significant reduction of 6.72% in the coefficient of friction (COF) compared to B30. B10 (Malaysian commercial diesel) exhibited very poor lubricity and COF among all tested fuels. Both ternary fuel blends showed a promising reduction in wear rate. All contaminated lubricant samples showed an increment in COF due to the dilution of combustible fuels. Lub + B10 (lubricant + B10) showed the highest increment of 42.29% in COF among all contaminated lubricant samples. B30 + TiO2 showed the maximum reduction (6.76%) in brake-specific fuel consumption (BSFC). B30 + DMC showed the maximum increment (8.01%) in brake thermal efficiency (BTE). B30 + DMC exhibited a considerable decline of 32.09% and 25.4% in CO and HC emissions, respectively. The B30 + TiO2 fuel blend showed better lubricity and a significant improvement in engine characteristics

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

Enzyme classification with peptide programs: a comparative study

<p>Abstract</p> <p>Background</p> <p>Efficient and accurate prediction of protein function from sequence is one of the standing problems in Biology. The generalised use of sequence alignments for inferring function promotes the propagation of errors, and there are limits to its applicability. Several machine learning methods have been applied to predict protein function, but they lose much of the information encoded by protein sequences because they need to transform them to obtain data of fixed length.</p> <p>Results</p> <p>We have developed a machine learning methodology, called peptide programs (PPs), to deal directly with protein sequences and compared its performance with that of Support Vector Machines (SVMs) and BLAST in detailed enzyme classification tasks. Overall, the PPs and SVMs had a similar performance in terms of Matthews Correlation Coefficient, but the PPs had generally a higher precision. BLAST performed globally better than both methodologies, but the PPs had better results than BLAST and SVMs for the smaller datasets.</p> <p>Conclusion</p> <p>The higher precision of the PPs in comparison to the SVMs suggests that dealing with sequences is advantageous for detailed protein classification, as precision is essential to avoid annotation errors. The fact that the PPs performed better than BLAST for the smaller datasets demonstrates the potential of the methodology, but the drop in performance observed for the larger datasets indicates that further development is required.</p> <p>Possible strategies to address this issue include partitioning the datasets into smaller subsets and training individual PPs for each subset, or training several PPs for each dataset and combining them using a bagging strategy.</p

Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data

We describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated-ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read density. To demonstrate that PING predictions from widely available sonicated data can have sufficient spatial resolution to be to be useful for biological inference, we use Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome positioning around transcription factor binding sites due to tamoxifen stimulation, to discriminate functional and non-functional transcription factor binding sites more effectively than with enrichment profiles, and to confirm that the pioneer transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA

An essential role for the Id1/PI3K/Akt/NFkB/survivin signalling pathway in promoting the proliferation of endothelial progenitor cells in vitro

The enhancement of re-endothelialisation is a critical therapeutic option for repairing injured blood vessels. Endothelial progenitor cells (EPCs) are the major source of cells that participate in endothelium repair and contribute to re-endothelialisation by reducing neointima formation after vascular injury. The over-expression of the inhibitor of differentiation or DNA binding 1 (Id1) significantly improved EPC proliferation. This study aimed to investigate the effects of Id1 on the phosphatidylinositol-3-kinase (PI3K)/Akt/nuclear factor kappa B (NFκB)/survivin signalling pathway and its significance in promoting EPC proliferation in vitro. Spleen-derived EPCs were cultured as previously described. Id1 was presented at low levels in EPCs, and was rapidly up-regulated by stimulation with vascular endothelial growth factor. We demonstrated that transient transfection of Id1 into EPCs activated the PI3K/Akt/NFκB/survivin signalling pathway and promoted EPC proliferation. The proliferation of EPCs was extensively inhibited by silencing of endogenous Id1, and knockdown of Id1 expression led to suppression of PI3K/Akt/NFκB/survivin signalling pathway in EPCs. In addition, blockade by the PI3K-specific inhibitor LY294002, Akt inhibitor, the NFκB inhibitor BAY 11-7082, the survivin inhibitor Curcumin, or the survivin inhibitor YM155 reduced the effects of Id1 transfection. These results suggest that the Id1/PI3K/Akt/NFκB/survivin signalling pathway plays a critical role in EPC proliferation. The Id1/PI3K/Akt/NFκB/survivin signalling pathway may represent a novel therapeutic target in the prevention of restenosis after vascular injury

Simultaneous Quantitation of Amino Acid Mixtures using Clustering Agents

A method that uses the abundances of large clusters formed in electrospray ionization to determine the solution-phase molar fractions of amino acids in multi-component mixtures is demonstrated. For solutions containing either four or 10 amino acids, the relative abundances of protonated molecules differed from their solution-phase molar fractions by up to 30-fold and 100-fold, respectively. For the four-component mixtures, the molar fractions determined from the abundances of larger clusters consisting of 19 or more molecules were within 25% of the solution-phase molar fractions, indicating that the abundances and compositions of these clusters reflect the relative concentrations of these amino acids in solution, and that ionization and detection biases are significantly reduced. Lower accuracy was obtained for the 10-component mixtures where values determined from the cluster abundances were typically within a factor of three of their solution molar fractions. The lower accuracy of this method with the more complex mixtures may be due to specific clustering effects owing to the heterogeneity as a result of significantly different physical properties of the components, or it may be the result of lower S/N for the more heterogeneous clusters and not including the low-abundance more highly heterogeneous clusters in this analysis. Although not as accurate as using traditional standards, this clustering method may find applications when suitable standards are not readily available