Respiratory pathogens like Streptococcus pneumoniae can cause severe pneumonia. Nonetheless, mechanically ventilated intensive care patients, who have a high risk of contracting pneumonia, rarely develop pneumococcal pneumonia. Mechanically ventilated patients are at risk of contracting pneumonia. Therefore, these patients often receive prophylactic systemic antimicrobial therapy. Intriguingly however, a previous study showed that antimicrobial activity in bronchoalveolar aspirates (here referred to as “sputa”) from ventilated patients was only partially explained by antibiotic therapy. Here we report that sputa from these patients presented distinct proteome signatures depending on the presence or absence of antimicrobial activity. Moreover, we show that the same distinction applied to antibodies against Streptococcus pneumoniae , which is a major causative agent of pneumonia. Specifically, the investigated sputa that inhibited growth of S. pneumoniae , while containing subinhibitory levels of the antibiotic cefotaxime, presented elevated levels of proteins implicated in innate immune defenses, including complement and apolipoprotein-associated proteins. In contrast, S. pneumoniae -inhibiting sputa with relatively high cefotaxime concentrations or noninhibiting sputa contained higher levels of proteins involved in inflammatory responses, such as neutrophil elastase-associated proteins. In an immunoproteomics analysis, 18 out of 55 S. pneumoniae antigens tested showed significantly increased levels of IgGs in inhibiting sputa. Hence, proteomics and immunoproteomics revealed elevated levels of antimicrobial host proteins or S. pneumoniae antigen-specific IgGs in pneumococcal growth-inhibiting sputa, thus explaining their anti-pneumococcal activity. IMPORTANCE Respiratory pathogens like Streptococcus pneumoniae can cause severe pneumonia. Nonetheless, mechanically ventilated intensive care patients, who have a high risk of contracting pneumonia, rarely develop pneumococcal pneumonia. This suggests the presence of potentially protective antimicrobial agents in their lung environment. Our present study shows for the first time that bronchoalveolar aspirates, “sputa,” of ventilated patients in a Dutch intensive care unit were characterized by three distinct groups of proteome abundance signatures that can explain their anti-pneumococcal activity. Importantly, this anti-pneumococcal sputum activity was related either to elevated levels of antimicrobial host proteins or to antibiotics and S. pneumoniae -specific antibodies. Further, the sputum composition of some patients changed over time. Therefore, we conclude that our study may provide a novel tool to measure changes that are indicative of infection-related conditions in the lungs of mechanically ventilated patients.
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Saliva diagnostics have become increasingly popular due to their non-invasive nature and patient-friendly collection process. Various collection methods are available, yet these are not always well standardized for either quantitative or qualitative analysis. In line, the objective of this study was to evaluate if measured levels of various biomarkers in the saliva of healthy individuals were affected by three distinct saliva collection methods: 1) unstimulated saliva, 2) chew stimulated saliva, and 3) oral rinse. Saliva samples from 30 healthy individuals were obtained by the three collection methods. Then, the levels of various salivary biomarkers such as proteins and ions were determined. It was found that levels of various biomarkers obtained from unstimulated saliva were comparable to those in chew stimulated saliva. The levels of potassium, sodium, and amylase activity differed significantly among the three collection methods. Levels of all biomarkers measured using the oral rinse method significantly differed from those obtained from unstimulated and chew-stimulated saliva. In conclusion, both unstimulated and chew-stimulated saliva provided comparable levels for a diverse group of biomarkers. However, the results obtained from the oral rinse method significantly differed from those of unstimulated and chew-stimulated saliva, due to the diluted nature of the saliva extract.
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For the future circular economy, renewable carbon feedstocks manifest considerable promise for synthesizing sustainable and biodegradable polyhydroxyalkanoate (PHA). In this study, 16 wt% and 30 wt% PHA (cell dry weight) are respectively produced by thermophilic Caldimonas thermodepolymerans from beechwood xylan and wheat arabinoxylan as the sole carbon source. Moreover, an in silico study of the potential xylan-degrading proteins was conducted using proteome sequencing and CAZyme specialized bioinformatic tools. This study demonstrates the feasibility of utilizing complex polysaccharide substrates for PHA biosynthesis, thereby potentially eliminate additional processing steps and reducing overall production costs for sustainable plastic.
MULTIFILE
Next-generation sequencing technology allows culture- independent analysis of species and genes present in a complex microbial community. Such metagenomics may overcome the inability to culture microbes in isolation. Microbial communities of interest are for example responsible for making biogas. Many applications in metagenomics focus on 16S RNA analysis. We here evaluate the possibility of whole genome analysis (WGS) as approach for metagenomics studies.Samples (Table 1) from three biogas installations fed with different feedstock were used for DNA isolation and WGS analysis. Short (75b) Illumina paired-end DNA sequence reads were generated and assembled into larger continuous stretches (contigs),AcknowledgementsResults show that WGS is feasible for complex community analysis. Large groups of organisms (for example the class Methanomicrobia) are present in all samples with a possible role in the biogas production pathway.Assemble reads into contigs•meta-velveth as metagenomics reads assemblerSequencesimilaritysearch•proteome reference database from all currently available Bacteria and Achaea genomesAssign hits to taxa•Lowest common ancestor method incorporated in MEGAN4Such studies will help to identify and use microbial species for future improvements of biogas production dependence on process parameters and feedstock.
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Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
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Om inzicht te krijgen in spierveroudering is genexpressie gemeten in vastus lateralis biopten van jonge en oude mannen en vrouwen. We vonden dat tijdens het ouder worden bij beide geslachten dezelfde categorieën genen in spieren worden aan- en uitgeschakeld (“gereguleerd”); de mate van deze zogenaamde differentiële expressie was echter geslachtsspecifiek. Bij mannen was oxidatieve fosforylering het meest in het oog springende proces, en bij vrouwen was dit celgroei gemedieerd door AKT-signalering. De conclusie is dat dezelfde processen zijn geassocieerd met skeletspierveroudering bij mannen en vrouwen, maar dat de differentiële expressie van die processen geslachtsspecifiek is.
MULTIFILE
The full potential of predictive maintenance has not yet been utilised. Current solutions focus on individual steps of the predictive maintenance cycle and only work for very specific settings. The overarching challenge of predictive maintenance is to leverage these individual building blocks to obtain a framework that supports optimal maintenance and asset management. The PrimaVera project has identified four obstacles to tackle in order to utilise predictive maintenance at its full potential: lack of orchestration and automation of the predictive maintenance workflow, inaccurate or incomplete data and the role of human and organisational factors in data-driven decision support tools. Furthermore, an intuitive generic applicable predictive maintenance process model is presented in this paper to provide a structured way of deploying predictive maintenance solutions https://doi.org/10.3390/app10238348 LinkedIn: https://www.linkedin.com/in/john-bolte-0856134/
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Background: Lung fibroblasts are implicated in abnormal tissue repair in chronic obstructive pulmonary disease (COPD). The exact mechanisms are unknown and comprehensive analysis comparing COPD- and control fibroblasts is lacking. Aim: To gain insight in the role of lung fibroblasts in COPD pathology using unbiased proteomic and transcriptomic analysis. Methods: Protein and RNA was isolated from cultured parenchymal lung fibroblasts of 17 stage IV COPD patients and 16 non-COPD controls. Proteins were analyzed using LC-MS/MS and RNA through RNA sequencing. Differential protein and gene expression in COPD was assessed via linear regression, followed by pathway enrichment, correlation analysis and immunohistological staining in lung tissue. Proteomic and transcriptomic data was compared to investigate the overlap and correlation between both levels of data. Results: We identified 40 differentially expressed (DE) proteins and zero DE genes between COPD and control fibroblasts. The most significant DE proteins were HNRNPA2B1 and FHL1. Thirteen of the 40 proteins were previously associated with COPD, including FHL1 and GSTP1. Six of the 40 proteins were related to telomere maintenance pathways, and were positively correlated with the senescence marker LMNB1. No significant correlation between gene and protein expression was observed for the 40 proteins. Conclusions: The 40 DE proteins in COPD fibroblasts include previously described COPD proteins (FHL1, GSTP1) and new COPD research targets like HNRNPA2B1. Lack of overlap and correlation between gene and protein data supports the use of unbiased proteomics analysis and indicates that different types of information are generated with both methods.
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Five methods were compared to determine the best technique for accurate identification of coagulase-negative staphylococci (CoNS) (n=142 strains). MALDI-TOF MS showed the best results for rapid and accurate CoNS differentiation (correct identity in 99.3%). An alternative to this approach could be Vitek2 combined with partial tuf gene sequencing.
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Accumulation of non-degradable plastic waste in the environment might be prevented by the use of biodegradable polyhydroxyalkanoate (PHA). In this study, the thermophile Schlegelella thermodepolymerans produced up to 80 wt% PHA based on dry cell mass. The largest PHA granules were found in the cells within 48 h using 20 g/L xylose, a C/N ratio of 100, an initial pH of 7, at 50 °C. The substrate consumption, pH changes, and cell growth were monitored, revealing the time dependency of PHA production in S. thermodepolymerans. The metabolic pathways from xylose to PHA were identified based on proteomic analysis, revealing involvement of classic phaCAB, de novo fatty acid biosynthesis, and fatty acid β-oxidation. In addition, it was shown that S. thermodepolymerans degraded extracellular PHA with a high efficiency at 50 °C.
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