Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p><it>Scheffersomyces stipitis</it> is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as <it>Saccharomyces cerevisiae</it>, the onset of fermentation in <it>S. stipitis</it> is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though <it>S. stipitis</it> has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of <it>S. stipitis</it> during aerobic growth on glucose under batch and chemostat cultivations.</p> <p>Results</p> <p>Starting from the analysis of physiological data, we confirmed through ¹³C-based flux analysis the fully respiratory metabolism of <it>S. stipitis</it> when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for <it>S. cerevisiae</it> under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with <it>S. cerevisiae</it>. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through <it>in silico</it> transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways.</p> <p>Conclusions</p> <p>The work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for <it>S. stipitis</it> under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for <it>S. cerevisiae</it> under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, <it>in silico</it> analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of <it>S. stiptis</it> is investigated in details and is compared to <it>S. cerevisiae</it>. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of <it>S. stipitis</it> as cell factory.</p

Biochar from Pine Wood, Rice Husks and Iron-Eupatorium Shrubs for Remediation Applications: Surface Characterization and Experimental Tests for Trichloroethylene Removal

Nowadays porous materials from organic waste, i.e., Biochar (BC), are receiving increased attention for environmental applications. This study adds information on three BCs that have undergone a number of studies in recent years. A Biochar from pine wood, one from rice husk and one from Eupatorium shrubs enriched with Iron, labelled as PWBC, RHBC and EuFeBC respectively, are evaluated for Trichloroethylene (TCE) removal from aqueous solution. Physical-chemical description is performed by SEM-EDS and BET analysis. The decrease of TCE over time follows a pseudo-second order kinetics with increased removal by the PWBC. Freundlich and Langmuir models well fit equilibrium test data. The optimized values of the maximum adsorbed amount, qmax (mg g−1), follows this order 109.41 PWBC &gt; 30.35 EuFeBC &gt; 21.00 RHBC. Fixed-bed columns are also carried out. Best performance is again achieved by PWBC, which operates for a higher number of pore volume, followed by EuFeBC and RHBC. Continuous testing confirms batch studies and makes it possible to evaluate the workability of materials in configurations closer to reality. Results are promising for potential environmental application. In particular, the characterization of several classes of contaminants opens the doors to possible uses in mixed contamination case

Assessment of Long-Term Fermentability of PHA-Based Materials from Pure and Mixed Microbial Cultures for Potential Environmental Applications

The use of polyhydroxyalkanoates (PHA) as slow-release electron donors for environmental remediation represents a novel and appealing application that is attracting considerable attention in the scientific community. In this context, here, the fermentation pattern of different types of PHA-based materials has been investigated in batch and continuous-flow experiments. Along with commercially available materials, produced from axenic microbial cultures, PHA produced at pilot scale by mixed microbial cultures (MMC) using waste feedstock have been also tested. As a main finding, a rapid onset of volatile fatty acids (VFA) production was observed with a low-purity MMC-deriving material, consisting of microbial cells containing 56% (on weight basis) of intracellular PHA. Indeed, with this material a sustained, long-term production of organic acids (i.e., acetic, propionic, and butyric acids) was observed. In addition, the obtained yield of conversion into acids (up to 70% gVFA/gPHA) was higher than that obtained with the other tested materials, made of extracted and purified PHA. These results clearly suggest the possibility to directly use the PHA-rich cells deriving from the MMC production process, with no need of extraction and purification procedures, as a sustainable and effective carbon source bringing remarkable advantages from an economic and environmental point of view

Assessment of long-term fermentability of pha-based materials from pure and mixed microbial cultures for potential environmental applications

The use of polyhydroxyalkanoates (PHA) as slow-release electron donors for environmental remediation represents a novel and appealing application that is attracting considerable attention in the scientific community. In this context, here, the fermentation pattern of different types of PHA-based materials has been investigated in batch and continuous-flow experiments. Along with commercially available materials, produced from axenic microbial cultures, PHA produced at pilot scale by mixed microbial cultures (MMC) using waste feedstock have been also tested. As a main finding, a rapid onset of volatile fatty acids (VFA) production was observed with a low-purity MMC-deriving material, consisting of microbial cells containing 56% (on weight basis) of intracellular PHA. Indeed, with this material a sustained, long-term production of organic acids (i.e., acetic, propionic, and butyric acids) was observed. In addition, the obtained yield of conversion into acids (up to 70% gVFA/gPHA) was higher than that obtained with the other tested materials, made of extracted and purified PHA. These results clearly suggest the possibility to directly use the PHA-rich cells deriving from the MMC production process, with no need of extraction and purification procedures, as a sustainable and effective carbon source bringing remarkable advantages from an economic and environmental point of view

Effect of Helicobacter pylori Vacuolating Toxin on Maturation and Extracellular Release of Procathepsin D and on Epidermal Growth Factor Degradation

Abstract The effect of vacuolating toxin (VacA) fromHelicobacter pylori on endosomal and lysosomal functions was studied by following procathepsin D maturation and epidermal growth factor (EGF) degradation in HeLa cells exposed to the toxin. VacA inhibited the conversion of procathepsin D (53 kDa) into both the intermediate (47 kDa) and the mature (31 kDa) form. Nonprocessed cathepsin D was partly retained inside cells and partly secreted in the extracellular medium via the constitutive secretion pathway. Intracellular degradation of EGF was also inhibited by VacA with a similar dose-response curve. VacA did not alter endocytosis, cell surface recycling, and retrograde transport from plasma membrane totrans-Golgi network and endoplasmic reticulum, as estimated by using transferrin, diphtheria toxin, and ricin as tracers. Subcellular fractionation of intoxicated cells showed that procathepsin D and nondegraded EGF accumulate in lysosomes. Measurements of intracellular acidification with fluorescein isothiocyanate-dextran revealed a partial neutralization of the lumen of endosomes and lysosomes, sufficient to account for both mistargeting of procathepsin D outside the cell and the decreased activity of lysosomal proteases

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation >= 0.99) and high consistency between the two platforms for analysis of gene expression levels (correlation >= 0.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data

Proinflammatory effects of bare and PEGylated ORMOSIL-, PLGA- and SUV-NPs on monocytes and PMNs and their modulation by f-MLP

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Long-Term Drug Survival and Effectiveness of Secukinumab in Patients with Moderate to Severe Chronic Plaque Psoriasis: 42-Month Results from the SUPREME 2.0 Study

Purpose: SUPREME, a phase IIIb study conducted in Italy, demonstrated safety and high efficacy of secukinumab for up to 72 weeks in patients with moderate-to-severe plaque-type psoriasis. SUPREME 2.0 study aimed to provide real-world data on the long-term drug survival and effectiveness of secukinumab beyond 72 weeks. Patients and Methods: SUPREME 2.0 is a retrospective observational chart review study conducted in patients previously enrolled in SUPREME study. After the end of the SUPREME study, eligible patients continued treatment as per clinical practice, and their effectiveness and drug survival data were retrieved from medical charts. Results: Of the 415 patients enrolled in the SUPREME study, 297 were included in SUPREME 2.0; of which, 210 (70.7%) continued secukinumab treatment throughout the 42-month observation period. Patients in the biologic-naïve cohort had higher drug survival than those in the biologic-experienced cohort (74.9% vs 61.7%), while HLA-Cw6–positive and HLA-Cw6–negative patients showed similar drug survival (69.3% and 71.9%). After 42 months, Psoriasis Area and Severity Index (PASI) 90 was achieved by 79.6% of patients overall; with a similar proportion of biologic-naïve and biologic-experienced patients achieving PASI90 (79.8% and 79.1%). The mean absolute PASI score reduced from 21.94 to 1.38 in the overall population, 21.90 to 1.24 in biologic-naïve and 22.03 to 1.77 in biologic-experienced patients after 42 months. The decrease in the absolute PASI score was comparable between HLACw6–positive and HLA–Cw6-negative patients. The baseline Dermatology Life Quality Index scores also decreased in the overall patients (10.5 to 2.32) and across all study sub-groups after 42 months. Safety was consistent with the known profile of secukinumab, with no new findings. Conclusion: In this real-world cohort study, secukinumab showed consistently high long-term drug survival and effectiveness with a favourable safety profile

Long-Term Drug Survival and Effectiveness of Secukinumab in Patients with Moderate to Severe Chronic Plaque Psoriasis: 42-Month Results from the SUPREME 2.0 Study

Purpose: SUPREME, a phase IIIb study conducted in Italy, demonstrated safety and high efficacy of secukinumab for up to 72 weeks in patients with moderate-to-severe plaque-type psoriasis. SUPREME 2.0 study aimed to provide real-world data on the long-term drug survival and effectiveness of secukinumab beyond 72 weeks.Patients and Methods: SUPREME 2.0 is a retrospective observational chart review study conducted in patients previously enrolled in SUPREME study. After the end of the SUPREME study, eligible patients continued treatment as per clinical practice, and their effectiveness and drug survival data were retrieved from medical charts.Results: Of the 415 patients enrolled in the SUPREME study, 297 were included in SUPREME 2.0; of which, 210 (70.7%) continued secukinumab treatment throughout the 42-month observation period. Patients in the biologic-naive cohort had higher drug survival than those in the biologic-experienced cohort (74.9% vs 61.7%), while HLA-Cw6-positive and HLA-Cw6-negative patients showed similar drug survival (69.3% and 71.9%). After 42 months, Psoriasis Area and Severity Index (PASI) 90 was achieved by 79.6% of patients overall; with a similar proportion of biologic-naive and biologic-experienced patients achieving PASI90 (79.8% and 79.1%). The mean absolute PASI score reduced from 21.94 to 1.38 in the overall population, 21.90 to 1.24 in biologic-naive and 22.03 to 1.77 in biologic-experienced patients after 42 months. The decrease in the absolute PASI score was comparable between HLA-Cw6-positive and HLA-Cw6-negative patients. The baseline Dermatology Life Quality Index scores also decreased in the overall patients (10.5 to 2.32) and across all study sub-groups after 42 months. Safety was consistent with the known profile of secukinumab, with no new findings. Conclusion: In this real-world cohort study, secukinumab showed consistently high long-term drug survival and effectiveness with a favourable safety profile