Raw metaproteomic data of "Modulated Production of Extracellular Vesicles Provides Protective and Effective Signaling Routes in Natural Scenarios"
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia Coli Staphylococcus Aureus
SUBMITTER: 
Qiansheng Huang
PROVIDER: PXD065377 | iProX | Tue Jun 24 00:00:00 BST 2025
REPOSITORIES: iProX
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Project description:In cheese production, microorganisms are usually added at the beginning of the process as primary starters to drive curd acidification, while secondary microorganisms, with other pro-technological features important for cheese ripening, are added as selected cultures. This research aimed to investigate the possibilities of influencing and selecting the raw milk microbiota using artisanal traditional methods, providing a simple method to produce a natural supplementary culture. We investigated the production of an enriched raw milk whey culture (eRWC), a natural adjunct microbial culture produced from mixing an enriched raw milk (eRM) with a natural whey culture (NWC). The raw milk was enriched by spontaneous fermentation for 21 d at 10°C. Three milk enrichment protocols were tested: heat treatment before incubation, heat treatment plus salt addition, and no treatment. The eRMs were then co-fermented with NWC (ratio of 1:10) at 38°C for 6 h (young eRWC) and 22 h (old eRWC). Microbial diversity during cultures' preparation was evaluated through the determination of colony forming units on selective growth media, and next-generation sequencing (16S rRNA gene amplicon sequencing). The enrichment step increased the streptococci and lactobacilli but reduced microbial richness and diversity of the eRMs. Although the lactic acid bacteria viable count was not significantly different between the eRWCs, they harbored higher microbial richness and diversity than NWC. Natural adjunct cultures were then tested in cheese making trials, following the microbial development, and assessing the chemical quality of the 120 d ripened cheeses. The use of eRWCs slowed the curd acidification in the first hours of cheese making but the pH 24 h after production settled to equal values for all the cheeses. Although the use of diverse eRWCs contributed to having a richer and more diverse microbiota in the early stages of cheese making, their effect decreased over time during ripening, showing an inferior effect to the raw milk microbiota. Even if more research is needed, the optimization of such a tool could be an alternative to the practice of isolating, geno-pheno-typing, and formulating mixed-defined-strain adjunct cultures that require knowledge and facilities not always available for artisanal cheese makers.
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Project description:The reported study concerns the introduction of renewable raw materials into the formulation of rigid polyurethane foams in the quest for the sustainable development of polymer composites. In this study, rigid polyurethane foam composites were prepared using 75 wt.% of rapeseed oil-based polyol and 15 parts per hundred parts of polyol (php) of natural fillers such as chokeberry pomace, raspberry seeds, as well as hazelnut and walnut shells. The influence of the used raw materials on the foaming process, structure, and properties of foams was investigated using a FOAMAT analyzer and a wide selection of characterization techniques. The introduction of renewable raw materials limited reactivity of the system, which reduced maximum temperature of the foaming process. Moreover, foams prepared using renewable raw materials were characterized by a more regular cell structure, a higher share of closed cells, lower apparent density, lower compressive strength and glass transition temperature, low friability (<2%), low water absorption (<1%), high dimensional stability (<±0.5%) and increased thermal stability. The proper selection and preparation of the renewable raw materials and the rational development of the polyurethane recipe composition allow for the preparation of environmentally-friendly foam products with beneficial application properties considering the demands of the circular economy in the synthesis of rigid foams.
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Project description:The current study underlines biotechnological valorization of the accumulated and the non-efficiently utilized agro-industrial orange peel waste to produce polygalacturonase (PGase), an industrially important enzyme with augmented demands in enzymes markets, from Bacillus licheniformis SHG10. Sequential statistical optimization of PGase production was performed through one variable at a time (OVAT) approach, Plackett-Burman (PB) and response surface methodology (RSM). The impact of introduction of six raw agro-industrial wastes (orange, lemon, banana, pomegranate, artichoke peel wastes and wheat bran) and other synthetic carbon sources separately into the fermentation broth on PGase productivity was studied through OVAT approach. Orange peel waste as sole raw carbon source in basal medium proved to be the best PGase inducer. It promoted PGase productivity with relative specific activity of 166% comparable with the effect imposed by synthetic citrus pectin as a reference inducer. Three key determinants (orange peel waste, pH of the production medium and incubation temperature) had RSM optimal levels of 1.76% (w/v), 8.0 and 37.8°C, respectively along with maximal PGase level (2.69 μg galacturonic acid. min(-1). mg(-1)) within 48 hrs. Moreover, SHG10 PGase exhibited activity over a wide range of pH (3-11) and an optimal activity at 50°C. Data greatly encourage pilot scale PGase production from B. licheniformis SHG10.
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Project description:Stress acclimation is an effective mechanism that plants acquired for adaption to dynamic environmental conditions. After undergoing cold acclimation, plants become more tolerant to cold stress. In order to understand the mechanism of cold acclimation, we performed a systematic, comprehensive study of cold response and acclimation in Cassava (Manihot esculenta), a staple crop and major food source in the tropical regions of the world. We profiled mRNA genes and small-RNA species, using next generation sequencing, and performed an integrative analysis of the transcriptome and microRNAome of Cassava across the normal condition, a moderate cold stress at 14M-BM-0C, a harsh stress at 4M-BM-0C after cold acclimation at 14M-BM-0C, and a cold shock from 24M-BM-0C to 4M-BM-0C. Two results from the analysis were striking. First, the moderate stress and cold shock, despite a difference of 10M-BM-0C between the two, triggered comparable degrees of perturbation to the transcriptome; in contrary, further harsh stress after cold acclimation resulted in a much smaller degree of transcriptome variation. Second and more importantly, about two thirds of the up- or down-regulated genes after moderate stress reversed their expression to down- or up-regulation, respectively, under harsh stress after cold acclimation, resulting in a genome-wide rewiring of regulatory networks. MicroRNAs, which are key post-transcriptional gene regulators, were major players in this massive rewiring of genetic circuitry. Further, a function enrichment analysis of the perturbed genes revealed that cold acclimation helped the plant to develop immunity to further harsh stress by exclusively inducing genes with functions of nutrient reservoir; in contrast, many genes with functions of viral reproduction were induced by cold shock. Our study revealed, for the first time, the molecular basis of stress acclimation in plants, and shed lights on the role of microRNA gene regulation in cold response and acclimation in Euphorbia. Three organs/tissues (folded leaf, fully expanded leaf and roots) of Cassava cultivar SC124 harvested at 6h, 24h and 5d for three cold treatments of CA, CCA and CS, for gene expression profiling at the stages of initial response, secondary response, and functional adaption to cold stresses. Total RNA of each sample was isolated individually, and then pooled with an equal amount from each sample into one for profiling. As a result, four mRNA libraries and four small-RNA libraries, corresponding to the conditions of CA, CCA, CS and NC, were constructed.
2014-08-18 | E-GEOD-52176 | biostudies-arrayexpress
Project description:RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and clinical science. Its immense popularity is due in large part to the continuous efforts of the bioinformatics community to develop accurate and scalable computational tools to analyze the enormous amounts of transcriptomic data that it produces. RNA-seq analysis enables genes and their corresponding transcripts to be probed for a variety of purposes, such as detecting novel exons or whole transcripts, assessing expression of genes and alternative transcripts, and studying alternative splicing structure. It can be a challenge, however, to obtain meaningful biological signals from raw RNA-seq data because of the enormous scale of the data as well as the inherent limitations of different sequencing technologies, such as amplification bias or biases of library preparation. The need to overcome these technical challenges has pushed the rapid development of novel computational tools, which have evolved and diversified in accordance with technological advancements, leading to the current myriad of RNA-seq tools. These tools, combined with the diverse computational skill sets of biomedical researchers, help to unlock the full potential of RNA-seq. The purpose of this review is to explain basic concepts in the computational analysis of RNA-seq data and define discipline-specific jargon.
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Project description:N-demethylases have been reported to remove the methyl groups on primary or secondary amines, which could further affect the properties and functions of biomacromolecules or chemical compounds; however, the substrate scope and the robustness of N-demethylases have not been systematically investigated. Here we report the recreation of natural evolution in key microdomains of the Thermomicrobium roseum sarcosine oxidase (TrSOX), an N-demethylase with marked stability (melting temperature over 100 °C) and enantioselectivity, for enhanced substrate scope and catalytic efficiency on -C-N- bonds. We obtained the structure of TrSOX by crystallization and X-ray diffraction (XRD) for the initial framework. The natural evolution in the nonconserved residues of key microdomains-including the catalytic loop, coenzyme pocket, substrate pocket, and entrance site-was then identified using ancestral sequence reconstruction (ASR), and the substitutions that accrued during natural evolution were recreated by site-directed mutagenesis. The single and double substitution variants catalyzed the N-demethylation of N-methyl-L-amino acids up to 1800- and 6000-fold faster than the wild type, respectively. Additionally, these single substitution variants catalyzed the terminal N-demethylation of non-amino-acid compounds and the oxidation of the main chain -C-N- bond to a -C=N- bond in the nitrogen-containing heterocycle. Notably, these variants retained the enantioselectivity and stability of the initial framework. We conclude that the variants of TrSOX are of great potential use in N-methyl enantiomer resolution, main-chain Schiff base synthesis, and alkaloid modification or degradation.
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Project description:Mycobacterium ulcerans produces a macrolide exotoxin, mycolactone which suppresses immune cells activity, is toxic to most cells and the key virulence factor in the pathogenesis of Buruli ulcer disease. Mycolactone is reported to mediate the production of reactive oxygen species in keratinocytes; cells that play critical role in wound healing. Increased levels of reactive oxygen species have been shown to disrupt the well-ordered process of wound repair; hence, the function of wound-healing cells such as macrophages, keratinocytes, and fibroblast could be impaired in the presence of the reactive oxygen species mediator, mycolactone. To ensure regeneration of tissues in chronic ulcers, with proper and timely healing of the wounds, natural antioxidants that can combat the effects of induced reactive oxygen species in wound-healing cells ought to be investigated. Reactive oxygen species activity was determined in mycolactone-treated RAW 264.7 macrophages and the scavenging ability of the antioxidants (ascorbic acid, gallic acid, and green tea kombucha) against mycolactone-induced reactive oxygen species (superoxide anions) was assessed using fluorescein probe (DCF-DA) and nitroblue tetrazolium dye. Cytotoxicity of the antioxidants, mycolactone, and the protective effect of the antioxidants on the cells upon treatment with mycolactone were determined using the Alamar blue assay. The expression levels of endogenous antioxidant enzyme genes (superoxide dismutase, catalase, and glutathione peroxidase) in response to mycolactone-mediated reactive oxygen species were determined using RT-qPCR. Mycolactone induced the production of reactive oxygen species in RAW 264.7 macrophages, and the resulting superoxide anions were scavenged by some of the antioxidants. The selected endogenous antioxidant enzyme genes in the macrophages were upregulated in the presence of the antioxidants and mycolactone. The exogenously supplied ascorbic acid and green tea kombucha offered moderate protection to the macrophages against the toxicity of mycolactone. We conclude that the results provide insights into alternate and adjunct therapeutic approaches in Buruli ulcer treatment, which could significantly attenuate the toxicity of the pathogenic factor; mycolactone.
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Project description:Zika virus (ZIKV) is a major human pathogen. ZIKV can replicate in female and male reproductive organs, thus facilitating the human-human transmission cycle. Viral shedding in the semen can increase the risk of ZIKV transmission through sexual mode. Therefore, the vaginal and anorectal mucosa are relevant sites for ZIKV infection. However, the pathobiology of ZIKV transmission through the rectal route is not well understood. Here, we utilize a mouse model system to investigate the immunopathological consequences following ZIKV infection of the rectal mucosa compared to a subcutaneous route of infection. We show that ZIKV-rectal inoculation results in viremia with subclinical infection. ZIKV infects the mucosal epithelium and submucosal dendritic cells, inducing immune and inflammatory cell infiltration. Rectal transmission of ZIKV resulted in the generation of serum-neutralizing antibody responses. Mass cytometry analyses of splenocytes showed a significantly reduced level of inflammatory monocyte and neutrophil cellular responses in the rectal route group. Furthermore, immunological priming through the rectal mucosa with an attenuated ZIKV strain resulted in significant protection from lethal subcutaneous ZIKV challenge, further eliciting robust memory CD4-positive (CD4+) and CD8+ T-cell and ZIKV-specific serum-neutralizing antibody responses. Thus, our study provides deeper immunopathobiological insights on rectal transmission and highlights a rational strategy for mucosal immunization. This model system recapitulates clinical aspects of human ZIKV disease outcome, where most infections are well controlled and result in subclinical and asymptomatic outcomes.IMPORTANCE Zika virus is a clinically significant human pathogen that is primarily transmitted and spread by Aedes species mosquitoes but is also sexually transmissible. The recent pandemic in the Americas led to an unprecedented increase of newborn babies with developmental brain and eye abnormalities. To date, there is no licensed vaccine or therapeutic intervention available for the fight against ZIKV. Understanding the sexual transmission of ZIKV through vaginal and rectal routes is necessary to restrict virus transmission and spread. This study examines the early immunological and pathological consequences of rectal and subcutaneous routes of ZIKV infection using a mouse model. We characterized the primary target cells of ZIKV infection and the subsequent mucosal immune responses to infection, and we demonstrate the protective effect of mucosal rectal immunization using an attenuated ZIKV strain. This mucosal vaccination approach can be further developed to prevent future ZIKV outbreaks.
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Project description:BackgroundA few recent large efforts significantly expanded the collection of human-associated bacterial genomes, which now contains thousands of entities including reference complete/draft genomes and metagenome assembled genomes (MAGs). These genomes provide useful resource for studying the functionality of the human-associated microbiome and their relationship with human health and diseases. One application of these genomes is to provide a universal reference for database search in metaproteomic studies, when matched metagenomic/metatranscriptomic data are unavailable. However, a greater collection of reference genomes may not necessarily result in better peptide/protein identification because the increase of search space often leads to fewer spectrum-peptide matches, not to mention the drastic increase of computation time. Video Abstract METHODS: Here, we present a new approach that uses two steps to optimize the use of the reference genomes and MAGs as the universal reference for human gut metaproteomic MS/MS data analysis. The first step is to use only the high-abundance proteins (HAPs) (i.e., ribosomal proteins and elongation factors) for metaproteomic MS/MS database search and, based on the identification results, to derive the taxonomic composition of the underlying microbial community. The second step is to expand the search database by including all proteins from identified abundant species. We call our approach HAPiID (HAPs guided metaproteomics IDentification).ResultsWe tested our approach using human gut metaproteomic datasets from a previous study and compared it to the state-of-the-art reference database search method MetaPro-IQ for metaproteomic identification in studying human gut microbiota. Our results show that our two-steps method not only performed significantly faster but also was able to identify more peptides. We further demonstrated the application of HAPiID to revealing protein profiles of individual human-associated bacterial species, one or a few species at a time, using metaproteomic data.ConclusionsThe HAP guided profiling approach presents a novel effective way for constructing target database for metaproteomic data analysis. The HAPiID pipeline built upon this approach provides a universal tool for analyzing human gut-associated metaproteomic data.
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Project description:Raw metaproteomic data of Chinese indoor dust derived extracellular vesicles. These dust samples were collected in the summer of 2022 and were immediately sent to the laboratory for processing. The extracellular vesicles of dust were subjected to ultracentrifugation, and they were further purified using iodixanol density gradient ultracentrifugation. After extracting the extracellular vesicles, metaproteomic sequencing was performed.
2025-08-30 | PXD067899 | Pride