Transcriptome analysis of Neisseria meningitidis strain MC58 in human whole blood
Ontology highlight
ABSTRACT:
ORGANISM(S): Neisseria meningitidis
SUBMITTER: Alessandro Muzzi
PROVIDER: E-TABM-1115 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival.
Echenique-Rivera Hebert H Muzzi Alessandro A Del Tordello Elena E Seib Kate L KL Francois Patrice P Rappuoli Rino R Pizza Mariagrazia M Serruto Davide D
PLoS pathogens 20110505 5
During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expressi ...[more]
Similar Datasets
Project description:Transcriptome analysis of Neisseria meningitidis strain MC58 during a time course growth in GC medium
2011-06-09 | E-TABM-1113 | biostudies-arrayexpress
Project description:Analysis of monocyte-derived dendritic cells (MoDC) gene expression signature induced by TLR agonists the in presence or in the absence of PP2.
2010-06-18 | E-TABM-1018 | biostudies-arrayexpress
Project description:The outcome of many infections depends on the initial interactions between agent and host. Aiming at elucidating the effect of the M. tuberculosis Mce1 protein complex on host transcriptional and immunological responses to infection with M. tuberculosis, RNA from murine macrophages at 15, 30, 60 min, 4 and 10 hrs post-infection with M. tuberculosis H37Rv or mce1 H37Rv was analyzed by whole-genome microarrays and RT-QPCR. Immunological responses were measured using a 23-plex cytokine assay. Compared to uninfected controls, 524 versus 64 genes were up-regulated by 15min post H37Rv- and mce1 H37Rv-infection, respectively. By 15min post-H37Rv infection, a decline of 17 cytokines combined with up-regulation of Ccl24 (26.5-fold), Clec4a2 (23.2-fold) and Ppar (10.5-fold) indicated an anti-inflammatory response initiated by IL-13. Down-regulation of Il13ra1 combined with up-regulation of Il12b (30.2-fold), suggested switch to a pro-inflammatory response by 4hrs post H37Rv-infection. Whereas no significant change in cytokine concentration or transcription was observed during the first hour post mce1 H37Rv-infection, a significant decline of IL-1b, IL-9, IL-13, Eotaxin and GM-CSF combined with increased transcription of Il12b (25.1-fold) and Inb1 (17.9-fold) by 4hrs, indicated a pro-inflammatory response. The balance between pro-and anti-inflammatory responses during the early stages of infection may have significant bearing on outcome.
2011-10-05 | E-TABM-1170 | biostudies-arrayexpress
Project description:Transcriptome analysis of of wt and PerR mutant Group A streptococcus strain 003Sm grown in the presence or absence of hydrogen peroxide, at early and late log
2011-11-18 | E-MTAB-646 | biostudies-arrayexpress
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:2D-LC/MS/MS analysis was used to examine time-dependent changes in proteome of E. coli O157:H7 strain Sakai upon an abrupt downshift in temperature (i.e., from 35°C to 14°C). Cell cultures were harvested at 30, 90, 160, and 330 min post-temperature downshift. It also should be noted that these time points were chosen with the aims to characterize the physiology of E. coli during dynamic changes in growth kinetics induced by an abrupt temperature downshift. Specifically, the samples taken at time 30 and 90 min were obtained during adaptation period, whereas the samples at time 160 and 330 min reflected the physiological state of E. coli during growth after the shift. MS/MS data obtained from each protein sample were processed by the Computational Proteomics Analysis System (CPAS), a web-based system built on the LabKey Server (v9.1, released 02.04.2009). The experimental mass spectra produced were subjected to a semi-tryptic search against the combined databases of E. coli O157:H7 Sakai (5,318 entries in total) downloaded from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, downloaded 25.11.2008) using X!Tandem v2007.07.01. These databases included the E. coli O157:H7 Sakai database (5230 entries, NC_002695.fasta) and two E. coli O157:H7 Sakai plasmid databases, plasmid pO157 (85 entries, NC_002128.fasta) and plasmid pOSAK1 (three entries, NC_002127.fasta). The parameters for the database search were as follows: mass tolerance for precursor and fragment ions: 10 ppm and 0.5 Da, respectively; fixed modification: cysteine cabamidomethylation (+57 Da); and no variable modifications. The search results were then analyzed using the PeptideProphet and ProteinProphet algorithms from the Trans Proteomic Pipeline v3.4.2. All peptide and protein identifications were accepted at PeptideProphet and ProteinProphet of ≥0.9, corresponding to a theoretical error rate of ≤2%.
2019-11-25 | PXD000573 | Pride
Project description:Background: Commercial Atlantic salmon is fed diets with high fat levels to promote fast and cost-effective growth. To avoid negative impact of obesity, food additives that stimulate fat metabolism and immune function are of high interest. TTA, tetradecylthioacetic acid, is a synthetic fatty acid that stimulates mitochondrial β -oxidation most likely by activation of peroxysome proliferator-activated receptors (PPARs). PPARs are important transcription factors regulating multiple functions including fat metabolism and immune responses. Atlantic salmon experiments have shown that TTA supplemented diets significantly reduce mortality during natural outbreaks of viral diseases, suggesting a modulatory role of the immune system. Results: To gain new insights into TTA effects on the Atlantic salmon immune system, a factorial, high-throughput microarray experiment was conducted using a 44K oligo nucleotide salmon microarray SIQ2.0 and the Atlantic salmon macrophage-like cell line ASK. The experiment was used to determine the transcriptional effects of TTA, the effects of TTA in poly(I:C) elicited cells and the effects of pretreating the cells with TTA. The expression patterns revealed that a large proportion of genes regulated by TTA were related to lipid metabolism and increased mitochondrial β -oxidation. In addition we found that for a subset of genes TTA antagonized the transcriptional effects of poly(I:C). This, together with the results from qRT-PCR showing an increased transcription of anti-inflammatory IL10 by TTA, indicates anti-inflammatory effects. Conclusions: We demonstrate that TTA has significant effects on macrophage-like salmon cells that are challenged by the artificial dsRNA poly(I:C). The immune stimulatory effect of TTA in macrophages involves increased lipid metabolism and suppressed inflammatory status. Thus, suggesting that TTA directs the macrophage-like cells towards alternative, anti-inflammatory, activation. This has positive implications for TTA as a feed additive. Factorial designed experiment: factor pretreatment = 2 levels (Control, TTA); factor treatment = 4 levels (Control, TTA, polyIC, TTA+polyIC). Experiment was performed with 2 biological replicates (different passages). 1 array hybridization failed and was excluded from the dataset. Therefore total number of arrays =15
2011-07-31 | E-GEOD-25328 | biostudies-arrayexpress
Project description:Multi-walled carbon nanotubes (MWCNTs) are among the most promising nanomaterials because of their physical and chemical properties. However, since they are biopersistent fiber-like materials which share similarities with asbestos, concerns have arisen about their health effects. With their various industrial usages, occupational exposure to MWCNTs may occur mainly by inhalation as these nanomaterials can get aerosolised. The number of toxicological studies on CNTs has steadily increased for the last decades. Different works showed that MWCNT exposure by inhalation or intratracheal instillation could lead to pulmonary toxicity, such as lung inflammation, genotoxicity, fibrosis or lung cancer (Kasai et al. 2015, Kasai et al. 2016, Porter et al. 2013, Suzui et al. 2016). To date, only one MWCNT (MWNT-7) has been classified as possibly carcinogen to human (Group 2B) while the others have not been as classifiable as to their carcinogenicity to humans (Group 3) because of the lack of data on their carcinogenic potential (IARC 2017). Because of the wide variety of CNTs with various length, diameter or functionalisation, additional effort is required to assess their pulmonary toxicity. As a complementary approach to conventional toxicological assays, the omics methods are useful technologies for the mechanistic understanding of the toxicological effects observed following exposure to chemicals and particulate matters. Importantly, they can also be used as predictive tools for identifying the mode of action of other particles with similar physical and chemical characteristics. These molecular approaches may also be used for the discovery of exposure markers or early markers of adverse effects, before the appearance of clinical signs of a disease (Rahman et al. 2017). Several studies assessed gene expression alteration following in vivo exposure to CNTs (Poulsen et al. 2015, Snyder-Talkington et al. 2013, Ellinger-Ziegelbauer and Pauluhn 2009). These omics approaches were used to identify genes and pathways modulated in response to exposure. However, there are still too few studies to assess the link between MWCNT physico-chemical properties, global gene or protein expression profiles, and long-term effects. In a previous study, we showed that inhalation of two pristine MWCNTs, the long and thick NM-401, and the short and thin NM-403, induced alveolar neutrophilic granulocyte influx, a hallmark of inflammation, which was proportional to the lung CNT BET surface deposited dose (Gate et al. 2019). However, due to their different physical and chemical properties, one could assume that these two CNTs may have diverse toxicological profiles, but the conventional toxicology approaches used in this early work were probably not sensitive enough to identify such differences. In order to gain additional insight about their toxicological properties, in the current study, we compare the alteration induced by the two MWCNTs on the transcriptome in the lung tissue and the proteome in the broncho-alveolar lavage fluid (BALF) after rat exposure by inhalation. The omics analyses were performed from 3 days up to 180 days.
2021-01-04 | PXD018900 | Pride
Project description:Multi-walled carbon nanotubes (MWCNTs) are among the most promising nanomaterials because of their physical and chemical properties. However, since they are biopersistent fiber-like materials which share similarities with asbestos, concerns have arisen about their health effects. With their various industrial usages, occupational exposure to MWCNTs may occur mainly by inhalation as these nanomaterials can get aerosolised. The number of toxicological studies on CNTs has steadily increased for the last decades. Different works showed that MWCNT exposure by inhalation or intratracheal instillation could lead to pulmonary toxicity, such as lung inflammation, genotoxicity, fibrosis or lung cancer (Kasai et al. 2015, Kasai et al. 2016, Porter et al. 2013, Suzui et al. 2016). To date, only one MWCNT (MWNT-7) has been classified as possibly carcinogen to human (Group 2B) while the others have not been as classifiable as to their carcinogenicity to humans (Group 3) because of the lack of data on their carcinogenic potential (IARC 2017). Because of the wide variety of CNTs with various length, diameter or functionalisation, additional effort is required to assess their pulmonary toxicity. As a complementary approach to conventional toxicological assays, the omics methods are useful technologies for the mechanistic understanding of the toxicological effects observed following exposure to chemicals and particulate matters. Importantly, they can also be used as predictive tools for identifying the mode of action of other particles with similar physical and chemical characteristics. These molecular approaches may also be used for the discovery of exposure markers or early markers of adverse effects, before the appearance of clinical signs of a disease (Rahman et al. 2017). Several studies assessed gene expression alteration following in vivo exposure to CNTs (Poulsen et al. 2015, Snyder-Talkington et al. 2013, Ellinger-Ziegelbauer and Pauluhn 2009). These omics approaches were used to identify genes and pathways modulated in response to exposure. However, there are still too few studies to assess the link between MWCNT physico-chemical properties, global gene or protein expression profiles, and long-term effects. In a previous study, we showed that inhalation of two pristine MWCNTs, the long and thick NM-401, and the short and thin NM-403, induced alveolar neutrophilic granulocyte influx, a hallmark of inflammation, which was proportional to the lung CNT BET surface deposited dose (Gate et al. 2019). However, due to their different physical and chemical properties, one could assume that these two CNTs may have diverse toxicological profiles, but the conventional toxicology approaches used in this early work were probably not sensitive enough to identify such differences. In order to gain additional insight about their toxicological properties, in the current study, we compare the alteration induced by the two MWCNTs on the transcriptome in the lung tissue and the proteome in the broncho-alveolar lavage fluid (BALF) after rat exposure by inhalation. The omics analyses were performed from 3 days up to 180 days.
2021-11-22 | PXD029842 | Pride
Project description:Xanthomonas axonopodis pv. citri (XAC) is the causal agent of citrus canker which is one of the most serious diseases of citrus. To understand the virulence mechanism of XAC, we designed and conducted genome-wide microarray analyses to characterize the regulons of HrpG and HrpX, which are critical for the pathogenicity of XAC. Our analyses revealed that the expression of 232 genes and 181 genes belonged to the HrpG and HrpX regulons, respectively. Totally, 123 genes were overlapped in the two regulons at any of the three time-points. Our results showed that HrpG and HrpX regulated all 25 T3SS genes, 22 T3SS effector genes, and 29 T2SS substrate genes. Our data showed that XAC regulates multiple cellular activities responding to the host environment, such as amino acid biosynthesis, oxidative phosphorylation, pentose-phosphate pathway, transport of sugar, iron and potassium, the phenolic compounds catabolism pathway (pcaQ) through HrpX and HrpG. We also identified 124 and 90 unknown genes controlled by HrpG and HrpX, respectively. Our data suggest that a cross-talk exists between HrpG and quorum sensing system in XAC. We also identified genes involved in chemotaxis and flagellar biosynthesis, production of extracellular enzymes, metabolic pathways, as well as signal transduction controlled by HrpG/HrpX. Our results suggest that HrpG and HrpX interplay with global signaling network and co-ordinate the expression of multiple virulence factors for modification and adaption of host environment during XAC infection. Two mutants and three time-points experiment. Four biological and dye-swap replicates of each strain per each time-point were used. Totally, there were three datasets of hrpG mutant: 1) hrpG mutant vs. wild type strain at time-point A; 2) hrpG mutant vs. wild type strain at time-point B; 3) hrpG mutant vs. wild type strain at time-point C. There are also three datasets of hrpX mutant: 1) hrpX mutant vs. wild type strain at time-point A; 2) hrpX mutant vs. wild type strain at time-point B; 3) hrpX mutant vs. wild type strain at time-point C.
2011-06-09 | E-GEOD-24016 | biostudies-arrayexpress