Caspofungin induced cell wall changes of Candida species influences macrophage interactions
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: MODEL1109130000MODEL1311110000MODEL1909260003MODEL1311110001MODEL1909260004MODEL1703310000MODEL1909260005MODEL1909260006
INSTRUMENT(S): Bruker Daltonics esquire series
ORGANISM(S): Candida Tropicalis Mya-3404 Candida Glabrata (yeast) (torulopsis Glabrata) Candida Parapsilosis Candida Dubliniensis Clavispora Lusitaniae Atcc 42720 Meyerozyma Guilliermondii Atcc 6260
TISSUE(S): Cell Suspension Culture
SUBMITTER: 
David Stead
LAB HEAD: Professor Carol Munro
PROVIDER: PXD019293 | Pride | 2020-05-20
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| AP11053_CW_06.mgf | Mgf | |||
| AP11053_CW_06.yep | Other | |||
| AP11065_LW_03.mgf | Mgf | |||
| AP11065_LW_03.yep | Other | |||
| AP11065_LW_04.mgf | Mgf |
Items per page: 5 1 - 5 of 109 |
Similar Datasets
Project description:Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. These ESTs were de novo assembled into 132,153 unique sequences. By combining the de novo assembled ESTs (132,153 sequences) with our previously identified EST sequences (341,984 sequences, unpublished data), and the ESTs available from GenBank (12,371 sequences), we built the first Alfalfa Gene Index (MSGI 1.0). MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1, 294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Transcript profiling of stem internodes of genotypes 708 and 773 was conducted by quantifying the number of Illumina EST reads that were mapped to sequences in MSGI 1.0. We identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index (MSGI 1.0) assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a cellulosic feedstock. Examination of 2 different tissue types at different developmental stages (Elongating vs. post-elongation stem internodes) in two alfalfa genotypes (708 and 773) with divergent cell wall composition in stems.
2011-04-21 | E-GEOD-26757 | biostudies-arrayexpress
Project description:Acanthamoeba castellanii, cause of keratitis and blindness, is an emerging pathogen because of its association with contact lens use. The cyst wall contributes to pathogenesis as cysts are resistant to sterilizing reagents in lens solutions and to antibiotics applied to the eye. Here we used structured illumination microscopy (SIM) and probes for sugar polymers to show that purified cyst walls of A. castellanii retain endocyst and ectocyst layers and conical structures (ostioles) that connect them. Mass spectrometry showed candidate cyst wall proteins (CWPs) are dominated by three families of lectins (named here Luke, Leo, and Jonah), because each binds to microcrystalline cellulose +/- chitin. Luke lectins contain two or three carbohydrate-binding modules (CBM49), which were first identified in a tomato cellulase. Leo lectins have two unique domains with eight cysteines each (8-Cys) +/- a Thr-, Lys-, and His-rich spacer. Jonah lectins contain one or three choice-of-anchor A (CAA) domains previously of unknown function. Representative members of each family were tagged with green fluorescent protein (GFP) and expressed under their own promoters in transfected parasites. A representative Jonah lectin with one CAA domain is made early during encystation and localizes to the ectocyst layer. In contrast, Leo and Luke lectins are made later and localize to the endocyst layer and ostioles. Probes for CWPs (anti-GFP antibodies) and for sugar polymers (maltose-binding protein-fusions with CWPs) suggest Jonah lectin and sugar polymers to which it binds are accessible in the ectocyst layer, while Luke and Leo lectins and sugar polymers to which they bind are mostly inaccessible in the ectocyst layer and ostioles. In summary, these results show the most abundant A. castellanii CWPs are three sets of lectins, which localize to either the ectocyst layer (Jonah) or endocyst layer and ostioles (Luke and Leo).
2019-05-21 | PXD011826 | Pride
Project description:p63 is a transcription factor central for epithelial homeostasis and development. In our model of epithelial to mesenchymal transition (EMT) in a human prostate cell culture model, p63 was one of the most down-regulated transcription factors during EMT. We therefore investigated the role of p63 in EMT by a gain and loss of function approach. Over-expression of the predominant epithelial isoform DNp63a in mesenchymal EPT1B8 cells led to gain of several epithelial characteristics without resulting in a complete mesenchymal to epithelial transition (MET). This was corroborated by a reciprocal effect when p63 was knocked down in epithelial EP156T cells. Global gene expression analyses found that DNp63a induced gene modules involving cell adhesion genes in mesenchymal like cells. Genome-wide analysis of p63 binding sites by ChIP-seq analyses confirmed binding of p63 to regulatory areas of genes associated with cell adhesion in prostate epithelial cells.CDH1 and ZEB1 are two elemental factors in the control of EMT. Over-expression and knock-down of these factors, respectively, were not sufficient alone or in combination with DNp63a to reverse the mesenchymal phenotype in EPT1 cells. The partial reversion of epithelial to mesenchymal transition might reflect the ability of DNp63a, as a key co-ordinator of several epithelial gene expression modules, to reduce epithelial to mesenchymal plasticity (EMP). The utility of DNp63a expression and the potential of reduced EMP in order to counteract metastasis warrant further investigation. Examination of p63 binding profile in prostate cell model EP156T with EPT1 as negative control.
2013-12-20 | E-GEOD-43111 | biostudies-arrayexpress
Project description:Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3’ ends. Here we show that polyadenylated 3’ termini in three yeast species (S. cerevisiae, K. lactis, D. hansenii) are remarkably heterogeneous. Instead of a few discrete 3’ ends, the average yeast gene has an “end zone”, a >200 bp window with >60 distinct poly(A) sites, the most utilized of which represents only 20% of the mRNA molecules. The pattern of polyadenylation within this zone varies across species, with D. hansenii possessing a higher focus on a single dominant point closer to the ORF terminus. Some polyadenylation occurs within mRNA coding regions with a strong bias towards the promoter. The polyadenylation pattern is determined by a highly degenerate sequence over a broad region and by a local sequence that relies on A residues after the cleavage point. Many dominant poly(A) sites are predicted to adopt a common secondary structure that may be recognized by the cleavage/polyadenylation machinery. We suggest that the end zone reflects a region permissive for polyadenylation, within which cleavage occurs preferentially at the A-rich sequence. In S. cerevisiae strains, D. hansenii genes adopt the S. cerevisiae polyadenylation profile, indicating that the polyadenylation pattern is mediated primarily by species-specific factors. Four sequencing lanes containing direct RNA sequence from S. cerevisiae (strains JGY2000 and two replicates of AB1380), K. lactis strain CLIB209, D. hansenii strain NCYC2572, and S. cerevisiae strains JYAC06 and JYAC07, each harboring D. hansenii sequences on a YAC. AB1380 is the non-YAC-containing S. cerevisiae parental strain for JYAC06 and JYAC07.
2013-07-03 | E-GEOD-47661 | biostudies-arrayexpress
Project description:Although Candida albicans and Candida dubliniensis are most closely related, both species significantly behave differently with respect to morphogenesis and virulence. In order to gain further insight into the divergent routes for morphogenetic adaptation in both species, we investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. Following genome-associated assembly of sequence reads we were able to generate experimentally verified databases containing 6016 and 5972 genes for C. albicans and C. dubliniensis, respectively. About 95% of the transcriptionally active regions (TARs) contain open reading frames while the remaining TARs most likely represent non-coding RNAs. Comparison of our annotations with publically available gene models for C. albicans and C. dubliniensis confirmed approximately 95% of already predicted genes, but also revealed so far unknown novel TARs in both species. Qualitative cross-species analysis of these databases revealed in addition to 5802 orthologs also 399 and 49 species-specific protein coding genes for C. albicans and C. dubliniensis, respectively. Furthermore, quantitative transcriptional profiling using RNA-Seq revealed significant differences in the expression of orthologs across both species. We defined a core subset of 84 hyphal-specific genes required for both species, as well as a set of 42 genes that seem to be specifically induced during hyphal morphogenesis in C. albicans. Species specific adaptation in C. albicans and C. dubliniensis is governed by individual genetic repertoires but also by altered regulation of conserved orthologs on the transcriptional level. We investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. In a first step, we reevaluated the in silico predicted gene models by collecting experimental data using FLX - technology for sequencing strand-specific and normalized cDNA libraries derived from blastospores and hyphae. In the second step, quantitative RNA-Seq (GAIIX) was applied to C. albicans hyphal cells and C. dubliniensis blastospore and hyphal cells to complement reevaluation of the gene models with FLX data as well as to measure differential gene expression across the species with two biological replicates.
2013-04-17 | E-GEOD-41749 | biostudies-arrayexpress
Project description:In this study, the cell wall proteomes of 3 different regions of alfalfa stems were compared. These three regions correspond to three phases in the stem development. The sequential extraction of cell wall proteins with CaCl2, EGTA and LiCl-complemented buffers was combined with a gel-based proteome approach and multivariate analysis. Although the highest similarities were observed between the apical and intermediate stem regions, the three proteome patterns are characteristic for each region. In the basal stem region, proteins that bind carbohydrates and have proteolytic activity, as well as enzymes involved in glycan remobilization, accumulate. Beta-amylase and ferritin likewise accumulate more in the basal stem segment. Therefore remobilization of nutrients appears to be an important process in the oldest stem segment. The intermediate and the apical region are sites of cell wall polymer remodelling, as suggested by the high abundance of proteins involved in the remodelling of the cell wall such as xyloglucan endoglucosylase, polygalacturonase non-catalytic subunit or beta-galactosidase. The most striking change between the different stem parts is however the strong accumulation of a DUF642-conserved domain containing protein in the apical region of the stem which suggests a particular role of this protein during the early development of stem tissues.
2019-11-12 | PXD010666 | Pride
Project description:To dissect local regulation into cis and trans contribution, we measured allelic differential expression in a hybrid cross of two yeast strains and compared it against allelic differential expression in a pool of spores of the same cross. RNA- and DNA-seq of a diploid S. cerevisiae hybrid and its haploid spores.
2015-02-04 | E-GEOD-61553 | biostudies-arrayexpress
Project description:Saccharibacteria (TM7) are obligate epibionts living on the surface of their host bacteria, and strongly correlated with dysbiotic microbiomes during periodontitis and other inflammatory diseases, suggesting they are putative pathogens. However, due to the recalcitrance of TM7 cultivation, no causal research has been conducted to investigate their role in inflammatory diseases. Here, we isolated multiple TM7 species on their host bacteria from periodontitis patients. These TM7 species reduced inflammation and consequential bone loss by modulating their host bacterial pathogenicity in mouse ligature-induced periodontitis model. Two host bacterial functions involved in collagen binding and utilization of eukaryotic sialic acid were identified as required for inducing bone loss and altered by TM7 association. This down-regulation of host bacterial pathogenicity by TM7 was shown for multiple TM7/host bacteria pairs, suggesting that, in contrast to their suspected pathogenic role, TM7 could protect mammalian hosts from inflammatory damage induced by their host bacteria.
2023-03-11 | PXD026999 | Pride
Project description:Plasmodesmata are cytosolic bridges, lined by the plasma membrane and traversed by endoplasmic reticulum, connecting cells and tissues, and critical for many aspects of plant biology. While plasmodesmata are notoriously difficult to extract, tissue fractionation and proteomic analyses can yield valuable knowledge of their composition. Here we have generated two novel proteomes to expand tissue and taxonomic representation of plasmodesmata: one from mature Arabidopsis leaves and one from the moss Physcomitrium patens and leveraged these and existing data to perform a comparative analysis to identify evolutionarily conserved protein families that are associated with plasmodesmata. Thus, we identified b-1,3-glucanases, C2 lipid-binding proteins and tetraspanins as core plasmodesmal components that likely serve as essential structural or functional components. Our approach has not only identified elements of a conserved plasmodesmal proteome, but also demonstrated the added power offered by comparative analysis for recalcitrant samples. Conserved plasmodesmal proteins establish a basis upon which ancient plasmodesmal function can be further investigated to determine the essential roles these structures play in multicellular organism physiology in the green lineages.
2023-01-13 | PXD038964 | Pride
Project description:The purpose of this experiment is to assess temporal transcriptomic change in Troy+ chief cells upon injury in the stomach corpus in mice. Troy+-eGFP cells were sorted at each time point after stomach injury by DMP777 treatment.
2022-05-05 | E-MTAB-10373 | biostudies-arrayexpress