Salinity changes and parasite infections induce metabolic shifts in cell metabolome of harmful algae
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Alexandrium Minutum (ncbitaxon:39455) Dinophyceae (ncbitaxon:2864) Parvilucifera Infectans (ncbitaxon:103983) Alveolata (ncbitaxon:33630)
SUBMITTER: 
Dr. Marine Vallet Ruchicka Oniel Georg Pohnert
PROVIDER: MSV000099020 | MassIVE |
REPOSITORIES: MassIVE
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Project description:Semi targeted metabolic profiling from microalgal cells in acid-water methanolic extracts using UHPLC-HRMS (Orbitrap Q Exactive). Dinoflagellate Alexandrium minutum were either healthy or infected with alveolate parasite Parvilucifera infectans, and cultivated under 20 PSU or 32 PSU. Samples were unpaired and extracted on Day 14 and 21. The samples were processed using ZIC-HILIC chromatography followed by PRM aquisition in the positive polarity mode for target PSP toxins. The supplementary files include, the study and result files from Compound Discoverer, the metadata table with normalization factor, sample code and conditions. The raw files of standards used confirm retention time and MS2 fragments of samples are included as well. Comparative toxin levels of Paralytic shellfish toxin was monitored in the enodmetabolome.
2025-11-30 | MSV000100057 | MassIVE
Project description:The genus Sirolpidium (Sirolpidiaceae) of the Oomycota includes several species of holocarpic obligate aquatic parasites. These organisms are widely occurring in marine and freshwater habitats, mostly infecting filamentous green algae. Presently, all species are only known from their morphology and descriptive life cycle traits. None of the seven species classified in Sirolpidium, including the type species, S. bryopsidis, has been rediscovered and studied for their molecular phylogeny, so far. Originally, the genus was established to accommodate all parasites of filamentous marine green algae. In the past few decades, however, Sirolpidium has undergone multiple taxonomic revisions and several species parasitic in other host groups were added to the genus. While the phylogeny of the marine rhodophyte- and phaeophyte-infecting genera Pontisma and Eurychasma, respectively, has only been resolved recently, the taxonomic placement of the chlorophyte-infecting genus Sirolpidium remained unresolved. In the present study, we report the phylogenetic placement of Sirolpidium bryopsidis infecting the filamentous marine green algae Capsosiphon fulvescens sampled from Skagaströnd in Northwest Iceland. Phylogenetic reconstructions revealed that S. bryopsidis is either conspecific or at least very closely related to the type species of Pontisma, Po. lagenidioides. Consequently, the type species of genus Sirolpidium, S. bryopsidis, is reclassified to Pontisma. Further infection trials are needed to determine if Po. bryopsidis and Po. lagenidioides are conspecific or closely related. In either case, the apparently recent host jump from red to green algae is remarkable, as it opens the possibility for radiation in a largely divergent eukaryotic lineage. Citation: Buaya AT, Scholz B, Thines M (2021). Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae. Fungal Systematics and Evolution 7: 223-231. doi: 10.3114/fuse.2021.07.11.
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Project description:The family of Zic transcription factors (TFs) are required for cerebellar development, and their binding is highly enriched at developmentally regulated enhancers active in cerebellar granule neurons at the progenitor stage around postnatal day 7 (P7) and the mature adult stage at P60 in the mouse cerebellum. Interestingly, Zic1/2 ChIP-seq data reveal that the Zics change their binding profile over time. To characterize these differences in Zic targeting between early and late cerebellar maturation, we compared the sequence underlying Zic Peaks, their relationship with active chromatin and gene expression at P7 and P60. From this we found Zic peaks tend to be large and bind open-active chromatin. Strikingly, Zic peaks shift from binding at promoter proximal regions at P7 to distal enhancer regions at P60. We hypothesize that other TFs collaborate with the Zic TFs to change their binding targets and affect their regulatory activity. A multi-tiered approach was used to predict TF binding at those Zic ChIP sites. We assessed motif enrichment (HOMER) and in-vivo TF binding profiles (BART) to determine putative TFs collaborating with Zic to drive this regulation. We then validated the presence of the predicted TFs in granule neurons using gene expression. This workflow identified known and novel distinct collaborators of Zic between early and late development. Early collaborates of Zic includes bHLH factors and chromatin remodelers whereas late collaborators of Zic are activity regulated TFs which are markers of synaptic maturation. To identify Zic’s developmental gene targets in cerebellar maturation, we used H3K4me3 PLAC-seq data, which captures promoter-enhancer loops from the adult mouse cerebellum and Hi-C data from the young mouse cerebellum to map genes to Zic bound enhancers. This revealed Zic as a transcriptional activator of late developmental genes in the cerebellum. Using this same approach with in vitro Zic KD, we were able to identify Zic dependent developmental gene targets which have functions in axonogenesis, axon guidance, and ion channel signaling, which are integral in proper maturation of a neuron. These integrated analyses reveal how Zic and other TFs regulate temporal expression of CGN developmental genes and provides information that will enhance our understanding of the molecular mechanisms that regulate the mode of TF function at enhancers.
2023-03-01 | GSE211309 | GEO
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2021-12-17 | E-MTAB-11303 | biostudies-arrayexpress
Project description:Plants have evolved elaborate mechanisms to sense, respond to and overcome the detrimental effects of high soil salinity. The role of calcium transients in salinity stress signaling is well established, but the physiological significance of concurrent salinity-induced changes in cytosolic pH remains largely undefined. Here, we analyzed the response of Arabidopsis roots expressing the genetically encoded ratiometric pH-sensor pHGFP fused to marker proteins for the recruitment of the sensor to the cytosolic side of the tonoplast (pHGFP-VTI11) and the plasma membrane (pHGFP-LTI6b). Salinity elicited a rapid alkalinization of cytosolic pH (pHcyt) in the meristematic and elongation zone of wild-type roots. The pH-shift near the plasma membrane preceded that at the tonoplast. In pH-maps transversal to the root axis, the epidermis and cortex had cells with a more alkaline pHcyt relative to cells in the stele in control conditions. Conversely, seedlings treated with 100 mM NaCl exhibited an increased pHcyt in cells of the vasculature relative to the external layers of the root, and this response occurred in both reporter lines. These pHcyt changes were substantially reduced in mutant roots lacking a functional SOS3/CBL4 protein, suggesting that the operation of the SOS pathway mediated the dynamics of pHcyt in response to salinity.
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Project description:DNA binding profiles of three maternal factors (Tcf7, Gata.a and Zic-r.a) in chordate 16-cell stage embryo. 16-cell stage ciona intestinalis embryos were collected from multiple batches and the extracted chromatin was immunoprecipitated by the antibodies which specifically recognize ciona Gata.a, Tcf7 and Zic-r.a, respectively.
2016-04-22 | GSE70902 | GEO
Project description:The Zinc finger of the cerebellum (ZIC) proteins have been implicated to function in normal tissue development. Mutations or deletions of ZIC genes have been found to be associated with neural-related abnormalities. Recent studies point out the critical functions of Zic proteins in cancers and the potential tumor suppressive functions in colon cancer development and progression. To elucidate the functional roles of Zic proteins in colorectal cancer, we employed CRISPR/Cas9 genome editing to knock out the Zic5 gene and analyze the chromatin localization pattern and transcriptional regulation of target gene expression. Zic5 regulates glucose metabolism through the regulation of expression of the GLUT1/SLC2A1 gene. Zic5 knockout is accompanied by an increased glycolytic state, tolerance to a low glucose condition, and derepression of metabolic genes especially GLUT1 gene expression. Reciprocally, the loss of Zic2 partially restored the glucose uptake by decreasing GLUT1 gene expression, pointing out the balance between the different Zic family proteins. Mechanistically, Zic5 is recruited by the β-catenin/TCF7l2 complex to the promoters of the target genes. Loss of β-catenin or TCF7l2 significantly diminishes the chromatin binding of Zic5 globally. Our studies suggest that the Wnt/β-catenin signaling pathway has a strong influence on the function of Zic proteins and glucose metabolism in colorectal cancers through GLUT1, thus interfering Wnt/β-catenin - Zic5 axis regulated aerobic glycolysis represents a potentially effective strategy to selectively target colon cancer cells.
2019-08-20 | GSE127960 | GEO
Project description:BackgroundMicrosporidians are obligate endoparasites infecting taxonomically diverse hosts. Both vertical (from mother to eggs) and horizontal (between conspecifics or between species) transmission routes are known. While the former may promote co-speciation and host-specificity, the latter may promote shifts between host species. Among aquatic arthropods, freshwater amphipod crustaceans are hosts for many microsporidian species. However, despite numerous studies, no general pattern emerged about host specificity and co-diversification. In south-eastern Europe, the gammarid Gammarus roeselii is composed of 13 cryptic lineages of Miocene to Pleistocene age but few genotypes of one lineage have spread postglacially throughout north-western Europe. Based on nearly 100 sampling sites covering its entire range, we aim to: (i) explore the microsporidian diversity present in G. roeselii and their phylogenetic relationships, especially in relation to the parasites infecting other Gammaridae; (ii) test if the host phylogeographical history might have impacted host-parasite association (e.g. co-diversifications or recent host shifts from local fauna).MethodsWe used part of the small subunit rRNA gene as source of sequences to identify and determine the phylogenetic position of the microsporidian taxa infecting G. roeselii.ResultsMicrosporidian diversity was high in G. roeselii with 24 detected haplogroups, clustered into 18 species-level taxa. Ten microsporidian species were rare, infecting a few individual hosts in a few populations, and were mostly phylogenetically related to parasites from other amphipods or various crustaceans. Other microsporidians were represented by widespread genera with high prevalence: Nosema, Cucumispora and Dictyocoela. Two contrasting host association patterns could be observed. First, two vertically transmitted microsporidian species, Nosema granulosis and Dictyocoela roeselum, share the pattern of infecting G. roeselii over most of its range and are specific to this host suggesting the co-diversification scenario. This pattern contrasted with that of Dictyocoela muelleri, the three species of Cucumispora, and the rare parasites, present only in the recently colonised region by the host. These patterns suggest recent acquisitions from local host species, after the recent spread of G. roeselii.ConclusionsMicrosporidians infecting G. roeselii revealed two scenarios of host-parasite associations: (i) ancient associations with vertically transmitted parasites that probably co-diversified with their hosts, and (ii) host shifts from local host species, after the postglacial spread of G. roeselii.
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Project description:Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral-algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress.
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Project description:Different strains of T. brucei induce different degrees of pathology in infected animals, and TREU927-infected mice display greater splenomegaly and anaemia than 247-infected mice. The analysis of differential host gene expression in infected spleens has allowed the identification of which pathways or processes are crucial in determining the progression of disease, for example IL10, LXR/RXR activation and alternative macrophage activation. We used microarray analysis to examine host gene expression between uninfected and infected mice, and between mice infected with the two trypanosome strains. Mouse spleens were dissected from infected or uninfected mice 10 days post infection, when the differences in pathology criteria (hepatomegaly, red blood cell numbers, reticulocyte percentage, IL10, IFNg and Il12 levels, and splenomegaly) were the greatest. This allowed a three-way comparison, uninfected vs 247-infected, uninfected vs 927-infected, and 247-infected vs 927-infected, allowing us to analyse genes that are differentially expressed between infected and uninfected spleens, but also crucially allows the differentiation between host gene expression with pathogenic (927) and less pathogenic (247) trypanosome strains.
2010-03-03 | E-GEOD-17049 | biostudies-arrayexpress