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Impact of wildfire ash on prokaryote plankton

ABSTRACT: Impact of wildfire ash on prokaryote plankton community composition and abundance in a coastal embayment, the Ría de Vigo (NW Spain)

PROVIDER: PRJEB51594 | ENA |

REPOSITORIES: ENA

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Project description:Impact of wildfire ash on prokaryote plankton abundance and community composition in a coastal embayment, the Ria de Vigo (NW Spain)

| PRJNA820456 | ENA

Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation

Project description:We performed RNA-seq and proteomics on naturally infested green ash (F. pennsylvanica) trees at low, medium and high levels of increasing emerald ash borer (A. planipennis) infestation. Our integrative analysis of the RNA-Seq and proteomics data identified 14 proteins and 4 transcripts that contribute most to the difference between highly infested and low infested trees.

2023-03-08 | GSE212332 | GEO

Single-organism multimodal characterisation of eukaryotic plankton with Ukiyo-e-Seq

Project description:We used single-cell sequencing data and imaging to investigate Eukaryotic plankton from environmental marine samples collected from Coogee, NSW, Australia.

2024-08-18 | GSE274796 | GEO

ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

Project description:ASH-1 orthologs are H3K36-specific methyltransferases that are conserved from fungi to humans but are poorly understood, in part because they are typically essential for viability. Here we examine the H3K36 methylation pathway of Neurospora crassa, which we find has just two H3K36 methyltransferases, ASH-1 and RNA polymerase II-associated SET-2. Our investigation of the interplay between SET-2 and ASH-1 uncovered a regulatory mechanism connecting ASH-1-catalyzed H3K36 methylation to repression of poorly transcribed genes. Our findings provide new insight into ASH-1 function, H3K27me2/3 establishment, and repression at facultative heterochromatin.

2018-08-14 | GSE118495 | GEO

High-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

Project description:In this study we applied MASC-seq (massive and parallel microarray sequencing, https://doi.org/10.1038/ncomms13182), a scRNA-seq method that facilitates sequencing of thousands of cells in parallel, and that couples microscope images with the single cell transcriptome data. For this method, fixed cells are spread over a microarray with 100 μm-sized spots of DNA capture probes with spot-specific indices. The cells are first imaged using a scanning microscope and then permeabilized, releasing their RNA out of the cells and bind to the probes on the array. cDNA is synthesized, harvested and sequenced, and, using the spot-specific barcode-sequences, cDNA sequences stemming from a specific spot (i.e., cell) can be linked to the microscope image of the corresponding cell. However, until now, the MASC-seq method has only been applied to mammalian cells. The aim of this study was to test and adapt the MASC-seq method for application on unicellular eukaryotic plankton. We applied and optimized the method on three cultured plankton representatives, abundant in communities of aquatic environments, Phaeodactylum tricornutum (a diatom, silica and polysaccharide cell walls 23), Heterocapsa sp. (a dinoflagellate, cellulose thecal plates 24) and Tetrahymena thermophila (a ciliate, lipid membrane 25) which all have different size and diverse cell surface structures common to plankton. We optimized several steps in the protocol to make it more suitable for planktonic cells and compared the results from MASC-seq generated single cell transcriptomes to bulk RNA sequencing.

2022-10-26 | E-MTAB-12261 | biostudies-arrayexpress

Effects of ash-2, hsf-1, or ash-2 + hsf-1 RNAi on gene expression in Day 1 adult Q40::YFP C. elegans

Project description:To determine how gene expression changes in long-lived ash-2-deficient worms expressing the amyloidogenic Q40::YFP, and to assess how simultaneous depletion of hsf-1 effects these transcriptomic changes.

2023-10-16 | GSE227652 | GEO

Ash genome

Project description:The study of ash genome

| PRJEB18069 | ENA

Ash microcosms

Project description:Ash microcosms Raw sequence reads

| PRJNA1092644 | ENA

ash tree

Project description:The non-native velvet ash Fraxinus velutina and native Manchurian ash F. mandshurica phloem Transcriptome

| PRJNA1125173 | ENA

Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes

Project description:Hymenoscyphus fraxineus, the causal agent of Ash Dieback (ADB), has been introduced to eastern Europe in the 1990s from where it spread causing decline in European ash populations. However, the genetic basis of the molecular response in tolerant and susceptible ash trees to this disease is still largely unknown. We performed RNA-sequencing to study the transcriptomic response to the disease in four ash genotypes (ADB-tolerant FAR3 and FS36, and ADB-susceptible UW1 and UW2), during a time-course of 7, 14, 21, and 28 days post-inoculation, including mock-infected trees as control samples for each sampling time point. The analysis yielded 395 and 500 Differentially Expressed Genes (DEGs) along the response for ADB-tolerant FAR3 and FS36, respectively, while ADB-susceptible UW1 and UW2 revealed 194 and 571 DEGs, respectively, with most DEGs found exclusively in just one of the genotypes. DEGs shared between tolerant genotypes FAR3 and FS36, included genes involved in the production of phytoalexins and other secondary metabolites with roles in plant defense. Moreover, we identified an earlier expression of genes involved in both pattern- and effector-triggered immunity (PTI and ETI) in ADB-tolerant genotypes, while in ADB-susceptible genotypes both responses were delayed (late response). Overall, these results revealed different transcriptomic expression patterns not only between ADB-tolerant and ADB-susceptible genotypes, but also within these two groups. This hints to individual response in the natural tolerance to ADB, possibly revealing diversified strategies across ash genotypes.

2025-01-29 | GSE278637 | GEO

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