Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamic transcriptional response of Microcoleus vaginatus to hydration and dehydration in a desert biological soil crust

ABSTRACT: Biological soil crusts (BSCs) are cyanobacteria-dominated microbial communities that cover extensive portions of the world’s arid and semi-arid deserts. The infrequent periods of hydration are often too short to allow for dormancy strategies based on sporulation; consequently, survival is based on the unique capabilities of vegetative cells to resuscitate from and re-enter a stress resistant dormant state, one of which is migration within the crust layers in response to hydration. In this study, we sought to characterize the events that govern the emergence of the dominant cyanobacterium from dormancy, its subsequent growth, and the events triggered by re-desiccation and a transition back to dormant state. We performed a 48 hour laboratory wetting experiment of a desert BSC and tracked the response of Microcoleus vaginatus using a whole genome transcriptional time-course including night/day periods. This allowed the identification of genes with a diel expression pattern, genes involved uniquely in the signaling after hydration and those that contribute primarily to desiccation preparation.

ORGANISM(S): Microcoleus vaginatus FGP-2 Microcoleus vaginatus Microcoleus vaginatus PCC 9802

PROVIDER: GSE40188 | GEO | 2012/10/30

SECONDARY ACCESSION(S): PRJNA173081

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Dynamic transcriptional response of Microcoleus vaginatus to hydration and dehydration in a desert biological soil crust

Project description:Biological soil crusts (BSCs) are cyanobacteria-dominated microbial communities that cover extensive portions of the world’s arid and semi-arid deserts. The infrequent periods of hydration are often too short to allow for dormancy strategies based on sporulation; consequently, survival is based on the unique capabilities of vegetative cells to resuscitate from and re-enter a stress resistant dormant state, one of which is migration within the crust layers in response to hydration. In this study, we sought to characterize the events that govern the emergence of the dominant cyanobacterium from dormancy, its subsequent growth, and the events triggered by re-desiccation and a transition back to dormant state. We performed a 48 hour laboratory wetting experiment of a desert BSC and tracked the response of Microcoleus vaginatus using a whole genome transcriptional time-course including night/day periods. This allowed the identification of genes with a diel expression pattern, genes involved uniquely in the signaling after hydration and those that contribute primarily to desiccation preparation. Desert BSC samples collected from Moab, UT, were hydrated over a period of 48 hours followed by drying induced by removal of water. At periodic times soil samples were harvested and used for RNA extraction and whole genome expression analysis using an expression array representing genes from two strains of M. vaginatus (PCC 9802 and FGP-2)

2012-10-30 | E-GEOD-40188 | biostudies-arrayexpress

An inflammatory memory of COVID-19 in airway basal stem cells impairs mucociliary differentiation (RNA-Seq)

Project description:Airway basal stem cells (BSCs) in chronic lung diseases accumulate memories to promote disease-specific pathogenesis. Whether acute lung infection also endows BSCs with an inflammatory memory to impair epithelial regeneration is unknown. Here, we derived multiple BSC lines from patients with and without COVID-19 (CoV19) using tracheal aspirate (TA) as a viable source of bronchial BSCs. While tested negative for SARS-CoV-2, BSC lines from CoV19 patients bore a proinflammatory gene signature, exhibited early cell cycle exist, and displayed goblet cell hypoplasia following differentiation in air-liquid interface (ALI). These phenotypes reproduced, at least partially, changes in BSCs in patients with CoV19 assessed by bioinformatic analysis of preexisting single cell transcriptomes of BSCs and by staining of lung sections for select markers. Such a memory in BSCs previously exposed to CoV19 was mediated by increases in chromosomal accessibility at key inflammatory gene loci associated with gene dysregulation and sustained STAT3 activation. Blockade of STAT3 hyperactivation in CoV19-exposed BSCs restored mucociliary differentiation in ALI. Taken together, BSCs acquire an epigenetic memory of CoV19 to impair epithelial regeneration. BSC derivation from TA provides a versatile approach to model airway epithelium in health and lung diseases.

2023-06-01 | GSE212411 | GEO

An inflammatory memory of COVID-19 in airway basal stem cells impairs mucociliary differentiation (ATAC-Seq)

2023-06-01 | GSE212410 | GEO

Gene expression in populations of the potato cyst nematode Globodera pallida in diapause or quiescence following hydration or exposure to tomato root diffusate

Project description:Plant-parasitic nematodes (PPN) need to be adapted to survive in the absence of a suitable host or in hostile environmental conditions. Various forms of developmental arrest (including desiccation, cryopreservation, hatching inhibition and dauer stages) are used by PPN in order to survive these conditions and spread to other areas. Potato cyst nematodes (PCN) (Globodera pallida and G. rostochiensis) are frequently in a dessicated state unhatched nematodes within the egg dispersal unit inside the cyst. Long term survival seems to be associated primarily with species that have a very restricted host range which requires surviving unhatched in the absence of the host for extended periods of time. This paper shows fundamental changes in the response of quiescent and diapaused eggs of G.pallida to hydration and following exposure to tomato root diffusate using microarray gene expression analysis from a broad set of genes. Surprisingly, many unique genes were activated in the population of diapaused eggs. Transport activity was activated in both quiescent and diapaused eggs; however, the transport function genes were very different between them. Hydrated quiescent and diapaused eggs were markedly different indicating differences in adaptation for long term survival.

2016-02-01 | E-MTAB-3824 | biostudies-arrayexpress

Tumor Cell Heterogeneity and Dormancy in Single Disseminated Prostate Cancer Cells

Project description:Prostate cancer (PCa) disseminated tumor cells (DTC) in the bone marrow (BM) can remain dormant for prolonged periods before recurrence. Our aim was to characterize individual prostate DTC, analyze tumor cell heterogeneity, and identify markers of tumor dormancy.

2014-09-16 | GSE48995 | GEO

soil

Project description:Hydration-Desiccation cycle - Raw reads

| PRJNA718159 | ENA

Analysis of light induced secondary seed dormancy in Aethionema arabicum, Cyprus accession

Project description:Light inhibits the seed germination in the Cypriot accession (CYP) of Aethionema arabicum. Extended light illumination also induces a secondary seed dormancy that inhibits the germination even if the seeds were transferred back to darkness. This analysis aims to compare the seed transcriptome before or after the dormancy was established by light illumination (100 µmol/m2s; white light). One day light treatment (1dL) inhibits the germination but the seeds are not yet dormant. Seven day (7dL) or 14-day (14dL) long light treatment induces dormancy, and the seeds stay dormant after 7 dal-light plus 7 day-dark (7dL7dD) treatment. To understand the dormancy establishment, transcriptome was compared between non-dormant (1dL) and dormant (7dL, 14dL, 7dL7dD) seed samples.

2023-09-01 | GSE237127 | GEO

affy_sunflower_2010_13-ROS and hormones in sunflower seed dormancy.

Project description:affy_sunflower_2010_13 - affy_sunflower_2010_13 - It concerns the interaction between ROS and hormones in dormancy release in sunflower seeds. ABA is responsible for dormancy maintenance, while GA and ethylene promote seed germination. Based on our results, ROS could represent good candidate to shift from a hormone signalling to another determining the dormancy state in sunflower seeds.-We aim to understand the mechanisms controlling sunflower seed dormancy at the transcriptomic level, by the application of treatments which maintain dormancy as ABA, or alleviate dormancy as ROS and ethylene. Transcripts comparison will be performed between dormant and non-dormant sunflower embryo imbibed 24h on water, on ABA, on methylviologen, a pro-oxidant compound or on ethylene. 12 arrays - SUNFLOWER; treated vs untreated comparison

2013-08-01 | E-GEOD-44165 | biostudies-arrayexpress

Modeling androgen deprivation therapy-induced prostate cancer dormancy and its clinical implications

Project description:Purpose: Treatment-induced tumor dormancy is a state in cancer progression where residual disease is present but remains asymptomatic. Dormant cancer cells are treatment-resistant and responsible for cancer recurrence and metastasis. Prostate cancer (PCa) treated with androgen-deprivation therapy (ADT) often enters a dormant state. ADT-induced PCa dormancy remains poorly understood due to the challenge in acquiring clinical dormant PCa cells and the lack of representative models. We, therefore, aimed to develop clinically relevant models that can be used for studying ADT-induced PCa dormancy. Experimental design: Dormant PCa models were established by castrating mice bearing PCa patient-derived xenografts (PDXs) of hormonal naïve or sensitive PCa. Dormancy status and tumor relapse were monitored and evaluated. Paired pre- and post-castration (dormant) PDX tissues were subjected to morphological and transcriptome profiling analyses. Results: We established eleven ADT-induced dormant PCa models that closely mimicked the clinical courses of ADT-treated PCa. We identified two ADT-induced dormancy subtypes that differed in morphology, gene expression, and relapse rates. We discovered transcriptomic differences in pre-castration PDXs that predisposed the dormancy response to ADT. We further developed a dormancy subtype-based, predisposed gene signature that was significantly associated with ADT response in hormonal naïve PCa and clinical outcome in castration-resistant PCa treated with ADT or androgen-receptor pathway inhibitors.

2022-01-11 | GSE193500 | GEO

Negev crust metatranscriptomes

Project description:Transcriptomic response of soil crust microbiota to hydration

| PRJEB52014 | ENA