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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. 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)

ORGANISM(S): Microcoleus vaginatus

SUBMITTER: Lara Rajeev

PROVIDER: E-GEOD-40188 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2012-10-30 | GSE40188 | GEO

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Project description:Hydration-Desiccation cycle - Raw reads

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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

Proteomic Insight into Early Establishment of Seed Dormancy in Xanthium Strumarium

Project description:Along with the inherent complexities of seed and dormancy, the use of different genotypes or mutants to study the molecular mechanisms underlying seed dormancy leads to potential biases and data misinterpretation. To provide a comprehensive insight into the actual protein activities involved in seed dormancy establishment, a SWATH-MS proteomics was performed on dormant and non-dormant developing seeds of Xanthium strumarium at five consecutive time intervals including three, 10, 20, and 30 days after burr emergence and full maturation. The amount of approximately 3.5% differentially abundant proteins (DAPs) with a ~94% stage-specificity supports considerable proteome overlap in the two seed types. More than 38% of all differentially abundant proteins were observed at the first stage, supporting the importance of this stage of seed development for seed fate determination. Rapid overrepresentation of proteins responsible for cell wall biosynthesis, cytokinesis, and seed development were detected for non-dormant seed at the first stage, while dormancy-associated proteins showed less abundance. In the middle of seed development, we identified DAPs involved in seed maturation and ABA signaling. Interestingly, higher abundant proteins in the mature non-dormant seed were mainly involved in the facilitation of seed germination. Taken together, the temporal pattern of the accumulated proteins demonstrated a delay in the initiation of active cell division, enriched response to ABA, and defect in the seed maturation in developing dormant seeds. Moreover, stored proteins in the mature dormant seed are responsible for delaying germination but not dormancy induction. Finally, assume that dormancy may be established at a stage of seed development earlier than previously thought.

2024-08-22 | PXD052504 | Pride

RNA-Seq of seed dormancy in red rice

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2018-05-10 | E-MTAB-6740 | biostudies-arrayexpress

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2011-07-19 | E-GEOD-23046 | biostudies-arrayexpress

affy_sunflower_2010_13-ROS and hormones in sunflower seed dormancy.

2013-08-01 | GSE44165 | GEO

Comparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivation

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2018-10-22 | MTBLS304 | MetaboLights

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