Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1182965 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31259033_1.fastq.gz | Fastqsanger.gz | |||
| SRR31259033_2.fastq.gz | Fastqsanger.gz | |||
| SRR31259034_1.fastq.gz | Fastqsanger.gz | |||
| SRR31259034_2.fastq.gz | Fastqsanger.gz | |||
| SRR31259035_1.fastq.gz | Fastqsanger.gz |
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Project description:The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.
2016-05-09 | GSE73915 | GEO
Project description:Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure.
2012-04-01 | GSE31587 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE30711: ChIP-Seq data from Arabidopsis thaliana under dark and far-red light GSE30712: Expression data from Arabidopsis thaliana under dark and far-red light Refer to individual Series
2011-12-31 | E-GEOD-30713 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) is the most abundant messenger RNA modification in higher eukaryotes. Functional studies of the RNA m6A modification in plants have been limited by mapping individual m6A-modified sites in whole transcriptomes. In this study, we introduce the method m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq) for quantitative whole-transcriptome profiling of m6A at single-nucleotide resolution under light and dark conditions in Arabidopsis. With this technology, we observed far-red but not red light, noticeably increase the m6A level. Further evidence showed that far-red light modulated mRNA stability and translation by m6A methylation. Additionally, our data uncovered that far-red light promoted m6A methylation of anthocyanin homeostasis related transcripts through the stabilization of FIONA1 (FIO1) and m6A methyltransferase complex, MTA (mRNA adenosine methylase A) and MTB, and the core component FIP37 (FKBP12 INTERACTING PROTEIN 37KD). Thus, with m6A stoichiometry information at single-base precision, we proposed a new mechanism for the regulation of anthocyanin accumulation under far-red light through m6A methylation.
2025-10-31 | GSE246071 | GEO
Project description:To study the transcriptomic profile of wt and brc1 mutant axillary buds during the shade avoidance response, we simulated a canopy shade with a low R/FR light ratio. We treated plants with white light supplemented with far-red light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1) for 8 hours. Control plants were left for 8 hours in white light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) .
2013-02-28 | GSE27273 | GEO
Project description:David2008 - Genome-scale metabolic network of
Aspergillus nidulans (iHD666)
This model is described in the article:
Analysis of Aspergillus
nidulans metabolism at the genome-scale.
David H, Ozçelik IS, Hofmann G,
Nielsen J.
BMC Genomics 2008; 9: 163
Abstract:
BACKGROUND: Aspergillus nidulans is a member of a diverse
group of filamentous fungi, sharing many of the properties of
its close relatives with significance in the fields of
medicine, agriculture and industry. Furthermore, A. nidulans
has been a classical model organism for studies of development
biology and gene regulation, and thus it has become one of the
best-characterized filamentous fungi. It was the first
Aspergillus species to have its genome sequenced, and automated
gene prediction tools predicted 9,451 open reading frames
(ORFs) in the genome, of which less than 10% were assigned a
function. RESULTS: In this work, we have manually assigned
functions to 472 orphan genes in the metabolism of A. nidulans,
by using a pathway-driven approach and by employing comparative
genomics tools based on sequence similarity. The central
metabolism of A. nidulans, as well as biosynthetic pathways of
relevant secondary metabolites, was reconstructed based on
detailed metabolic reconstructions available for A. niger and
Saccharomyces cerevisiae, and information on the genetics,
biochemistry and physiology of A. nidulans. Thereby, it was
possible to identify metabolic functions without a gene
associated, and to look for candidate ORFs in the genome of A.
nidulans by comparing its sequence to sequences of
well-characterized genes in other species encoding the function
of interest. A classification system, based on defined
criteria, was developed for evaluating and selecting the ORFs
among the candidates, in an objective and systematic manner.
The functional assignments served as a basis to develop a
mathematical model, linking 666 genes (both previously and
newly annotated) to metabolic roles. The model was used to
simulate metabolic behavior and additionally to integrate,
analyze and interpret large-scale gene expression data
concerning a study on glucose repression, thereby providing a
means of upgrading the information content of experimental data
and getting further insight into this phenomenon in A.
nidulans. CONCLUSION: We demonstrate how pathway modeling of A.
nidulans can be used as an approach to improve the functional
annotation of the genome of this organism. Furthermore we show
how the metabolic model establishes functional links between
genes, enabling the upgrade of the information content of
transcriptome data.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180016.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180016 | BioModels
Project description:Expression data from Col-0 and pil5 imbibed seeds after far-red or far-red/red light irradiation.
| PRJNA111417 | ENA
Project description:Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA). A twelve array study using total RNA recovered from six separate cultures of Aspergillus nidulans wild-type RDIT9.32 (veA) and six separate cultures of Aspergillus nidulans overexpressing rsmA (restorer of secondary metabolism A), using custom-designed, four-plex arrays. The experiment was divided into two runs. In the first run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans carrying a plasmid overexpressing rsmA under the control of the gpdA promoter were assayed. In the second run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans overexpressing rsmA at the native locus under the control of the gpdA promoter were assayed.
2012-01-17 | E-GEOD-34220 | biostudies-arrayexpress