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55 results for “phytochrome”
Data for Vibrational Couplings between Protein and Co-factor in Bacterial Phytochrome Agp1revealed by 2D-IR Spectroscopy
<p>2D-IR data for the bacteriophytochrome Agp1 in the Pr and Pfr states </p>
Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?
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Data for: Circular dichroism spectroscopy reveals multiple phytochrome photoproducts in equilibrium
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Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is highly conserved. Liverworts, hornworts and Selaginella apparently possess a single phytochrome, whereas independent gene duplications occurred within mosses, lycopods, ferns and seed plants, leading to diverse phytochrome families in these clades. Surprisingly, the phytochrome portions of algal and land plant neochromes, a chimera of phytochrome and phototropin, appear to share a common origin. Our results reveal novel phytochrome clades and establish the basis for understanding phytochrome functional evolution in land plants and their algal relatives.
Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis
Plants respond to shade-modulated light-signals, via the phytochrome (phy) system, by adaptive changes, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this information to the transcriptional network, we compared the genome-wide expression profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry controlling downstream response-elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. Collectively, these data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment via perturbations in the mutually antagonistic actions of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses.
Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes
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Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis
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RNAseq analysis of the response of Arabidopsis thaliana phytochrome mutants (PhyA PhyB) to fractional gravity under blue-light stimulation during spaceflight
Traveling to nearby extraterrestrial objects having a reduced gravity level (partial gravity) compared to Earth s gravity is becoming a realistic objective for space agencies. The use of plants as part of life support systems will require a better understanding of the interactions among plant growth responses including tropisms under partial gravity conditions. Here we present results from the Seedling Growth space experiments on the ISS to complement the previously released GLDS-251 dataset including seeds of Arabidopsis thaliana wildtype plants. Seeds were germinated and seedlings grew for six days under different gravity levels namely micro-g several intermediate partial-g levels and 1g and were subjected to irradiation with blue light for the last 48 hours. RNA was extracted was obtained for 20 wildtype samples for subsequent RNAseq analysis in GLDS-251 here we add 36 samples from similarly exposed PhyA and PhyB mutants.
Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways [RNA-seq]
GEO Series GSE48767. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Phytochrome-based extracellular matrix with reversibly tunable mechanical properties
GEO Series GSE125130. Homo sapiens. 78 samples. Type: Expression profiling by high throughput sequencing.
Arabidopsis phytochrome A directly targets numerous promoters for individualized modulation of genes in wide range of pathways [ChIP-seq]
GEO Series GSE48769. Arabidopsis thaliana. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The cyanobacterial phytochrome 2 regulates the expression of motility-related genes through the second messenger cyclic di-GMP
GEO Series GSE116409. Synechocystis sp. PCC 6803. 8 samples. Type: Expression profiling by array.
PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics
GEO Series GSE139296. Arabidopsis thaliana. 109 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
A cis-regulatory element of the PHYTOCHROME A gene confers the submergence escape capacity for amphibious plants
GEO Series GSE274369. Arabidopsis thaliana. 18 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant
GEO Series GSE36274. Physcomitrium patens. 4 samples. Type: Expression profiling by high throughput sequencing.
Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4
GEO Series GSE109038. Arabidopsis thaliana. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice
GEO Series GSE16796. Oryza sativa. 4 samples. Type: Expression profiling by array.
SUPPRESSOR OF PHYTOCHROME B4#3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days [RNA-seq]
GEO Series GSE189264. Arabidopsis thaliana. 18 samples. Type: Expression profiling by high throughput sequencing.
SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis
GEO Series GSE85883. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Expression data from epidermis specific phytochrome B or global phytochrome B line comparing to phyB-9 mutant.
GEO Series GSE87591. Arabidopsis thaliana. 8 samples. Type: Expression profiling by array.
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.