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LC-MS/MS of apoplast proteins from Arabidopsis wild type and ca1ca4 mutant plants

ABSTRACT: geLC-MS/MS analysiswas performed to identify proteins that are present in apoplastic fluid isolated from rosette leaves of 8-week-old wild type and carbonic anhydrase (ca1ca4) mutant Arabidopsis plants.

OTHER RELATED OMICS DATASETS IN: E-MTAB-4447PRJNA218542

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Jeff Anderson

LAB HEAD: Scott C Peck

PROVIDER: PXD000692 | Pride | 2014-08-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CA-1.RAW	Raw
	CA-1.dat-pride.pride.mgf.gz	Mgf
	CA-1.dat-pride.pride.mztab.gz	Mztab
	CA-1.dat-pride.xml.gz	Xml
	CA-10.RAW	Raw

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1 - 5 of 80

Publications

Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development.

Engineer Cawas B CB Ghassemian Majid M Anderson Jeffrey C JC Peck Scott C SC Hu Honghong H Schroeder Julian I JI

Nature 20140706 7517

Environmental stimuli, including elevated carbon dioxide levels, regulate stomatal development; however, the key mechanisms mediating the perception and relay of the CO2 signal to the stomatal development machinery remain elusive. To adapt CO2 intake to water loss, plants regulate the development of stomatal gas exchange pores in the aerial epidermis. A diverse range of plant species show a decrease in stomatal density in response to the continuing rise in atmospheric CO2 (ref. 4). To date, one ...[more]

PMID: 25043023

Similar Datasets

LC-MS/MS to identify proteins present in apoplastic fluid extracted from WT and ca1ca4 mutant Arabidopsis plants grown under low and high CO2 conditions

Project description:geLC-MS/MS analysis was performed to identify proteins that are present in apoplastic fluid isolated from rosette leaves of 8-week-old wild type and carbonic anhydrase (ca1ca4) mutant Arabidopsis. Plants were grown in either low (150 ppm) or high (500 ppm) CO2.

2014-08-22 | PXD000693 | Pride

Plasma membrane proteomics in the maize primary root elongation zone under water stress conditions

Project description:Maintenance of root growth is critical to plant adaptation to drought conditions. Previous work on the maize (Zea mays L.) primary root under water stress showed that cell elongation is maintained in the apical region of the growth zone but progressively inhibited further from the apex. These responses involve spatially differential and coordinated regulation of cellular growth processes, including modifications of both cell production rate and cell wall extensibility. As the interface between the cytoplasm and the apoplast (including the cell wall), the plasma membrane is likely to play major functions in the coordination of cell production and expansion. In addition, plasma membrane proteins may be involved in solute uptake for osmotic adjustment, pH regulation, ion homeostasis and other critical processes in roots growing under water-stressed conditions. Due to technical limitations, however, plasma membrane proteomic studies have not been reported for water-stressed tissues. Using a simplified method for enrichment of plasma membrane proteins, we compared the developmental distribution of plasma membrane proteins that are differentially regulated in the growth zone of well-watered and water-stressed roots.

2020-11-11 | PXD002027 | Pride

Genes expression in case of PEV caused by chromosomal rearrangement

Project description:Heterochromatic position effect variegation (PEV) is the epigenetic disruption of genes expression near the new-formed eu-heterochromatic border. We characterized the inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the opposite normal chromosome in combination with the inversion. Euchromatic breakpoint of In(2)A4 inversion was localized at 105 bp region (chr2L:21182214-21182318) of the second exon of the Mcm10 gene, the heterochromatic breakpoint is located at the block of dodecasatellite in 2L pericentromeric heterochromatin. In order to check the effects of heterochromatin on neighbor euchromatic genes and estimate the distance of inactivation spreading, we performed RNA-seq analysis of genes expression in larvae and adults females of genotypes A12/A12 (control) and In(2)A4/In(2)A4. Cis-influence of heterochromatin in the inversion causes not only repression, but also activation of genes, and the effects of heterochromatin are different at different developmental stages. Cis-actions affect only a few genes located near the heterochromatin Comparison of genes expression in wild type and demonstrating PEV larvae and adults in two repeats each

2015-10-25 | E-GEOD-71842 | biostudies-arrayexpress

Transcriptome analysis of capelin (Mallotus villosus) liver slice culture exposed to benzo[a]pyrene

Project description:Capelin (Mallotus villosus) is one of the important fish species in the arctic marine foodweb that could be vulnerable to contaminant exposure from offshore petroleum related activities. The study was conducted to map transcriptome responses in capelin liver slice culture exposed to benzo[a]pyrene (BaP). BaP is a polyaromatic hydrocarbon (PAH) which is among the most toxic compounds found in crude oil. Ex vivo liver slices culture was performed under 10 µM BaP exposure for 72 h and transcriptome analysis (RNA-seq) analysis was performed to characterize de novo transcriptome of the liver and identify genes responding to BaP exposure.

2024-09-08 | E-MTAB-13934 | biostudies-arrayexpress

Transcriptome analysis of long rough dab (Hippoglossoides platessoides) liver slice culture exposed to benzo[a]pyrene.

Project description:Long rough dab (Hippoglossoides platessoides) is an important flatfish fish species in the north Atlantic arctic and sub-arctic marine foodweb that could be vulnerable to contaminant exposure from offshore petroleum related activities. The study was conducted to map transcriptome responses in long rough dab precision cut liver slice (PCLS) culture exposed to benzo[a]pyrene (BaP). BaP is a polyaromatic hydrocarbon (PAH) which is among the most toxic compounds found in crude oil. PCLS culture was performed under 10 µM BaP exposure for 72 h and transcriptome analysis (RNA-seq) analysis was performed to characterize de novo transcriptome of the liver and identify genes responding to BaP exposure.

2024-09-09 | E-MTAB-13932 | biostudies-arrayexpress

Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

Project description:The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a M-bM-^@M-^\cleavable complexM-bM-^@M-^]. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment affected transcription initiation, elongation, termination, splicing and enhancer activity. Following removal of camptothecin, transcription spread as a wave from the 5M-bM-^@M-^Y-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. As a result, camptothecin preferentially inhibited the expression of large genes such as proto-oncogenes, and anti-apoptotic genes while smaller ribosomal protein genes, pro-apoptotic genes and p53 target genes showed relative higher expression. In addition, a set of mitotic regulator genes and histone genes were inhibited in a size-independent manner. Cockayne syndrome group B fibroblasts showed a very similar RNA synthesis recovery profile to normal fibroblasts suggesting that transcription-coupled repair is not involved in the repair of transcription-blocking TOP1 lesions. These findings of the effects of camptothecin on transcription have important implications for its anti-cancer activities and may aid in the design of improved combinatorial treatments involving Top1 poisons. Analysis of the effect of Camptothecin (CPT) on transcription. Normal fibroblasts and Cockayne syndrome group B fibroblasts were exposed to CPT for 60 minutes, after which a washout was performed. Nascent RNA was labeled using bromouridine for 15 minutes starting at time points: 1) 15 minutes before the washout; 2) Immediately after the washout; 3) 15 minutes after the washout. Test samples are compared to control cells that were not exposed to CPT.

2013-10-29 | E-GEOD-48678 | biostudies-arrayexpress

Bru-seq nascent RNA sequencing of human and mouse cells: correlation to replication timing and genome instability

Project description:Bru-seq nascent RNA sequencing (PubMed ID 23973811) was performed on two primary human fibroblast cell lines, mouse embryonic stem cells, and GM12878 human lymphoblastoid cells. Read data, which include both exon and intron signals, were used to identify transcription unit spans genome-wide, where a transcription unit is roughly correspondent to the longest expressed isoform of a gene. However, because algorithms were not constrained by annotated genes, transcription units need not and often do not correspond precisely to gene boundaries and include extragenic transcription. Transcription units were then compared to separate data sets that comprised induced copy number variants, common fragile sites, and Repli-seq replication timing. The objective was to discover the relationships between transcription unit span and size, local genomic instability, and replication timing. This GEO sample series provides the span and intensity of transcription units called genome-wide in the various samples. Correlations to genome stability and replication timing are provided in the associated manuscript. In addition, one human fibroblast line and the mouse embryonic stem cells had paired samples treated and untreated with low dose aphidicolin. Gene RPKM signal intensities are provided for these samples, although comparing these was not the principal objective of the study. Bru-seq single-read nascent RNA sequencing on human 090 fibroblasts +/- aphidicolin treatment, human UMHF1 fibroblasts (3 replicates), human GM12878 lymphoblastoid cells, and mouse embryonic stem cells+/- aphidicolin treatment.

2014-10-17 | E-GEOD-55862 | biostudies-arrayexpress

RNA-seq of polar cod (Boreogadus saida) liver slice culture exposed to benzo[a]pyrene and ethynylestradiol

Project description:Polar cod, a key fish species in the arctic marine foodweb is vulnerable to effects of pollution from offshore petroleum related activities in the Arctic and sub-arctic region. The study was conducted to map transcriptome responses to in Polar cod (Boreogadus saida) liver slice culture exposed to benzo[a]pyrene (BaP) in the presence or absence of physiological levels of ethynylestradiol (EE2). BaP is a polycyclic aromatic hydrocarbon (PAH), also found in crude oil contaminants. PAHs such as BaP are among the most toxic compounds of crude oil. Precision-cut liver slice cultures from five female polar cod (n = 5/ group, paired design) were exposed to BaP alone (10 µM), or in combination with low concentrations of EE2 (5 nM), to mimic physiological estradiol levels in early vitellogenic female fish. Transcriptome analysis (RNA-seq) was performed after 72 h exposure in culture. The results provide a global view of transcriptome responses to BaP, EE2 and their mixture. In the mixture exposure, BaP resulted attenuation of EE2 stimulated gene expression (anti-estrogenic effects). The results from this ex vivo experiment suggest that pollutants that activate the Ahr pathway such as the PAH compound BaP can result in anti-estrogenic effects that may lead to endocrine disruption in polar cod.

2021-05-24 | E-MTAB-10509 | biostudies-arrayexpress

Impacts of HLA-B57 micropolymorphism (MRM)

Project description:Comparison of peptide ligands of major histocompatibility class (MHC) I isolated by immunoaffinity purification from the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the MHC class I alleles HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01.

2018-10-24 | PXD009850 | Pride

Effects of physiological and synthetic IAP antagonism on c-IAP dependent signaling

Project description:Cellular inhibitor of apoptosis proteins 1 and 2 (c-IAP1/2) play central roles in signal transduction mediated by numerous receptors that participate in inflammatory and immune responses. In certain pathways, such as activation of NF-kB, their degradation is a major regulatory event and is physiologically induced by activation of receptors. Additionally, a number of synthetic compounds have been developed that also target the c-IAPs and induce their degradation. However, the extent of a synthetic IAP antagonist’s ability to mirror the transcriptional program by a physiological signal remains unclear. Here we take a systems approach to compare the transcriptional programs triggered by activation of CD30, a well-characterized receptor previously shown to induce the degradation of the c-IAPs, to SM-164, a synthetic IAP antagonist that specifically triggers c-IAP degradation. Employing a technique that allows the specific analysis of newly transcribed RNA, we have generated comparative transcriptome profiles for CD30 activation and SM-164 treatment. Analysis of these profiles revealed that the genes regulated by each stimulus were not completely shared, indicating novel functions of IAP antagonists and consequences of c-IAP1/2 degradation. The data identified a role for c-IAP1/2 in the regulation of the ribosome and protein synthesis, which was subsequently confirmed by biological assays. These findings expand our knowledge of the roles of c-IAP1/2 in signaling and provide insight into the mechanism of synthetic IAP antagonists, furthering our understanding of their therapeutic potential. This submission contains two different experiments. In experiment 1, cells were exposed to drug treament (DMSO or SM-164) for 3 hours. In experiment 2, cells were exposed to an adherent layer of CHO cells either expressing or not CD30L. Each treatment in each experiment was conducted once, leading to a total of 4 samples.

2015-02-09 | E-GEOD-64927 | biostudies-arrayexpress

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