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Affy_ams_maize-Cell wall maize mutant during arbuscular mycorrhizal symbiosis

ABSTRACT: affy_ams_maize - aafy_ams_maize - Main objectives of this study: - role of plant cell wall during AM symbiosis - regulation pattern during AM symbiosis - understanding of the original mycorrhizal phenotype of bm4 - search of candidate-genes to study AM symbiosis-After 7 days in phytochambers, plantlets were transplanted in 2L of humidified bedrock with 3000 spores for inoculation conditions or without spore for mock conditions then plants have grown in greenhouse. Maize roots have been sampled 7 weeks post-inoculation and freezed in liquid nitrogen then stocked at -80M-BM-0C. Total RNA was isolated from frozen root tissue by using the RNeasy Plant Mini Kit (Qiagen) following the manufacturerM-bM-^@M-^Ys instructions. Keywords: treated vs untreated comparison 8 arrays - maize

ORGANISM(S): Zea mays

SUBMITTER: stephanie huguet

PROVIDER: E-GEOD-22950 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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affy_diversity_maize-Understanding the Diversity of Maize Cell Wall

Project description:affy_diversity_maize - affy_diversity_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of two maize lines Cm484 (line of good digestibility) and F98902 (line of bad digestibility) at the same developmental stage (male flowering). Keywords: organ comparison 4 arrays - maize

2011-07-14 | E-GEOD-22948 | biostudies-arrayexpress

The membrane proteome of Medicago truncatula roots displays qualitative and quantitative changes in response to arbuscular mycorrhizal symbiosis

Project description:Arbuscular mycorrhizal (AM) symbiosis that associates roots of most land plants with soilborne fungi (Glomeromycota), is characterized by reciprocal nutritional benefits. Fungal colonization of plant roots induces massive changes in cortical cells where the fungus differentiates an arbuscule, which drives proliferation of the plasma membrane, and the de novo synthesis of the periarbuscular membrane. Despite the recognized importance of membrane proteins in sustaining AM symbiosis, the root microsomal proteome elicited upon mycorrhiza still remains to be explored. In this study, we first examined the qualitative composition of the root membrane proteome of Medicago truncatula after microsome enrichment and subsequent in depth analysis by GeLC-MS/MS. The results obtained highlighted the identification of 1226 root membrane protein candidates whose cellular and functional classifications predispose plastids and protein synthesis as prevalent organelle and function, respectively. Changes at the protein abundance level between the membrane proteomes of mycorrhizal and nonmycorrhizal roots were further monitored by spectral counting, which retrieved a total of 97 proteins that displayed a differential accumulation upon AM symbiosis. Besides the canonical markers of the periarbuscular membrane, new candidates supporting the importance of membrane trafficking events during mycorrhiza establishment/functioning were identified, including flotillin-like proteins.

2014-06-30 | PXD000875 | Pride

Comparison of gene expression in roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor

Project description:The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor. The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturer's instructions. We carried out six hybridizations (NimbleGen) with samples derived from Populus trichocarpa and Populus deltoides mycorrhizal root tips. Three samples (biological replicates) originated from Populus trichocarpa (GSM648401, GSM648403, GSM648405) and three biological replicates from Populus deltoides (GSM648408, GSM648411, GSM648414). cDNA was synthesized using CLONTECH Super Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

2011-01-15 | E-GEOD-26416 | biostudies-arrayexpress

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2020-12-31 | E-MTAB-8969 | biostudies-arrayexpress

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2015-12-31 | E-GEOD-72770 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

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Project description:The experiment intended to identify biomarker genes for arsenite exposure in rice roots. These biomarker genes were tested as alternative endpoints in an sediment-contact test with rice (Brinke et al. Environ Sci Pollut R 22.16 (2015): 12664-12675)

2017-10-01 | E-MTAB-5430 | biostudies-arrayexpress

Proteome analysis reveals alterations in protein profile upon ectomycorrhiza establishment in oak roots

Project description:Trees establish a symbiotic relationship with specialized soil fungi, called ectomycorrhizae, which is essential for nutrition, growth and health of temperate forest ecosystems. Understanding the mechanisms governing the establishment and functioning of ectomycorrhiza is important because of the role of forests in sequestering CO2 and also to develop ways to optimize tree productivity and sustainability. Here, we investigated the response of an oak species to ectomycorrhiza formation using a two dimensional differential in gel electrophoresis (2D-DIGE) and MALDI-TOF/TOF mass spectrometry proteomics approach. At the root level, changes in the abundance of 34 unique oak proteins were detected and revealed proteins involved in carbon and energy metabolism, protein processing and degradation, response to oxidative stress, lipid metabolism/transport, nitrogen and phosphorous assimilation and cell wall modification. Proteins supporting the importance of the secretory pathway functioning, in particular of the endoplasmic reticulum, during ectomycorrhiza functioning were identified. These proteins were identified as components of the endoplasmic reticulum folding/chaperoning machinery and proteins involved in the ER quality control system. This study constitutes an important contribution for the understanding of the mechanisms underlying the response of plants to ectomycorrhizal symbiosis establishment.

2017-07-14 | PXD003009 | Pride

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Project description:Alnus glutinosa belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program and to identify new key plant genes that control nodulation during symbiosis in A. glutinosa. Symbiosis between A. glutinosa and Frankia was obtained after inoculation of young plant with a concentrated culture of the bacteria. Inoculation was performed in a medium depleted in nitrogen which favors the induction of nitrogen fixing symbiosis. For this study we considered two stages of symbiosis: - an early stage where inoculated roots were harvested 7 days after inoculation with the bacteria and compared to two controls (non-inoculated roots grown with or without nitrogen and harvested at the same time) - a late stage where nodules (nitrogen-fixing specific organs) were harvested 21 days after inoculation and compared to non-inoculated roots harvested on the day of inoculation (which is our reference time 0d). Three biological replicates were used for each condition. Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for A. glutinosa, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent

2011-04-11 | E-GEOD-24153 | biostudies-arrayexpress

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