Transcription profiling of Populus x canescens - WT and PcISPS-RNAi
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus tremula x Populus alba
SUBMITTER: Katja Behnke
PROVIDER: E-MEXP-2120 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Arabipdosis thaliana (ecotype Col-0) was infected with the root pathogen Plasmodiophora brassicae. Gene expression of the host plant has been analyzed at two time points after inoculation (10 and 23 days after inoculation) compared to the correspondend control plants.
2005-02-25 | E-MEXP-254 | biostudies-arrayexpress
Project description:We present the first results of a high coverage Dual RNA-Seq experiment of an R. solani AG1-IB 7/3/14 and L. sativa interaction model with focus on the R. solani transcriptome. With this experiment it is our goal to expand the knowledge regarding the pathosystem L. sativa R. solani AG1-IB through the determination of genes, of pivotal importance for this interaction and who can therefore be seen as putative pathogenicity determinants of R. solani infection within this specific host species.
2017-05-17 | E-MTAB-4762 | biostudies-arrayexpress
Project description:Simulating predicted future climate conditions, stress response and stress-related memory after one week of recovery were transcriptionally characterised in young and old leaves, phloem-bark, developing xylem and roots of 3-month-old Grey poplar plants that had undergone three weeks of stress or were kept under control conditions. The control conditions include ambient or elevated CO2 levels (380 μL L-1 and 500 μL L-1, respectively) with a daily maximum temperature of 27 °C. The stress conditions include a periodic and a chronic drought-heat scenario at elevated CO2 levels (500 μL L-1) with a daily maximum temperature of 33 °C. The periodic stress treatment included three cycles of reduced irrigation (50%, 60% and 70% reduction compared with the controls), each one lasting for six days; between the cycles, there were recovery periods with a duration of two days and a daily maximum temperature of 27 °C. In the chronic stress treatment, irrigation was gradually reduced for 22 days, down to 70% reduction compared with the controls. Three biological replicates were examined per group defined by a specific environmental condition (droughtPER: periodic stress, droughtCHR: chronic stress, control500: elevated CO2 control, control380: ambient CO2 control), a specific harvesting time (S: stress phase, R: recovery phase) and a specific tissue (LE1: young leaves, LE2: old leaves, PHL: phloem-bark, XYL: developing xylem, ROO: roots). For stress phase ambient CO2 control in old leaves, one replicate failed quality control.
2019-01-11 | E-MTAB-6121 | biostudies-arrayexpress
Project description:In the present study molecular interactions between potato plants, Colorado potato beetle (CPB) larvae and Potato virus YNTN (PVYNTN) were investigated by analyzing gene expression in potato leaves. mRNA samples of secondary PVYNTN-infected (CPB_PVY) and healthy potato plants (CPB_H) cultivar Igor and of RNAi coi1-silenced (CPB_coi1) and non-transformed (CPB_NT) potato plants cultivar Desiree collected 24 h post CPB infestation and respective control non-infested samples (CONT_PVY, CONT_H, CONT_coi1, CONT_NT).
2014-10-23 | E-GEOD-56333 | biostudies-arrayexpress
Project description:In order to identify genes specifically induced during various developmental stages of Adventitious Root (AR) formation (described in Ahkami et al. 2009) in leafy cuttings of Petunia hybrida (line W115) and to describe the series of physiological processes during adventitious rooting, a microarray-based transcriptome analysis in the stem base of the cuttings was conducted. The microarray was described by Breuillin et al. (2010) and included a normalized cDNA library from different time points after taking the cuttings from mother plant. Because physiological processes and molecular changes specifically involved in AR formation were considered as of major interest, rather than those associated with wound responses, a filtration approach was chosen to eliminate primarily wound-responsive genes. This study is mainly focused on changes in transcript abundances of genes related to specific metabolic pathways or cellular events including primary metabolism, membrane transport, cell division or signalling during various phases of AR formation. The overall design of the custom microarray used in this study is described in Breuillin et al. (2010). In brief, a database of 24,816 unigene sequences (including 4,700 ESTs from P. hybrida cutting base and all public available P. hybrida and P. axillaris sequences) was used for construction of a custom microarray.
2014-05-17 | E-GEOD-57752 | biostudies-arrayexpress
Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level. Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers VM-CM-6tsch VB 1514 (VM-CM-6tch Industrietechnik GmbH, Germany) with a 16/8 h (light/dark) photoperiod at 22/18 M-BM-0C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity. The Pseudomonas syringae pv. tomato strain DC3000 culture was grown overnight in 10 ml of Kings B solution supplemented with antibiotics rifampicin (50 M-NM-<g mlM-bM-^HM-^R1) and kanamycin (25 M-NM-<g mlM-bM-^HM-^R1). Overnight culture was washed once in 10 mM MgCl2 and final cell densities were adjusted to approximately 0.20 at 600 nm (approximately 1.5 M-CM-^W 108 cfu mlM-bM-^HM-^R1) in 10 mM MgCl2. Plants were mock-challenged with 10 mM MgCl2 or inoculated with DC3000 strain, 3-4 leaves were infiltrated on the abaxial surface with a needleless 1-ml syringe.Whole rosettes were cut at the hypocotyls and harvested from Pseudomonas infested and mock-infected plants after 72 hours treatment. 4 biological replicates were prepared from each treatment, each containing rosettes from 15 individual plants. Differences in transcriptional responses were measured by comparing genes expression of Pseudomonas infected plants against mock-infected control plants.
2013-06-01 | E-GEOD-39246 | biostudies-arrayexpress
Project description:Analysis of the effect of heterologous expression of a soybean DREB2 gene (GmDREB2A;2)on the transcriptome of transgenic Arabidopsis plants. For the genetic modification of Arabidopsis, we introduced gene casettes that express our genes of interest into the genome viaT-DNA transfer using Agrobacterium tumefaciens.
2012-12-04 | E-MEXP-3692 | biostudies-arrayexpress
Project description:Animal venoms are a rich source of novel biomolecules with tremendous potential in medicine and agriculture. Ants represent one of the most species-rich lineages of venomous animals. However, only a fraction of their biodiversity has been studied so far. Here, we investigated the venom compositions from Myrmica rubra and Myrmica ruginodis, two members of the Myrmicinae subfamily of ants. We applied a proteo-transcriptomics based venomics workflow. Our analysis revealed that venoms of both species are composed of several protein classes, such as venom serine protease, cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins (CAP), Kunitz-type serine protease inhibitors or venom acid phosphatase. Several protein classes identified are known venom allergens, and for the first time we detected phospholipase A1 in the venom of M. ruginodis. We also identified two novel toxins of the epidermal growth factor (EGF) family in its venom proteome and an array of additional EGF-like toxins in venom gland transcriptomes of both species. They display similarity to known toxins from the related myrmecine Manica rubida and the Australian red bulldog ant Myrmecia gullosa of the Myrmeciinae subfamily and may serve as nociceptive weapons in defensive scenarios. Our work suggests that the venoms of M. rubra and M. ruginodis contain many high molecular proteins and enzymes with putatively cell damaging functions. Nevertheless, the presence of EGF-like toxins underpins that myrmicine ants also recruited smaller peptide components into their venom arsenal. Although little is known about the bioactivity and function of these EGF-like toxins, their presence in Myrmecinae and Myrmeciinae suggests that they play an important role for the venom systems of Formicoidea. Our work adds to the emerging picture of ant venoms as a source for novel biomolecules. This underlines the importance to incorporate such taxa in future venom bioprospecting programs.
2022-06-09 | PXD033537 | Pride
Project description:In fungi, sexual compatibility is controlled by mating type loci that prevent self-fertilization. In the plant pathogenic fungus Ustilago maydis, the b mating type locus encodes a pair of unrelated homeodomain proteins, termed bE and bW. After fusion of two compatible, haploid cells, the bE and bW proteins form a heterodimeric complex, but only if they are derived from different, compatible alleles. The active bE/bW complex is required and sufficient to initiate pathogenic development of U. maydis, which is prerequisite for sexual reproduction of the fungus. However, the role of the b heterodimer during later stages of pathogenic development was unclear. To analyze b function during in planta development, we generated a temperature-sensitive bE allele (bEts) encoding a protein with a single amino acid alteration at the border of the homeodomain. This mutation leads to a stop in pathogenic development at the restrictive temperature in planta, while bEts strains show normal development at permissive temperature. At restrictive temperature, hyphae develop enlarged, bulbous cells at their tips that contain multiple nuclei, indicating a severe defect in cell division. DNA array analysis of bEts mutant strains in planta revealed a b-dependent regulation of genes coding for secreted proteins that were shown to influence fungal virulence. Our data demonstrate that in U. maydis the b heterodimer is not only essential to establish the heterodikaryon after mating of two compatible sporidia and to initiate fungal pathogenicity, but also to sustain in planta proliferation and ensure sexual reproduction. Maize plants were infected with a mixture of either FB1 and FB2 (wild-type), or RAb1ts and RAb2ts (temperature-sensitive b heterodimer) and kept at 22°C (permissive conditions). Control samples of FB1/FB2 and RAb1ts and RAb2ts were taken 5 days post inoculation at 22 °C (1 replicate each), to see if strains expressing the bts heterodimer show wildtype-like biotrophic development. To measure the impact of the b heterodimer on pathogenic development, infected plants were shifted for 9 hours to resrictive conditions (31°C) 111 hours post infection. After the temperature shift FB1/FB2 (3 replicates) infections developed normal, whereas RAb1ts/RAb2ts (3 replicates) infections were not able to further proliferate in planta because of a none-functional b heterodimer.
2010-05-18 | E-GEOD-16501 | biostudies-arrayexpress
Project description:Plants have the ability to shed organs that are no longer in use. In Arabidopsis thaliana abscission of floral organs involves cell wall remodeling and cell expansion prior to cell wall dissolution. IDA encodes a secreted peptide that signals through the leucine-rich repeat receptor-like kinases (LRR-RLKs) HAESA (HAE) (At4g28490) and HASEA-LIKE2 (HSL2) (At5g65710). Arabidopsis thaliana (ecotype Colombia-0) plants were kept in growth chambers with a 16/8 h (light/dark) photoperiod at 22 M-BM-0C, and 100 mE m-2 s-1 light intensity. 4 biological replicates were prepared from each sample, each containing abscission zone regions of siliques position 4 to 8 (when counting from the flowe at anthesis at the top of the inflorescence) from plants with at least 20 siliques. Differences in transcriptional responses were measured by comparing genes expression in abscission zones of ida-2 plants (SALK_133209) against abscission zones from control plants.
2013-12-30 | E-GEOD-48107 | biostudies-arrayexpress