Microarray transcription profiling of healthy and PVYNTN infected potato tuber tissues (necrotic and non-necrotic)
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum tuberosum
SUBMITTER: Ales Sedlar
PROVIDER: E-MTAB-5776 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Field-grown tubers of potato were examined for infection by Tobacco rattle virus and consequent production of corky ringspot or spraing symptoms. A microarray study identified tuber genes that are differentially expressed in response to TRV infection and to spraing production, showing that hypersensitive response (HR) pathways are activated in spraing-symptomatic tubers. This was confirmed by quantitative RT-PCR (Q-RT-PCR) of a selected group of HR-related genes and by histochemical staining of excised tuber tissue with spraing symptoms. Q-RT-PCR of TRV in different areas of the same tuber slice showed that non-symptomatic areas contained higher levels of virus than did spraing-symptomatic areas. This suggests that spraing formation is associated with an active plant defence that reduces the level of virus in the infected tuber. Expression of two plant defence genes was similarly upregulated in spraing-symptomatic tubers that were infected with another virus, Potato mop-top-virus, suggesting that spraing is a generalised response to virus infection of tubers.
2016-11-15 | E-MTAB-4670 | biostudies-arrayexpress
Project description:A comparison between two suppression subtractive hybridization cDNA libraries. One library is enriched with cDNAs from Potato virus A (PVA) resistant potato genotypes (non-necrotic resistance, nnr) 24h post-inoculation and the other library from PVA-susceptible potato 24h post-inoculation.
2006-03-23 | E-MEXP-289 | biostudies-arrayexpress
Project description:Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits. Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV). Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens. Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV. 3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum. Control plants were mock inoculated using sap from healthy plants. All plants were maintained in a growth chamber at 22C for 18 days. 8 plants were inoculated with each virus or mock inoculated. This experiment was repeated twice. 4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations. RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates. Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples. RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2. Total RNA was purified using Trizol according to TIGRs listed protocol. RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907). Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer. Keywords: Reference design 23 hybs total
2007-09-01 | E-GEOD-8256 | biostudies-arrayexpress
Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing. Small RNA sequencing and degradome sequencing of control and cold treated Solanum tuberosum tubers
2015-12-24 | E-GEOD-43237 | biostudies-arrayexpress
Project description:Wildtype potato plants (Solara) and transgenic plants overexpressing a codon-optimizied version of SP6A (SP6Acop) were grown for 2 months in a greenhouse (16h light, 21°C day/ 19°C night temperature). Tubers were harvested and stored at room temperature. After 19 days dormant buds were taken from tubers of WT and 3 different transgenic lines (#3, 7, 9) and analysed by microarray.
2019-04-08 | E-MTAB-7387 | biostudies-arrayexpress
Project description:Most MS-based approaches to study protein-protein interactions require homogenization of the cells, which leads to loss of the cellular structures, dilution of proteins and formation of incorrect protein complexes. Furthermore, several purification and washing steps are needed, which can lead to the loss of (weaker) interactions. We recently developed a new method for studying protein complexes without interfering with the cellular integrity; Virotrap. By trapping and purifying protein complexes in virus-like particles, we avoid cell lysis and preserve intact complexes during the purification process. Here, we present a protein-protein interaction network of the TNFR1-induced NF-κB and apoptosis pathway, using TRADD, FADD, TRAF2, cIAP1, NEMO, TANK, HOIL1, HOIP, SHARPIN, A20, ABIN1 and ABIN2 as baits in Virotrap. Virotrap was applied both under resting conditions as well as upon TNF stimulation, which reveals dynamic interactions in TNFR1-induced NF-κB signaling. The found interactions compromise both known interactors as well as novel ones that might serve as valuable resource for further unraveling the molecular mechanisms controlling inflammation, cellular proliferation and cell death.
2018-11-06 | PXD009366 | Pride
Project description:Aphids, sap-sucking insects in the order Hemiptera, are among the most prolific insect vectors of plant viruses Plant viruses from the family Luteoviridae are transmitted exclusively by aphids in a circulative manner and cause significant crop yield losses. Circulative plant viruses must cross the aphid gut and other tissues prior to transmission to a new host plant. The discovery of proteins that control acquisition and transmission in the insect vector is the biggest challenge for the vector biology field and will have practical applications for growers by providing new molecular targets for the development of precision vector management tools. The green peach aphid, Myzus persicae, is a vector of the Potato leafroll virus (PLRV), a polerovirus in the Luteoviridae. PLRV transmission efficiency was significantly reduced when a clonal lineage of M. persicae was reared on turnip (T-Myzus) as compared to the weed physalis (P-Myzus). The effect on PLRV transmission efficiency was transient and caused by a host-switch response. Using 2-D DIGE, we revealed that the major difference in the proteome profile of P- and T-Myzus was the lysosomal cysteine protease cathepsin B, with multiple size and charge isoforms of this enzyme up-regulated in T-Myzus. Quantitative, shotgun proteomics revealed a specific upregulation in the expression of other lysosomal proteins in T-Myzus as compared to P-Myzus, including cathepsin B, cathepsin B-16, beta-glucuronidase, peroxidasin, legumain-like, and aminopeptidase-N. The titer of PLRV was over 1.5 fold higher in P-Myzus than in T-Myzus at 24h and 72h after the beginning of virus acquisition, suggesting that virus acquisition in P-Myzus was more efficient. Cathepsin B and PLRV localization were starkly different in P- and T-Myzus midguts, the site of PLRV acquisition into the insect. In P-Myzus midguts, an abundance of PLRV was observed inside midgut cells, and cathepsin B was sequestered in a subcellular compartment. In contrast, there is near complete co-localization of cathepsin B and PLRV at the cell membranes in viruliferous T-Myzus. Inhibition of cathepsin and other cysteine proteases with E64 restored the ability of T-Myzus to transmit PLRV in a dose-dependent manner, suggesting that the activities of lysosomal cysteine proteases at the cell membrane in T-Myzus is responsible for the change in virus transmission phenotype in these aphids. T-Myzus individuals weighed more and had more progeny than P-Myzus individuals. These data are all consistent with the hypothesis that there is an induction of lysosomal exocytos in the midgut of T-Myzus linked to the ability of the aphid to acquire PLRV. These data also show that the ability of the generalist aphid M. persicae to transmit PLRV is influenced by the host plant the aphids are reared on, information that is useful to growers for polerovirus management in field crops.
2016-12-14 | PXD004893 | Pride
Project description:Spongospora subterranea is a soil-borne plant pathogen responsible for economically significant root and powdery scab diseases of potato. However, Tthe obligate biotrophic nature of S. subterranea has made detailed study of the pathogen problematic. Here, we first compared the benefits of sporosori partial purification utilizing Ludox gradient centrifugation. We then undertook optimization efforts for protein isolation comparing the use of a urea buffer followed by Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) and a sodium dodecyl sulfate (SDS) buffer followed by suspension-trapping (S-Trap). Label-free, quantitative proteomics was then used to evaluate the efficiency of sporosori purification and protein preparation methods. The purification protocol produced a highly purified suspension of S. subterranea sporosori without affecting the viability of the spores. Results indicated that the use of a combination of SDS and S-Trap for sample clean-up and digestion obtained a significantly higher number of identified proteins compare to using urea and SP3, with 218 and 652 proteins identified using SP3 and S-Trap methods, respectively. Analysis of proteins by mass spectrometry showed that the number of identified proteins increased by approximately 40% after the purification of spores by Ludox. These results suggested a potential use of the described spore purification and protein preparation methods for proteomics study of obligate biotrophic pathogens such as S. subterranea.
2021-09-09 | PXD019776 | Pride
Project description:The goal of the current research is to identify factors that involved with heat induced russeting of the potato tuber skin. Potato plants of the variety Desirèe were grown in pots filled with perlite, in a greenhouse under natural winter conditions (Nov 2005- Jan 2006, average temperatures range of 10-18°C). For the exposure of tubers to heat stress (H) hot water (33-35°C) was circulated in tubes lined at the internal side of the pots. The heat was applied one week before tubers harvest. Tubers were harvested at two time points: 8 weeks post sprouting and a week post mechanical vine killing. The skin (S) of young tubers was peeled by hand, as the remaining phelloderm (PH) layers, the periderm of young tubers (P) and the periderm of mature tubers (ST) were peeled using a scalpel blade. Leaves (L) and tuber flesh (TF) samples were collected as well. For each RNA sample 4 biological replicates were prepared; each one represents pooled tissues from 4-6 plants grown at different location in the greenhouse. RNA was extracted using CTAB protocol, and was further purified by RNeasy Mini Kit (Qiagen) using the On-Column DNase Digestion protocol. Keywords: Loop design 28 hybs total
2007-08-31 | E-GEOD-8283 | biostudies-arrayexpress
Project description:Cancer cachexia and the associated skeletal muscle wasting are considered poor prognostic factors, although effective treatment has not yet been established. Recent studies have indicated that the pathogenesis of skeletal muscle loss may involve dysbiosis of the gut microbiota and the accompanying chronic inflammation or altered metabolism. In this study, we evaluated the possible effects of modifying the gut microenvironment with partially hydrolyzed guar gum (PHGG), a soluble dietary fiber, on cancer-related muscle wasting and its mechanism using a colon-26 murine cachexia model. Compared to a fiber-free (FF) diet, PHGG contained fiber-rich (FR) diet attenuated skeletal muscle loss in cachectic mice by suppressing the elevation of the major muscle-specific ubiquitin ligases Atrogin-1 and MuRF1, as well as the autophagy markers LC3 and Bnip3. Although tight junction markers were partially reduced in both FR and FF diet-fed cachectic mice, the abundance of Bifidobacterium, Akkermansia, and unclassified S24-7 family increased by FR diet, contributing to the retention of the colonic mucus layer. The reinforcement of the gut barrier function resulted in the controlled entry of pathogens into the host system and reduced circulating levels of lipopolysaccharide-binding protein (LBP) and IL-6, which in turn led to the suppression of proteolysis by downregulating the ubiquitin-proteasome system and autophagy pathway. These results suggest that dietary fiber may have the potential to alleviate skeletal muscle loss in cancer cachexia, providing new insights for developing effective strategies in the future.
2021-11-23 | E-MTAB-11094 | biostudies-arrayexpress