Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561604 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10013580_1.fastq.gz | Fastqsanger.gz | |||
| SRR10013580_2.fastq.gz | Fastqsanger.gz | |||
| SRR10013581_1.fastq.gz | Fastqsanger.gz | |||
| SRR10013581_2.fastq.gz | Fastqsanger.gz | |||
| SRR10013582_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
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Project description:Jacobaea vulgaris HSS cDNA sequences
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Project description:Introduction: Usually whole plant or whole leaf extracts are analyzed to study the chemical ecology of insect-plant interactions. For herbivore species the contact with the leaf surface enables them to estimate the quality of the plant. The relationship between the leaf-surface and leaf-tissue secondary metabolites (SMs) could offer important new insights in insect-plant interactions mediated by SMs. Pyrrolizidine alkaloids (PAs), typical defense chemicals in Jacobaea species, are repellent for generalist herbivores but are attractive to specialists.</br> Objectives: Explore whether the PAs on the leaf surface are a reliable representation of the PAs in the leaf tissue in PA-containing plants.</br> Method: The concentration of individual PAs present on the leaf surface and in the corresponding leaf tissue from 37 genotypes (one plant from each genotype) of an F2 generation of a cross between Jacobaea vulgaris and Jacobaea aquatica was measured by high performance liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). PAs were removed from the leaf surface by extraction with a slightly acidic aqueous solution.</br> Results: The total amount of PAs present on the surface of the leaves was only 0.015% (range: 0.001-0.163%) of the total amount present in the leaf tissue. Most PAs present in the leaf tissue were also found on the surface, except for jaconine, dehydrojaconine, dehydrojacoline and usaramine N-oxide. Positive correlations between leaf-surface and leaf-tissue concentrations were found for most of the jacobine-like and otosenine-like PAs, but correlations for total PA, senecionine- and erucifoline-like PAs were not significant.</br> Conclusion: These results indicate that PA variation on the leaf surface only partially reflects the PA variation in the leaf tissue. Because most herbivores are affected in a different manner by individual PAs, this result means that the leaf surface does not give a reliable estimate of plant quality to herbivores.
2018-05-01 | MTBLS429 | MetaboLights
Project description:In this study, we characterized the fatty acid production in Neochloris aquatica at transcriptomics and biochemical levels under limiting, normal, and excess nitrate concentrations in different growth phases. At the stationary phase, N. aquatica mainly produced saturated fatty acids such as stearic acid under the limiting nitrate concentration, which is suitable for biodiesel production. However, it produced polyunsaturated fatty acids such as α-linolenic acid under the excess nitrate concentration, which has nutritional values as food supplements. In addition, RNA-seq was employed to identify genes and pathways that were being affected in N. aquatica for three growth phases in the presence of the different nitrate amounts. Genes that are responsible for the production of saturated fatty acids were upregulated in the cells grown under a limiting nitrogen amount while genes that are responsible for the production of polyunsaturated fatty acid were upregulated in the cells grown under excess nitrogen amount. Further analysis showed more genes differentially expressed (DEGs) at the loga- rithmic phase in all conditions while a relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase under limiting and excess nitrogen. Our results provide a foundation for identifying developmentally important genes and understanding the biological processes in the different growth phases of the N. aquatica in terms of biomass and lipid production.
2022-03-27 | GSE163658 | GEO
Project description:Microbial biodiversity and structure in soil affects the composition of pyrrolizidine alkaloids in Jacobaea vulgaris
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Project description:The saliva of the common octopus (Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioural studies and molecular analysis on O. vulgaris and related species suggests that it should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the salivary gland transcriptome of O. vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.
2018-09-24 | PXD010298 | Pride
Project description:A Phaseolus vulgaris genome-wide analysis led to identify the small RNAs (sRNA) of this agronomical important legume. It revealed newly identified P. vulgaris-specific microRNAs (miRNAs) that could be involved in the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. We aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli-Nod factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to identify 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF-induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples, however these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events.
2017-05-01 | GSE81176 | GEO
Project description:Jahnula aquatica CBS 123560 transcriptome
| PRJNA519656 | ENA
Project description:Beta vulgaris subsp. vulgaris reference transcriptome
| PRJNA219421 | ENA
Project description:Beta vulgaris subsp. vulgaris Transcriptome sequencing
| PRJNA246329 | ENA
Project description:Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria, a group of microbes that can perform dissimilatory sulfate reduction coupled to the oxidation of various substrates as carbon and energy sources. In the absence of sulfate, they can also ferment organic acids in syntrophy with methanogens. They exhibit high metabolic diversity switching from one energy mode to another depending on nutrients availability in the environments. Hence, they play a central role in shaping ecosystems. Despite, intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remains far from being fully understood. Alternatively, few metabolic models were also proposed to explain D. vulgaris bioenergetics. However, they appeared to be not easily adaptable to various environmental conditions. To lift off these limitations, here we constructed a new transparent and robust metabolic model of D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
2024-02-01 | PXD046638 | Pride