Plant health identification of Coleoptera
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NextSeq 500
ORGANISM(S): Anoplophora Glabripennis
SUBMITTER: University of Hohenheim
PROVIDER: PRJEB66443 | EVA | 2023-10-01
REPOSITORIES: EVA
Dataset's files
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls. Microarray assessments were conducted on larvae exposed for 7-days to Sacramento River water collected at Hood and pooled laboratory controls. Assessments were carried out in quadruplicate, using 3 fish per treatment. RNA was extracted from frozen whole, individual organisms, using Trizol Reagent (Invitrogen) as per manufacturer's guidelines. Total RNA from 5 fish was pooled per treatment and cDNA was synthesized from a total of 2ug total RNA, amplified using a SuperScripttm Indirect RNA Amplification System (Invitrogen). Resulting aRNA was labeled with Alexa fluor dyes (Invitrogen) as per manufacturerM-bM-^@M-^Ys instructions. Two color microarray assessments were carried out on quadruplicate treatments, using 5M-BM-5g of aRNA for pooled controls vs exposed sample, (total 4 samples). Microarray hybridizations were performed manually, and incubated in a waterbath at 42C for 16 hours. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment.
2012-09-20 | E-GEOD-40991 | biostudies-arrayexpress
Project description:This project aims to study exoskeleton proteins from four species of crustaceans including two crabs, one shirmp and one crayfish through proteomic methods.
2023-07-10 | PXD043631 |
Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls.
2012-09-20 | GSE40991 | GEO
Project description:This project aims at sequencing a few Terrisporobacter species.
| PRJEB22086 | ENA
Project description:Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease.The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/Phytophthora parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy.The present project aims at analyzing the compatible interaction between A. thaliana roots and Phytophthora parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom designed Phytophthora parasitica biochip will enable analyzing of Phytophthora parasitica gene expression during the same stages. The pathosystem involving A. thaliana and Phytophthora parasitica was described in Attard A, Gourgues M, Callemeyn-Torre N, Keller H. 2010. The New phytologist 187: 449–460. The protocol for recovery of RNA from purified appressoria was described in Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre JY, Gourgues M. 2010. New Phytol 185: 248–257.
2014-03-01 | GSE51252 | GEO
Project description:1. Research project objectives/Research hypothesis Phytopathogenic microfungi are plant parasites commonly found in the human environment. They may pose a potential threat to human health, as fungi are a generally known and prominent source of allergens. Allergic diseases are considered the epidemics of the twentieth century and are estimated to affect more than 30% of the population in industrialized countries with a still dramatically increasing incidence. However, the cause of existing allergies is not always identified by commonly used skin or blood tests. The essential allergenic fungi belong to the genera Alternaria, Aspergillus, Cladosporium, Penicillium, and Fusarium; however, it cannot be excluded that very common native and invasive phytopathogenic microfungi causing mass plant infestations are also a source of allergens. Therefore, we hypothesize that humans can inhale common phytopathogenic microfungi as a potential cause of allergic reactions. The subject of the research will be eight phytopathogenic microfungal species belonging to Erysiphales, Puccinales, Peronosporales, and Albuginales orders collected in their natural environment, comprehensive biochemical characteristics thereof, and determination of their potential impact on human asthma development. Both these species and their host plants are currently very common in Poland. The hosts include herbaceous plants, shrubs, planted species as well as ornamental plants or wild species that are very popular in parks and gardens. Phytopathogenic fungi cause massive infestation of plants and release vast amounts of spores. Such dissemination of plants and their parasites increases the risk of human contact with potential allergens. 2. Research project methodology Collected fungi will be identified both with microscopic and molecular methods (the fungal DNA sequences will be compared with relevant sequences available in the GenBank database with the use of the BLAST tool; also, a phylogenetic tree will be constructed using the MEGA7 program with the Neighbor-Joining method). We will carry out precise biochemical characteristics of fungal crude extracts; using the modern spectral methods will facilitate structural analysis of fatty acids and carbohydrates (gas-liquid chromatography-mass spectrometry) and protein identification (liquid chromatography-mass spectrometry). Fungal crude extracts will be used in in vitro studies to determine their cytotoxic potential in a human airway epithelial cell line and their ability to induce cytokines involved in allergic reactions – TNFα, TGFβ, GM-CSF, IL-1β, and IL-6. Based on in vitro results, chosen crude fungal extracts will induce acute and chronic asthma in a murine model (compared to positive controls – ovalbumin and Aspergillus fumigatus). We will study the remodeling of mouse lungs, serum IgE, and cytokine levels (IL-4, -5, -13, TNF-α, TGF-β), as well as the content of blood leukocytes (including eosinophils). 3. Expected impact of the research project on the development of science Prospective results will contribute to the extension of our basic knowledge about environmental threats to human health connected with native and invasive phytopathogenic microfungal species. Although many fungal allergens have been characterized in recent years, which proved very useful in diagnosing, the actual role of common and close-to-human plant parasites remains unknown. Biochemical characteristics of chosen microfungi will complete general knowledge about these still neglected plant parasites. At the same time, fatty acid profiles will be helpful to as chemotaxonomic markers for rapid identification and classification thereof. Additionally, including invasive plant parasites in our research has great significance not only for the Polish region but also for countries of their origin, which underlines the universal character of the presented project. Summing up, our research will cover a multi-faceted area: (i) taxonomy of microfungi – determination of rare in nature fungal components which will help in rapid classification thereof, (ii) molecular biology – genetic identification of fungal species, and identification of protein, fatty acids, and carbohydrates in inhaled fungal material with advanced spectroscopic methods, (iii) human health – indication of the allergic potential of phytopathogenic microfungi as a public health threat.
2025-06-25 | PXD058325 | Pride
Project description:The project aims to reveal the differentially expressed microRNAs in patients with ovarian cancer compared with normal controls.
2022-07-14 | GSE134289 | GEO
Project description:The RNA sequencing analysis was undertaken to investigate the transcriptomic changes in adult wheat inoculated with Puccinia graminis f. sp. tritici the causal agent of stem rust disease. The project firstly aims to compare gene expression in one susceptible wheat line with two wheat lines exhibiting adult plant resistance to the stem rust. Secondly, the project aims to examine the temporal changes in gene expression in wheat after inoculation. Wheat plants was grown until maturity under greenhouse conditions. Plants were inoculated with Puccinia graminis f. sp. tritici and the flag leaf sheath sampled for RNA sequencing. The project aims to give essential insight into the adult plant resistance response in wheat to Puccinia graminis f. sp. tritici inoculation.
2022-10-30 | E-MTAB-9681 | biostudies-arrayexpress
Project description:GenomeTrakr Project: Vibrio species New York State Department of Health. Wadsworth Center
| PRJNA828570 | ENA
Project description:If relapses occur in only 20% of T-ALL children, 70% will have a dismal outcome, justifying the need for new therapeutic options. Transcriptomic plasticity is a property of leukemic cells to adapt their functions and resist to treatments. The project aims at analyzing, at a single cell resolution, the variations of the gene expression, between diagnostic and relapse. This will allow identification of relapse-associated genes as potential new targets for future innovative treatments.
2024-05-17 | GSE262271 | GEO