Hippobosca camelina
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ABSTRACT:
PROVIDER: PRJNA1120633 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Camelina is an annual oilseed plant that is gaining momentum as a biofuel winter cover crop. Understanding gene regulatory networks (GRNs) is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. Also, we performed RNA-seq assays of Camelina's seed at 5, 8, and 11 days post-anthesis (DPA) to improve the transcriptomic resolution of the early stages of the Camelina seed development. We identified ~350 TFs highly co-expressed with lipid-related genes (LRGs). After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16/22 TF using DNA affinity purification sequencing (DAP-seq). Enrichment analyses supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes and aspects unique to Camelina. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confident and shortlist of Camelina TFs involved in controlling lipid metabolism during seed development.
2022-01-13 | GSE184283 | GEO
Project description:This study was performed to investigate assess the impacts of CO and/or CM containing diets on Atlantic salmon hepatic gene expression in order to identify candidate molecular biomarkers of responses to camelina-containing diets. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial (Control diet: FO; Test diet: 100% FO replacement with CO, with solvent-extracted FM and inclusion of 10% CM (100COSEFM10CM). A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to FO controls at week 16.
2015-05-12 | GSE56784 | GEO
Project description:This study was performed to investigate assess the impacts of CO and/or CM containing diets on Atlantic salmon hepatic gene expression in order to identify candidate molecular biomarkers of responses to camelina-containing diets. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial (Control diet: FO; Test diet: 100% FO replacement with CO, with solvent-extracted FM and inclusion of 10% CM (100COSEFM10CM). A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to FO controls at week 16. Atlantic salmon were fed for 16 weeks with the FO or 100COSEFM10CM diet (three tanks per diet). Liver samples were taken from 7 fish from each tank at week 16. A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual livers of fish from the 2 treatment groups: FO and 100COSEFM10CM. For each treatment group we used 9 biological replicates (3 fish from each of 3 tanks). All test samples were labeled with Cy5. The common reference was a pool of 18 RNA samples from livers of fish from all individuals invovled in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 18 arrays
2015-05-12 | E-GEOD-56784 | biostudies-arrayexpress
Project description:Soil salinity presents a notable challenge to agriculture and to increasing the use marginal lands for farming. Here we provide a detailed analysis of the physiology, chemistry and gene expression patterns in roots and shoots of Camelina sativa in response to salt stress. Salt treatment reduced shoot, but not root length. Root and shoot weight were affected by salt, as was photosynthetic capacity. Salt treatment did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels. Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt. Genes encoding proteins involved in chelation and storage were highly up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots. In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated, probably to improve desiccation tolerance. Partial genome expression partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa genomes. Genome I and II were involved in the response to salinity stress to about the same degree, while about 10 % more differentially-expressed genes were associated with Genome III. This study has provided valuable information and insight into the response of camelina to salt stress. Examination of this data and comparison to similar studies in more halophytic species will allow development of even more salt-tolerant varieties of this emerging industrial crop.
2017-08-10 | GSE102422 | GEO
Project description:In recent decades, the food system has been faced with the significant problem of increasing food waste. Indeed, as reported by the Food and Agriculture Organisation of the United Nations (FAO), approximately 1.3 billion tonnes of food are lost or wasted globally each year (FAO, 2011). For this reason, the European Union has implemented multiple strategies to ensure the sustainability of the food/feed sector. Among these, the Agenda 2030, later supported by the Green Deal, plays a major role, whose goal is to ensure a competitive, clean and circular economy (Fetting, 2020; Vastolo et al., 2022). For this reason, scientific research is investigating the use of non-edible biomass produced along the food chain as co-products (any product obtained from different agro-industrial processes) for livestock (Pinotti et al., 2020; Rakita et al., 2021). As shown by Govoni et al. (2023), the introduction of co-products (11-16%) to replace energy-rich food crops (such as cereals) would conserve 15.4-27.8 Mha of land, 3-19.6 km3 of blue water and 74.2-137.8 km3 of green water, representing an important strategy to ensure environmental sustainability. To date, although many co-products have already been tested (grape marcs, beet pulp, hempseed cake), several more are attracting the interest of the scientific community (Serena and Knudsen, 2007; Muhlack et al., 2018; Lanzoni et al., 2023a). Among these are camelina (Camelina Sativa L. Crantz) and cardoon (Cynara cardunculus), due to both the low environmental footprint and the high nutritional profile (Turco et al., 2019; Singh et al., 2023). More specifically, camelina and cardoon seeds are characterised by a good protein (25.9±2.07% and 16.7% on DM, respectively) and a high lipid (38.9±1.26% and 25-30% on DM, respectively) content (Genovese et al., 2015; Turco et al., 2019; Singh et al., 2023). As reported by Singh et al. (2023) and Petropoulos et al. (2018), the high fatty acid profile of camelina and cardoon seeds, rich in polyunsaturated fatty acids (55.6% and 65.43±0.08, respectively) and low in saturated fatty acids (9.04% and 13.23±0. 07%, respectively), prompted the food and feed industry to isolate the lipid fraction for nutritional and nutraceutical purposes, creating in parallel waste products. Among them, camelina cake (CAMC), cardoon cake (CC) and cardoon meal (CM) could be used in animal feed due to their high nutritional profile, as reported by Lolli et al. (2020), Nannucci et al. (2021) and Serrapica et al. (2019). However, the characterisation of the antioxidant profile and the study of bioactive peptides are still at an early stage. Therefore, in light of the above, the aim of this work was to investigate the modulation of total phenolic content (TPC) and antioxidant activity during the in vitro digestion process with 2′-azinobis-(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), ferric reducing antioxidant power (FRAP) and oxygen radical absorbance capacity (ORAC) assays of CAMC, CC, and CM. In parallel, peptidomics analyses of in vitro digested CAMC, CC, and CM have been carried out.
2024-07-03 | PXD049333 | Pride
Project description:Hippobosca camelina isolate:Hippobosca camelina Laisamis isolate Genome sequencing
| PRJNA1119285 | ENA
Project description:This study was performed to investigate the effect of camelina oil-based diets on the immune function of Atlantic cod, as measured by gene expression in spleen. Atlantic cod were fed with one of three practical diets (three tanks per diet): a control diet using herring oil as a lipid source (FO diet), and two experimental diets using vegetable oil from Camelina sativa to replace 40% or 80% of herring oil (40CO and 80CO diets). We studied both the effect of the diet alone on basal spleen gene expression levels, as well as the effect of the diet after fish were injected with the synthetic double-stranded RNA polyriboinosinic polyribocytidylic acid (pIC), which mimics a viral immune stimulus.
2014-12-31 | GSE54358 | GEO
Project description:Fish were fed a standard fish meal (FM) diet or a diet with partial replacement of FM with solvent extracted camelina meal (CM) (8%, 16% or 24% CM inclusion) during a 16-week feeding trial. A significant decrease in growth performance was seen in fish fed the CM inclusion diets. A 44k oligonucleotide array experiment was used to identify any differentially expressed transcripts in the distal intestine of the fish fed the 24% CM diet compared to the control. The expression level of these genes was validated using quantitative polymerase chain reaction, which was also used to measure transcript expression in the fish fed the 8% CM and 16% CM diets. Histopathological analysis was used to quantify any physical signs in inflammation in the distal intestine of the Atlantic salmon fed the CM-containing diets.
2015-11-13 | GSE68732 | GEO
Project description:Vegetable oils (VO) are possible substitutes for fish oil in aquafeeds but are limited by their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA). However, oilseed crops can be modified to produce n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, representing a potential option to fill the gap between supply and demand of these important nutrients. Camelina sativa was metabolically engineered to produce a seed oil with around 15 % total n-3 LC-PUFA to potentially substitute for fish oil in salmon feeds. Post-smolt Atlantic salmon (Salmo salar) were fed for 11-weeks with one of three experimental diets containing either fish oil (FO), wild-type Camelina oil (WCO) or transgenic Camelina oil (DCO) as added lipid source to evaluate fish performance, nutrient digestibility, tissue n-3 LC-PUFA, and metabolic impact determined by liver transcriptome analysis. The DCO diet did not affect any of the performance or health parameters studied and enhanced apparent digestibility of EPA and DHA compared to the WCO diet. The level of total n-3 LC-PUFA was higher in all the tissues of DCO-fed fish than in WCO-fed fish with levels in liver similar to those in fish fed FO. Endogenous LC-PUFA biosynthetic activity was observed in fish fed both the Camelina oil diets as indicated by the liver transcriptome and levels of intermediate metabolites such as docosapentaenoic acid, with data suggesting that the dietary combination of EPA and DHA inhibited desaturation and elongation activities. Expression of genes involved in phospholipid and triacylglycerol metabolism followed a similar pattern in fish fed DCO and WCO despite the difference in n-3 LC-PUFA contents.
2016-12-05 | E-MTAB-4621 | biostudies-arrayexpress
Project description:New de novo sources of omega 3 (n-3) long chain polyunsaturated fatty acids (LC-PUFA) are required as alternatives to fish oil in aquafeeds in order to maintain adequate levels of the beneficial fatty acids, eicosapentaenoic and docosahexaenoic (EPA and DHA, respectively). The present study investigated the use of an EPA+DHA oil derived from a transgenic Camelina sativa in feeds for Atlantic salmon (Salmo salar) containing low levels of fishmeal (35 %) and fish oil (10 %), reflecting current commercial formulations, to determine the impacts on intestinal transcriptome, tissue fatty acid profile and health of farmed salmon. Post-smolt Atlantic salmon were fed for 12-weeks with one of three experimental diets containing either a blend of fish oil/rapeseed oil (FO), wild-type camelina oil (WCO) or transgenic camelina oil (DCO) as added lipid source. The DCO diet did not affect any of the fish performance or health parameters studied. Analyses of the mid and hindgut transcriptomes showed only mild effects on metabolism. Flesh of fish fed the DCO diet accumulated almost double the amount of n-3 LC-PUFA than fish fed the FO or WCO diets, indicating that these oils from transgenic oilseeds offer the opportunity to increase the n-3 LC-PUFA in farmed fish to levels comparable to those found twelve years ago.
2017-05-31 | E-MTAB-5529 | biostudies-arrayexpress