Ontology highlight
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PROVIDER: PRJNA1051575 | ENA |
REPOSITORIES: ENA
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Project description:Background Rice farming faces a serious challenge from the brown planthopper (BPH), with the pyramiding of BPH14 and BPH15 genes delivering effective protection in elite rice strains. However, the molecular basis behind this resistance is still unclear. Results The study investigated miRNA levels in BPH14/BPH15 pyramiding line (B1415) and their recurrent parent (RP) under BPH infestation employing high-throughput sequencing and revealed 136 differentially expressed miRNAs (DEMs) among 550 known miRNAs. An integrated analysis highlighted that 587 miRNA-mRNA pairs linking 95 DEMs to 537 targeted genes were enriched in phenylpropanoid and lignin metabolism, circadian rhythms, and amino acid metabolism. The candidate DEMs, miR172d-3p, and miR396 family members were identified as negative regulators to decrease their target genes Os06g0708700 (encoding a nodulin-like protein) and Os11g0129700 (encoding an AP2 domain transcription factor), suggesting their key roles in rice against BPH. Conclusions Our investigation provides the first insights into miRNA-mediated defense mechanisms in the B1415. Identifying miRNAs and their target mRNAs in BPH resistance opens a new avenue for rice breeding programs, offering potential targets for improving pest resistance. Understanding these molecular interactions paves the way for developing more resistant rice cultivars, thereby contributing to sustainable rice production and food security.
2024-10-02 | GSE278202 | GEO
Project description:Nutrition affects milk composition influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not completely known. MicroRNAs (miRNA) are small non-coding RNA that work as important post-transcriptional gene expression regulators by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, and which may give clues to decipher the regulations of milk components biosynthesis and secretion. Using high-throughput sequencing technology, miRNomes of the lactating mammary gland have been established from 4 goats fed ad libitum and 6 goats food deprived during 48h. Food deprivation affected the expression of 30 miRNA (padj<0.1), 16 were downregulated and 14 were upregulated. Prediction tools Diana-microT suggests a potential role of several nutriregulated miRNA in the lipid metabolism. Among putative targets 19 differently expressed genes (DEG) previously identified in the same sample, were found. Functions of these 19 DEG revealed their involvement in tissue remodeling. This study constitutes the first evidence of nutriregulated miRNA in the ruminant mammary gland. The characterization of these 30 miRNA could contribute to a better understanding of genes regulations in the mammary gland in response to nutrition.
2015-07-01 | GSE61025 | GEO
Project description:Nutrition affects milk composition influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not completely known. MicroRNAs (miRNA) are small non-coding RNA that work as important post-transcriptional gene expression regulators by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, and which may give clues to decipher the regulations of milk components biosynthesis and secretion. Using high-throughput sequencing technology, miRNomes of the lactating mammary gland have been established from 4 goats fed ad libitum and 6 goats food deprived during 48h. Food deprivation affected the expression of 30 miRNA (padj<0.1), 16 were downregulated and 14 were upregulated. Prediction tools Diana-microT suggests a potential role of several nutriregulated miRNA in the lipid metabolism. Among putative targets 19 differently expressed genes (DEG) previously identified in the same sample, were found. Functions of these 19 DEG revealed their involvement in tissue remodeling. This study constitutes the first evidence of nutriregulated miRNA in the ruminant mammary gland. The characterization of these 30 miRNA could contribute to a better understanding of genes regulations in the mammary gland in response to nutrition. MicroRNA profiles of mammary glands from 10 Alpine goats at the peak of lactation (48 ± 2 days post-partum) generated by a HiSeq 2500 using Illumina Solexa technic.
2015-07-01 | E-GEOD-61025 | biostudies-arrayexpress
Project description:Cashew is one of the most prevalent causes of tree nut allergies. However, the cashew proteome is far from complete, which limits the quality of peptide identification in mass spectrometric analyses. In this study, bioinformatics tools were utilized to construct a customized cashew protein database and improve sequence quality for proteins of interest, based on a publicly available cashew genome database. As a result, two additional isoforms for cashew 2S albumins and five other isoforms for cashew 11S proteins were identified, along with several other potential allergens. Using the optimized protein database, the protein profiles of cashew nuts subjected to different oil-roasting conditions (138 °C and 166 °C for 2-10 minutes) were analyzed using discovery LC-MS/MS analysis. The results showed that cashew 2S protein is most heat-stable, followed by 11S and 7S proteins, though protein isoforms might be affected differently. Preliminary target peptide selection indicated that out of the 29 potential targets, 18 peptides were derived from the newly developed database. In the evaluation of thermal processing effects on cashew proteins, several Maillard reaction adducts were also identified. The cashew protein database developed in this study allows for comprehensive analyses of cashew proteome and development of high-quality allergen detection method.
2022-06-07 | PXD027543 | Pride
Project description:Plant-parasitic nematodes can cause a hugh damage and crop loss becoming a threat for food security. We use Caenorhabditis elegans as a model organism to study the effect of the new nematicide cyclobutrifluram. RNA for two different biological replicates was isolated from animals of each condition: nematicide exposure/ no exposure; and then sequenced to detect differentially expressed genes in exposed vs. non-exposed samples.
2023-09-30 | E-MTAB-13189 | biostudies-arrayexpress
Project description:Compost application for sustainable vineyards nutrition in hilly areas
| PRJEB64206 | ENA
Project description:Soil salinity is a major environmental constraint affecting crop growth and threatening global food security. Plants adapt to salinity by optimizing performance of stomata, the microscopic sphincters inserted into the wax-covered epidermis of the shoot, which balance CO2 intake for photosynthetic carbon gain and concomitant water loss. Stomata are formed by two guard cells (GCs) that are morphologically and functionally distinct from the other leaf cells. In order to better understand the molecular mechanisms underlying stomatal function under saline conditions we used proteomics approach to study isolated GCs from the salt-tolerant sugar beet species.
2020-05-27 | PXD017583 | Pride
Project description:The research on alternative and sustainable feed ingredients is a challenge to reduce the feed-food competition between humans and monogastrics, in particular pigs. Former food products (FFPs) drop out from the industrial production of food such as pasta, bread, snacks and chips. They have a high nutritional and energetic value and represent an alternative and sustainable feed ingredient. The aim of this study was to apply label-free quantitative peptidomics to assess the impact of the inclusion of FFPs on serum peptidome.
2024-10-17 | PXD047855 | Pride
Project description:Water availability is a key determinant of terrestrial plant productivity. Many climate models predict that water stress will increasingly challenge agricultural yields and exacerbate projected food deficits. To ensure food security and increase agricultural efficiency, crop water productivity must be increased. Research over past decades has established that the phytohormone abscisic acid (ABA) is a central regulator of water use and directly regulates stomatal opening and transpiration. In this study, we investigated whether the water productivity of wheat could be improved by increasing its ABA sensitivity. We show that overexpression of a wheat ABA receptor increases wheat ABA sensitivity, which significantly lowers a plant’s lifetime water consumption. Physiological analyses demonstrated that this water-saving trait is a consequence of reduced transpiration and a concomitant increase in photosynthetic activity, which together boost grain production per liter of water and protect productivity during water deficit. Our findings provide a general strategy for increasing water productivity that should be applicable to other crops because of the high conservation of the ABA signaling pathway.
2019-01-03 | GSE79522 | GEO
Project description:Soybean (Glycine max) and mung bean (Vigna radiata) are key legumes with global importance, but their mechanisms for coping with cold stress—a major challenge in agriculture—have not been thoroughly investigated, especially in a comparative study. This research aimed to fill this gap by examining how these two major legumes respond differently to cold stress and exploring the role of uniconazole, a potential stress mitigator. Our comprehensive approach involved transcriptomic and metabolomic analyses, revealing distinct responses between soybean and mung bean under cold stress conditions. Notably, uniconazole was found to significantly enhance cold tolerance in mung bean by upregulating genes associated with photosynthesis, while its impact on soybean was either negligible or adverse. To further understand the molecular interactions, we utilized advanced machine learning algorithms for protein structure prediction, focusing on photosynthetic pathways. This enabled us to identify LOC106780309 as a direct binding target for uniconazole, confirmed through isothermal titration calorimetry. This research establishes a new comparative approach to explore how soybean and mung bean adapt to cold stress, offers key insights to improve the hardiness of legumes against environmental challenges, and contributes to sustainable agricultural practices and food security.
2024-07-19 | GSE193328 | GEO