Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1098997 | ENA |
REPOSITORIES: ENA
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Project description:The red seaweed, Asparagopsis taxiformis, is a promising ruminant feed-additive with significant anti-methanogenic properties, which could provide a global solution to climate-change. Emerging genomics in this species has provided a strong foundation for in-depth molecular investigations, including proteomics. Here, we investigated the A. taxiformis (L6) proteome of sporophyte and gametophyte (male and female), using soluble and insoluble extraction methods followed by mass spectrometry. A combined total of 741 and 2007 unique non-redundant proteins were identified using genome-derived and transcriptome-derived databases, respectively. Genome-derived proteins were used for further analysis including a relatively large proportion of proteins that were annotated as ion binding proteins (i.e. iron, zinc, manganese, potassium and copper), which may play a role in heavy metal bioremediation. In addition, we identified 44 photosynthesis-related proteins (e.g. phycobilisomes, photosystem I, photosystem II and ATPase) and 58 stress-related proteins (e.g. heat shock proteins and vanadium-dependent haloperoxidases). Forty proteins were predicted to be secreted, supporting a role for them in extracellular activities such as mucilage development and defence. Two Gal-2,6-Sulfurylases II proteins are likely necessary for carrageenan biosynthesis, as well as development of reproductive-associated structures. These findings provide a comprehensive overview of expressed proteins in A. taxiformis (L6) at two different life stages, highlighting the potential of proteomic approaches and warrant further studies for understanding protein functions.
2023-01-26 | PXD035669 | Pride
Project description:Microvesicle generation is an integral part of the aging process of red blood cells in vivo and in vitro. Extensive vesiculation impairs function and survival of red blood cells after transfusion, and microvesicles contribute to transfusion reactions. The triggers and mechanism of microvesicle generation are largely unknown. In this study, we combined morphological, immunochemical, proteomic, lipidomic and metabolomic analyses in order to obtain an integrated understanding of the mechanisms underlying microvesicle generation during storage of red blood cell concentrates. Our data indicate that changes in membrane organization, triggered by altered protein conformation, constitute the main mechanism of vesiculation, and precede changes in lipid organization. The resulting selective accumulation of membrane components in microvesicles is accompanied by the recruitment of plasma proteins involved in inflammation and coagulation. Our data may serve as a basis for further dissection of the fundamental mechanisms of red blood cell aging and vesiculation, for identifying the cause-effect relationship between blood bank storage and transfusion complications, and for assessing the role of microvesicles in pathologies affecting red blood cells.
2020-04-03 | PXD017056 | Pride
Project description:Raw data of the LC-HRMS analysis of Asparagopsis armata and A. taxiformis samples, pertaining to the publication entitled:
Development of a Multiblock Metabolomics Approach to Explore Metabolite Variations of two Algae of the Genus Asparagopsis Linked to Interspecies and Temporal Factors (https://doi.org/10.1016/j.algal.2023.103138)
LC-HRMS analyses were performed with a Vanquish UHPLC system from ThermoScientific (MA, USA) equipped with a Q Exactive Plus mass spectrometer with an electrospray ionization source (negative mode).
MeOH are the injection solvent blanks
Extraction blanks are blank samples extracted in the same way as algal samples.
Pool is a set of samples for analytical drift correction (pool 1-3 and 13-15 are priming pools which are then not included in the analysis)
2023-04-04 | MSV000091631 | MassIVE
Project description:Rationale: Sepsis is a leading cause of morbidity and mortality; early diagnosis and prediction of progression is difficult to determine. The integration of metabolomic and transcriptomic data in an experimental model of sepsis may be a novel method to identify molecular signatures of clinical sepsis. Objectives: Develop a biomarker panel for earlier diagnosis and prognostic characterization of sepsis patients to inform personalized clinical management and improve understanding of the pathophysiology of sepsis progression. Methods: Mild to severe sepsis, lung injury and death was recapitulated in Macaca fascicularis by intravenous inoculation of Escherichia coli. Plasma samples were obtained at time of challenge and at one, three, and five days later or time of euthanasia. Necropsy was performed and blood, lung, kidney and spleen samples were obtained. An integrative analysis of comprehensive metabolomic and transcriptomic datasets was performed to identify and parameterize a biomarker panel. Measurements and Main Results: Pathogen invasion, respiratory distress, lethargy and mortality was dose dependent. Severe infection and death were associated with metabolomic and transcriptomic changes indicative of mitochondrial, peroxisomal and liver dysfunction. Analysis of reciprocal pulmonary transcriptome and plasma metabolome data revealed an integrated host response that suggested dysregulated fatty acid catabolism resulting from peroxisome-proliferator activated receptor signaling. A representative 4-metabolite model effectively diagnosed sepsis in primates (AUC 0.966) and in two human sepsis cohorts (AUC=0.78 and 0.82). Conclusion: A model to guide early management of patients with sepsis was developed by analysis of reciprocal metabolomic and transcriptomic data in primates that diagnosed sepsis in humans. Transcriptomic analysis of lungs from Cynomolgus macaques challenged with E. coli
2015-07-03 | E-GEOD-59075 | biostudies-arrayexpress
Project description:Potato, S. tuberosum, is one of the most important global crops, but has high levels of waste due to tuber greening under light, which is associated with the accumulation of neurotoxic glycoalkaloids. Here, we have investigated the effect of monochromatic far-red, red, and blue light on the regulation of chlorophyll and glycoalkaloid accumulation in tubers of a commercial variety, King Edward. Transcriptomic analysis of tubers exposed to red, blue, and white light showed that light induction of photosynthesis and tetrapyrrole-related genes grouped into two distinct patterns with one group showing much stronger induction in blue at 6 h and 24 h and a second group showing only red induction at 24 h.
2020-02-25 | E-MTAB-7707 | biostudies-arrayexpress
Project description:The aim of this study was to elucidate changes in gene expression related to the induced anti-herbivory response in the brown seaweed Fucus vesiculosus. Microarray hybridizations were used to identify genes differentially expressed in response to grazing by the periwinkle Littorina obtusata. This study shows that modifications in gene expression occur simultaneously to a reduced palatability and that defence induction entails reallocation of resources from primary to secondary metabolism with down-regulation of photosynthesis.
2013-12-13 | GSE53262 | GEO
Project description:Transcriptomic and metabolomic changes might predict frailty in SAMP8 mice
| PRJNA1127529 | ENA