Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unraveling Genotypic Proteomic Shifts in Salvia hispanica Seeds Exposed to Accelerated Aging

ABSTRACT: This Project investigates the impact of elevated temperatures and relative humidity on the aging process of chia seeds (Salvia hispanica L.). The study employs proteomics to examine molecular responses to accelerated aging in two chia genotypes. The results underscore the importance of evaluating changes in proteins of aged seeds to gain insights into the biological mechanisms responsible for maintaining chia seed integrity during the aging process.

INSTRUMENT(S):

ORGANISM(S): Salvia Hispanica

TISSUE(S): Seed

DISEASE(S): Disease Free

SUBMITTER: Concha Gil

LAB HEAD: María Reguera

PROVIDER: PXD049229 | Pride | 2024-08-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BR_normalizada_NCBI.mgf	Mgf
	BR_normalizada_NCBI.mzML	Mzml
	BR_normalizada_NCBI.mzid.gz	Mzid
	E_BR1.raw	Raw
	E_BR2.raw	Raw

Items per page:

1 - 5 of 30

Similar Datasets

Physiological and proteomic changes in soft wheat seeds during accelerated aging

Project description:Wheat (Triticum aestivum L.), one of the most important crops in the world, is a staple food used for making flour, noodles, alcoholic beverages, biofuel and a variety of other products. In wheat, kernel texture and biochemical composition vary with different hardnesses. Previous study of our research group indicated that physiological properties changes including germination ratio, and physiological enzymatic activities in wheat with different hardnesses were different. A comparative proteomic analysis of soft and hard wheat embryos by our research group identified more proteins associated with anti-resistance in soft wheat than that in hard wheat. Additionally, quantitative proteomic analysis of medium-hard wheat ‘Aikang58’ seeds showed that 162 differentially expressed proteins (DEPs) participated in metabolism, energy supply, and defense/stress responses were identified during artificial ageing were identified in our previous research. However, the dynamic physiological and quantitative proteomic changes in soft wheat seeds during accelerated aging remain unclear, thus need to be elucidated. In this work, we conducted the first Tandem Mass Tag (TMT)-based dynamic quantitative proteomic analysis of elite Chinese soft wheat cultivar ‘Yangmai 15’ seeds during artificial ageing. The uncovered differentially expressed proteins (DEPs) with different functions might provide new insights into the comprehensive understanding of deterioration in soft wheat seeds.

2018-10-08 | PXD009156 | Pride

Shotgun proteomics of quinoa seeds from plants grown under irrigated and rainfed conditions

Project description:Quinoa is an Andean crop whose cultivation has been extended to many different parts of the world in the last decade. It shows a great capacity for adaptation to diverse climate conditions, including environmental stressors, and moreover, the seeds are very nutritious in part due to their high protein content which is rich in essential amino acids. They also contain good amounts of other nutrients such as unsaturated fatty acids, vitamins, or minerals and are gluten-free seeds. Also, the use of quinoa hydrolysates and peptides has been linked to numerous health benefits. Altogether, these aspects have situated quinoa as a crop able to contribute to food security worldwide. Aiming to deepen our understanding of the protein quality and function of quinoa seeds and how they can vary when this crop is subjected to water-limiting conditions, a shotgun proteomics analysis was performed to obtain the proteomes of quinoa seeds harvested from two different water regimes in field: rainfed and irrigated conditions. Also, a quantitative analysis was developed to determine the total number of proteins identified in both samples, which of them are present in both conditions, and also, which ones were present exclusively in seeds under rainfed or irrigated conditions.

2023-04-04 | PXD038953 | Pride

Proteome analysis of rice seeds during artificial aging treatment for understanding the role of antioxidant machinery

Project description:Seed longevity is a crucial trait in agriculture as it determines the ability of seeds to maintain viability during dry storage. However, the molecular mechanism underlying seed aging and reduced seed longevity are currently not well understood. Here we report the comparative proteome and metabolome profiling of three rice cultivars varying in aging tolerance including an aging tolerant indica cultivar Dharial, an aging sensitive japonica cultivar Ilmi, and a moderately aging tolerant cultivar A2 that was generated by crossing between Dharial and Ilmi. Results obtained from comparative proteome and metabolome profiling suggest that aged seeds of all the cultivars utilize ubiquitin proteasome-mediated protein degradation which results in the accumulation of free amino acids in Ilmi while tolerant cultivars utilize those for energy production and synthesis of heat shock proteins, especially hsp20/alpha crystallin family protein. Additionally, aging tolerant cultivar seems to activate brassinosteroid signalling and suppress jasmonate signaling to initiate a signaling cascade that allows efficient detoxification of aging induced ROS to maintain the seed longevity during aging. Taken together, these results provide an in-depth understand of aging induced changes in rice seeds.

2024-01-10 | PXD043955 | Pride

Small extracellular vesicles from young plasma reverse age-related functional declines by improving mitochondrial energy metabolism

Project description:Aging and the chronic diseases associated with aging have become a great burden to modern society. Recent animal studies on heterochronic parabiosis have revealed that young blood has a powerful rejuvenating effect on aged tissues, but which components of the young blood are responsible for the rejuvenating effects remains unclear. In this study, we found that small extracellular vesicles (sEVs) purified from the plasma of young mice could counteract pre-existing aging at the molecular, mitochondrial, cellular and physiological levels. In detail, injection of young sEVs into aged mice extended lifespan, attenuated senescent phenotypes and mitigate age-associated impairments on various tissues (hippocampus, muscle, heart, testis, bone, etc). Mechanistical studies using iTRAQ-based quantitative proteomic analyses combined with GO term cluster revealed that the altered proteomes in aged tissues of young sEVs-treated mice were specifically related to their roles in regulating cellular senescence, metabolic process, epigenetic modification, genomic stability, etc, which are the cardinal features associated with aging. Particularly, the sEVs derived from young mice and young human donors could stimulate PGC-1α (a master regulator of mitochondrial biogenesis and energy metabolism) expression in vitro and in vivo through their rejuvenating miRNA cargos, thereby facilitating mitochondrial regeneration and counteracting mitochondrial deficits in aged tissues. Taken together, this study demonstrates that young sEVs can reverse degenerative changes and age-related dysfunctions through stimulating PGC-1α expression and regenerating intact mitochondria.

2024-03-31 | PXD030350 | Pride

Contribution of the Unfolded Protein Response (UPR) transcription factor XBP1 to brain aging

Project description:In this project we aimed to evaluate the contribution of endoplasmic reticulum stress sensor IRE1 and its downstream transcription factor XBP1s to mammalian brain aging. We compared traits associated to aging at behavioral, electrophysiological, morphological and proteomic levels. We used transgenic animals overexpressing XBP1s in brain tissue and also wild type animals injected with adeno-associated virus to overexpress XBP1s in the brain during aging.

2022-11-04 | PXD020539 | Pride

Germination of Leafy Spurge (Euphorbia esula) Seeds under Constant and Alternating Temperature

Project description:Transcriptome changes were investigated for Euphorbia esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20°C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30°C (16:8 h). Incubation at 20°C for 21 followed by 20:30°C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes. Labeled cDNA was prepared from total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA) according to manufacture's protocols. Labeled cDNAs were hybridized to a custom made 23 K element microarray that contained 19,808 unigenes from the leafy spurge EST database and an additional 4,129 unigenes from a cassava EST database. A rolling circle dye swap hybridization scheme was used to compare gene expression between samples. There were three biological and two technical replications for each treatment. Microarray hybridization was visualized using a GenPix 4000B scanner (Axon Instruments/Molecular Devices Corp., Sunnyvale, CA) and spot intensities and background was quantified using GenPix Pro software. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other.

2010-06-01 | E-GEOD-18533 | biostudies-arrayexpress

Genomic profiling of type-1 adult diabetic and aged normoglycemic mice liver

Project description:Here we characterized and compared differential gene expression from diabetic and normoglycemic NOD mice and from aged and young-adults Balb/c mice. Total RNA from NOD diabetic (3 weeks with glicemia over 500mg/dl) and normoglycemic NOD mice from the same age was used. To compare the effects of aging in genomic expression, total RNA from young-adult Balb/c (9 weeks old) and middle-aged Balb/c (47 weeks old) were used.

2013-09-06 | E-GEOD-50613 | biostudies-arrayexpress

A gDNA microarray for genotyping Salvia species

Project description:Salvia is an important genus from the Lamiaceae with approximately 1000 species distributed globally. Several Salvia species are commercially important because of their medicinal and culinary properties. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus. In order to generate the Salvia Subtracted Diversity Array (SDA), a Suppression Subtractive Hybridization (SSH) was performed between a pool of ten Salvia species and a pool of non-angiosperm and angiosperms (excluding the Lamiaceae) to selectively isolate Salvia-specific sequences. A total of 285 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. DNA fingerprints were obtained for fifteen Salvia genotypes including three that were not part of the original subtraction pool. Hierarchical cluster analysis indicated that the Salvia-specific SDA was capable of differentiating closely related species of S. officinalis and S. miltiorrhiza and was also able to reveal genetic relationships consistent with geographical origins. Species-specific features were also found for S. elegans, S. officinalis, S. sclarea, S. przewalskii and S. runcinata.

2013-07-31 | E-GEOD-39403 | biostudies-arrayexpress

Brassica napus differentially expressed genes in seeds and silique walls

Project description:Identification of differentially expressed genes in seeds and silique walls at the seed-filling stage in Brassica napus through transcriptional profiling Two tissues, three biological replicates, one biological duplicate with two technical replicates

2016-07-03 | E-GEOD-61598 | biostudies-arrayexpress

scRNA-seq of stromal vascular cells from 48 week (aged) mouse subcutaneous adipose tissue compared to control 10 week (young) mouse SVF

Project description:Adipose tissue mass and adiposity change throughout the lifespan. During aging, while visceral adipose tissue (VAT) tends to increase, peripheral subcutaneous adipose tissue (SAT) decreases significantly. Unlike VAT, which is linked to metabolic diseases, SAT has beneficial effects. However, the molecular details behind aging-associated loss of SAT remain unclear. Here we compare scRNA-seq of total SVF of SAT from young and aging mice to identify a novel Aging-dependent Regulatory Cell (ARC) that emerges in SAT of aged mice. Inguinal white adipose tissue (iWAT) was used as a representative SAT; iWAT pads of 2 mice from each age group were subjected to collagenase digestion and treated with a hypotonic buffer to remove red blood cells before subjection to scRNA-seq by 10X Genomics Chromium Single Cell Kit. The findings showed that ARCs express adipogenic markers but lack adipogenic capacity and inhibit differentiation of neighboring adipose precursors.

2021-03-25 | E-MTAB-10221 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data