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Xenopus laevis oocyte mitochondria

ABSTRACT: Characterization of mitochondria in non-growing oocytes from xenopus laevis compared to somatic controls of the following tissues: heart, liver and white adipose tissue.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Heart, Liver, White Adipose Tissue, Oocyte

SUBMITTER: Aida Rodriguez-Nuevo

LAB HEAD: Elvan Boke

PROVIDER: PXD030576 | Pride | 2022-05-09

REPOSITORIES: Pride

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			Action	DRS
	2021LF002_ELBO_001_01_2ug_FR01.raw	Raw
	2021LF002_ELBO_001_01_2ug_FR03.raw	Raw
	2021LF002_ELBO_001_01_2ug_FR05.raw	Raw
	2021LF002_ELBO_001_01_2ug_FR07.raw	Raw
	2021LF002_ELBO_001_01_2ug_FR09.raw	Raw

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Publications

Oocytes maintain ROS-free mitochondrial metabolism by suppressing complex I.

Rodríguez-Nuevo Aida A Torres-Sanchez Ariadna A Duran Juan M JM De Guirior Cristian C Martínez-Zamora Maria Angeles MA Böke Elvan E

Nature 20220720 7920

Oocytes form before birth and remain viable for several decades before fertilization1. Although poor oocyte quality accounts for most female fertility problems, little is known about how oocytes maintain cellular fitness, or why their quality eventually declines with age2. Reactive oxygen species (ROS) produced as by-products of mitochondrial activity are associated with lower rates of fertilization and embryo survival3-5. Yet, how healthy oocytes balance essenti ...[more]

PMID: 35859172

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Xenopus laevis oocyte mitochondria

Project description:Characterization of mitochondria in non-growing oocytes from xenopus laevis.

2022-05-09 | PXD025366 | Pride

Comparison of human primordial oocyte follicles to ovarian somatic cells

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2022-05-09 | PXD025369 | Pride

Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

Project description:Turnover of nucleoplasmic transcripts by the multi-subunit RNA exosome is mediated by two adaptors; the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely been based on long-term factor depletion strategies. Here, we rapidly deplete a NEXT, a PAXT and a core-exosome component, uncovering direct consequences of their losses. Global proteome analyses displayed only minor changes, yet exposed the immediate co-depletion of exosome and adaptor subunits, reflecting possible sub-complex compositions. Parallel high-resolution 3’end sequencing of newly synthesized RNA confirmed earlier established long-term depletion phenotypes. Still, rapid NEXT depletion displayed a narrower phenotype, illustrated by its restricted effect on snoRNA-hosting introns, whereas long-term NEXT depletion data had suggested a more general role of the complex in mediating intron turnover. While this validates snoRNA-hosting introns as primary NEXT targets, our data suggest that nuclear 5’-3’ RNA decay is altered after prolonged NEXT depletion, obscuring interpretation. Further analysis of snoRNA-hosting introns also uncovered an unusual mode of core exosome-independent RNA decay. Due to its non-processive nature, we speculate that this reflects a hitherto undisclosed exosome-independent activity of the EXOSC10 ribonuclease.

2021-12-23 | PXD026774 | Pride

Gut bacterial nutrient preferences quantified in vivo

Project description:We quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. To determine nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. By in vivo isotope tracer feeding, mapped the contribution of different dietary nutrients vs circulating nutrients contribution to different gut bacterial genera.

2022-08-17 | PXD031015 | Pride

Targeting the Post-Synaptic Proteome in Alzheimer Disease with Psychosis

Project description:Individuals with Alzheimer Disease who develop psychotic symptoms (AD+P) experience more rapid cognitive decline and have reduced indices of synaptic integrity relative to those without psychosis (AD-P). We sought to determine whether the postsynaptic density (PSD) proteome is altered in AD+P relative to AD-P, analyzing PSDs from dorsolateral prefrontal cortex of AD+P, AD-P, and a reference group of cognitively normal elderly subjects. The PSD proteome of AD+P showed a global shift towards lower levels of all proteins relative to AD-P, enriched for kinases, proteins regulating Rho GTPases, and other regulators of the actin cytoskeleton. We computationally identified potential novel therapies predicted to reverse the PSD protein signature of AD+P. Five days of administration of one of these drugs, the C-C Motif Chemokine Receptor 5 inhibitor, maraviroc, led to a net reversal of the PSD protein signature in adult mice, nominating it as a novel potential treatment for AD+P.

2023-06-19 | PXD042025 | Pride

Uncovering diurnal rhythm disruptions of synaptic proteome signaling in prefrontal cortex and nucleus accumbens associated with opioid use disorder

Project description:This article presents a study that examines the proteomic alterations associated with opioid use disorder (OUD) in the human brain. The study investigates the interplay between pro-inflammatory signaling, extracellular matrix (ECM) remodeling, and synaptic plasticity in the corticostriatal circuitry associated with OUD. The findings reveal differential alterations in the synaptic proteomes across the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC), indicating that changes in certain synaptic subtypes are unique to each brain region. The proteomic alterations associated with OUD in DLPFC are mainly in glutamatergic, serotonergic, dopaminergic, and oxytocin signaling, while altered adrenergic signaling is enriched in NAc. The study also identifies alterations in proteins involved in circadian entrainment specifically in synaptic enrichments in both DLPFC and NAc of OUD subjects. These findings provide new evidence linking disrupted molecular rhythms in the regulation of distinct synaptic subtypes altered by opioids.

2023-10-25 | PXD041333 | Pride

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress

Transcription profiling of rat at pheochromocytoma cell line PC12 treated with trimethyltin at low and high doses

Project description:The rat pheochromocytoma cell line PC12 cells were cultured in complete DMEM till 80% confluence, then placed at 5000 cells per squared cm. Cells were then plated in 24-well plates for cell viability assay and in T75 flasks for RNA isolation. Medium was replaced with serum-free fresh medium for 12 hours prior to TMT treatment. Gene expression patterns were then analysed using Rat Expression Array 230A Experiment Overall Design: In this study we analize gene expression patterns in PC12 cells treated with Trimethyltin (TMT). We utilized control cells (untreated) and two different concentration (1 and 5) Experiment Overall Design: We used three biological replicates, for the three concentration tested, according to MIAME guidelines Experiment Overall Design: (total 9 chips were used in this study).

2009-04-29 | E-GEOD-5073 | biostudies-arrayexpress

Simultaneous characterisation of RNA and protein subcellular dynamics

Project description:Existing methods to analyse RNA localisation are constrained to specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation of RNA (LoRNA), which maps, at once, RNAs to membranous (nucleus, ER and mitochondria) and membraneless compartments (cytosol, nucleolus and phase-separated granules). Simultaneous interrogation of all RNA locations allows the system-wide quantification of RNA proportional distribution and the comprehensive analysis of RNA subcellular dynamics. Moreover, we have re-engineered the LOPIT (Localisation Of Proteins by Isotope Tagging) method, enabling integration with LoRNA, to jointly map RNA and protein subcellular localisation. Applying this framework, we obtain a global re-localisation map for 31839 transcripts and 5314 proteins during the unfolded protein response, uncovering that ER-localised transcripts are more efficiently recruited to stress granules than cytosolic RNAs, and revealing eIF3d is key to sustain cytoskeletal function. Overall, we provide the most exhaustive map to date of RNA and protein subcellular dynamics.

2022-01-25 | PXD030456 | Pride

Automated 16plex plasma proteomics with real-time search and ion mobility mass spectrometry enables large scale profiling in naked mole-rats and mice.

Project description:Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully Automated Multiplexed Proteome Profiling Platform (AutoMP3) using the Hamilton VantageTM liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single shot runs we combined 16plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS). We quantified over 40 proteins / min / sample, doubling the previously published rates. We applied AutoMP3 to investigate the naked mole-rat plasma proteome both as a function of circadian cycle and in response to ultraviolet (UV) treatment. In keeping with the lack of synchronized circadian rhythms in naked mole-rats, we find few circadian patterns in plasma proteins over the course of 48hr. Furthermore, we quantify many disparate changes between mice and naked mole-rats at both 48hr and one week after UV exposure. These species differences in plasma protein temporal responses could contribute to the pronounced cancer resistance observed in naked mole-rats.

2021-02-04 | PXD022891 | Pride

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