Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of copepods during diel vertical migration

ABSTRACT: One of the greatest cyclical patterns in the pelagic ecosystem is the daily vertical migration of various zooplankton and fish to depth, a process referred to as diel vertical migration (DVM). DVM is considered to be energetically costly as tiny plankton migrate hundreds of meters in a 24 hour period. To study the metabolic demands of DVM, the copepod Pleuromamma xiphias was collected during upwards and downwards migration off of Bermuda. Data-dependent acquisition on the Q-Exactive detected >1600 proteins, 180 of which were differentially abundant between the two sampling periods.

INSTRUMENT(S):

ORGANISM(S): Pleuromamma Xiphias

TISSUE(S): Whole Body

SUBMITTER: Emma Timmins-Schiffman

LAB HEAD: Amy Maas

PROVIDER: PXD005778 | Pride | 2017-02-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2016_June_20_copepod_13.pep.xml	Pepxml
	2016_June_20_copepod_13.raw	Raw
	2016_June_20_copepod_14.pep.xml	Pepxml
	2016_June_20_copepod_14.raw	Raw
	2016_June_20_copepod_15.pep.xml	Pepxml

Items per page:

1 - 5 of 73

Similar Datasets

Copepod Diel Vertical Migration Proteomics

Project description:This project characterizes the metabolic consequences of the daily physiological rhythms and diel vertical migration for the model subtropical copepod, Pleuromamma xiphias. P. xiphias were collected near the Bermuda Atlantic Time Series in plankton tows at different times of day, representing different parts of their daily vertical migration. Single copepods were isolated from the tows and flash-frozen for proteomics analysis.

2024-01-14 | PXD021156 | Pride

Induction of inverted morphology in brain organoids by vertical-mixing bioreactors

Project description:Organoid technology provides an opportunity to generate brain-like structures by recapitulating developmental steps in the manner of self-organization. We examined the vertical-mixing effect on brain organoid structures using bioreactors and established inverted brain organoids. The organoids generated by vertical mixing showed neurons that migrated from the outer periphery to the inner core of organoids, in contrast to orbital mixing. To uncover the mechanisms of the inverted structure, we investigated the direction of primary cilia, a cellular mechanosensor. Primary cilia of neural progenitors by vertical mixing were aligned in a multidirectional manner, and those by orbital mixing in a bidirectional manner. Single-cell RNA sequencing revealed that neurons of inverted brain organoids presented a GABAergic character of the ventral forebrain.

2021-10-27 | GSE184409 | GEO

Transcriptomics analysis of enteroendocrine cells after vertical sleeve gastrectomy

Project description:We report here the transcriptome of sorted enteroendocrine cells from duodenum, ileum and colon from mice after vertical sleeve gastrectomy or sham operation, weight matched or not. We analyze the effect of region of origin and surgery and gene expression and found that only region of origin had an impact on EEC transcriptome

2018-10-19 | GSE121489 | GEO

Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Project description:Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical E. coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.

2022-12-23 | GSE219270 | GEO

Pacific halibut white muscle DDA proteomics

Project description:White muscle samples from juvenile Pacific halibut were analyzed in discovery-driven proteomics to investigate the effects of temperature-induced growth manipulations and to identify protein markers of somatic growth. Juvenile Pacific halibut were either acclimated to 2C (low temperature) and 9C (control temperature) to elicit growth suppression and also initially acclimated to 2C and subsequently transferred to 9C to elicit growth compensation. This project was led by Josep Planas at the International Pacific Halibut Commission.

2019-10-11 | PXD012634 | Pride

Diel vertical migration of Arctic zooplankton during the polar night.

Project description:High-latitude environments show extreme seasonal variation in physical and biological variables. The classic paradigm of Arctic marine ecosystems holds that most biological processes slow down or cease during the polar night. One key process that is generally assumed to cease during winter is diel vertical migration (DVM) of zooplankton. DVM constitutes the largest synchronized movement of biomass on the planet, and is of paramount importance for marine ecosystem function and carbon cycling. Here we present acoustic data that demonstrate a synchronized DVM behaviour of zooplankton that continues throughout the Arctic winter, in both open and ice-covered waters. We argue that even during the polar night, DVM is regulated by diel variations in solar and lunar illumination, which are at intensities far below the threshold of human perception. We also demonstrate that winter DVM is stronger in open waters compared with ice-covered waters. This suggests that the biologically mediated vertical flux of carbon will increase if there is a continued retreat of the Arctic winter sea ice cover.

| S-EPMC2657746 | biostudies-literature

Peptidomics profiling of the murine gut after vertical sleeve gastrectomy

Project description:Profiling of the murine peptidome along the gastrointestinal tract and pancreas in vertical sleeve gastrectomy and sham operated mice. The study compares the peptidome of various portions of the GI tract using intact mass spectrometry and database searching. These peptides included most gut hormones including proglucagon derived peptides, PYY, GIP, somatostatin, neurotensin amongst others.

2019-02-09 | PXD011455 | Pride

Malaspina Microbial Vertical Profiles Metagenomes

Project description:Malaspina Expedition 2010 Microbial Picoplankton Vertical Profiles Metagenomes

| PRJEB52452 | ENA

vertical freshwater sediment

Project description:Vertical organization of freshwater sediment microbial communities: implications for microbial activities and burial processes

| PRJEB14189 | ENA

Arctic complexity: a case study on diel vertical migration of zooplankton.

Project description:Diel vertical migration (DVM) of zooplankton is a global phenomenon, characteristic of both marine and limnic environments. At high latitudes, patterns of DVM have been documented, but rather little knowledge exists regarding which species perform this ecologically important behaviour. Also, in the Arctic, the vertically migrating components of the zooplankton community are usually regarded as a single sound scattering layer (SSL) performing synchronized patterns of migration directly controlled by ambient light. Here, we present evidence for hitherto unknown complexity of Arctic marine systems, where zooplankton form multiple aggregations through the water column seen via acoustics as distinct SSLs. We show that while the initiation of DVM during the autumnal equinox is light mediated, the vertical positioning of the migrants during day is linked more to the thermal characteristics of water masses than to irradiance. During night, phytoplankton biomass is shown to be the most important factor determining the vertical positioning of all migrating taxa. Further, we develop a novel way of representing acoustic data in the form of a Sound Image (SI) that enables a direct comparison of the relative importance of each potential scatterer based upon the theoretical contribution of their backscatter. Based on our comparison of locations with contrasting hydrography, we conclude that a continued warming of the Arctic is likely to result in more complex ecotones across the Arctic marine system.

| S-EPMC4161229 | biostudies-literature

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