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Analysis of Gulf Toadfish Intestinal Precipitate Matrix

ABSTRACT: Marine teleosts produce CaCO3 in their intestine as part of their osmoregulatory strategy. This study aimed to characterize the proteinaceous matrix associated with these precipitates.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Opsanus Beta

SUBMITTER: Kevin Schauer

LAB HEAD: Martin Grosell

PROVIDER: PXD004134 | Pride | 2016-10-05

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	Insoluble_1-12_inj1.raw	Raw
	Insoluble_1-12_inj2.raw	Raw
	Insoluble_13-24_inj1.raw	Raw
	Insoluble_13-24_inj2.raw	Raw
	Mudpit_Insoluble_1-12_inj1 (F002371).mzid_Mudpit_Insoluble_1-12_inj1_(F002371).pride.mgf.gz	Mzid

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Publications

A proteinaceous organic matrix regulates carbonate mineral production in the marine teleost intestine.

Schauer Kevin L KL LeMoine Christophe M R CM Pelin Adrian A Corradi Nicolas N Warren Wesley C WC Grosell Martin M McDonald M Danielle MD

Scientific reports 20161003

Marine teleost fish produce CaCO<sub>3</sub> in their intestine as part of their osmoregulatory strategy. This precipitation is critical for rehydration and survival of the largest vertebrate group on earth, yet the molecular mechanisms that regulate this reaction are unknown. Here, we isolate and characterize an organic matrix associated with the intestinal precipitates produced by Gulf toadfish (Opsanus beta). Toadfish precipitates were purified using two different methods, and the associated ...[more]

PMID: 27694946

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Gulf toadfish intestinal fluid and intestinal CaCO3 matrix proteome

Project description:Marine teleosts produce CaCO3 in their intestine as part of their osmoregulatory strategy. This study aimed to characterize the proteinaceous matrix associated with these precipitates and compare its constituents to the proteins found in the intestinal fluid.

2016-09-29 | PXD004135 | Pride

Analysis of the Gulf toadfish intestinal proteome response to chronic hypersalinity exposure

Project description:The marine teleost intestine plays a vital role in whole body salt and water homeostasis. Marine fish must drink seawater in order to rehydrate, and processing of that seawater throughout the gastrointestinal tract allows for the extraction of water from this highly hyperosmotic source. Although the molecular mechanisms of this process have been the subject of much investigation, numerous questions remain. Here, Gulf toadfish (Opsanus beta) were acclimated to normal seawater (35 ppt) of hypersaline seawater (60 ppt) and changes in the anterior intestine, posterior intestine, and intestinal fluid proteomes were investigated using a shotgun proteomics approach employing isobaric TMT tags.

2018-06-26 | PXD005923 | Pride

USP8 maintains ESC stemness via deubiquitination of EPG5

Project description:The coiled-coil domain of EPG5 was synthesized as follows: Biotin-MNKNEAVSQQIHVLQKEVRQLQAE AAQ (from Beijing SciLight Biotechnology, LCC). 1 mg of this short peptide was incubated with ES cells lysates followed by immunoprecipitation with anti-biotin beads. The precipitates were extensively washed with lysis buffer then boiled with SDS loading buffer and subjected to SDS–PAGE. Total proteins were excised from the gels, then subjected to in-gel digestion and analysis by LC-MS/MS.

2019-02-25 | PXD012563 | Pride

Calcium effect to the Clostridium beijerinckii NCIMB 8052 degenerate strain for the solvent producing recovery

Project description:Solventogenic Clostridium species ferment carbohydrates to acetone, butanol and ethanol which are well-known next-generation biofuels. However, repeated subculture of or continuous fermentation by Clostridium often decreases and eventually terminates the solvent production and spore formation, which is a process called strain degeneration. Supplementation of CaCO3 to fermentation medium could partially recover metabolism of degenerated strain by more than 50% increase of cell growth and solvent production. The transcriptome profile of Clostridium beijerinckii NCIMB 8052 (DG-8052) and its response to CaCO3 treatment were analysed by microarray. Since fermentation by C. beijerinckii NCIMB 8052 is a biphasic process, gene expressions of two fermentations were compared at each stage, i.e. 12h and 24h fermentation time representing acidogenic phase and solventogenic phase, respectively. This study examined expression of 5168 genes capturing 98.6% of the C. beijerinckii NCIMB 8052 genome. With the addition of CaCO3, DG-8052 had 565 and 916 genes significantly up-regulated at acidogenic phase and solventogenic phase, respectively. According to the enrichment analysis of pathway and Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, these genes were significantly overrepresented in cellular functions such as Amino acid transport and metabolism, organic acid biosynthetic process, bacteria chemotaxis and defense mechanisms. On the other hand, there were 704 and 1044 genes significantly down-regulated at acidogenic phase and solventogenic phase, respectively. These repressed genes were mainly enriched in functions such as ion transmembrane transport, ATP synthesis, oxidative phosphorylation.

2017-01-02 | GSE81808 | GEO

Iron precipitates

Project description:Iron precipitates Raw sequence reads

| PRJNA432859 | ENA

mine drainage metagenome

Project description:AMD precipitates Targeted Locus (Loci)

| PRJNA273187 | ENA

Human Cell 293T BCAT1 IP GC-LC-MS

Project description:To identify the potential interaction protein that interacts with BCAT1 by IP-MS, we established the stable cell line with vector and BCAT1 in AGS. Then ten million cells were collected lysed in ice-cold 0.1% NP-40 buffer (50 mM Na2HPO4, pH 7.5, 150 mM NaCl) with protease inhibitors cocktail (Sigma, p8340). The supernatants were collected by centrifugation and incubated with 10 µL Anti Flag‐beads (Sigma, A2220at 4°C for overnight. After incubation, beads were washed with lysis buffer for 3 times. Precipitates were resuspended in 1 × SDS loading buffer and separated by SDS-PAGE (polyacrylamide gel electrophoresis). Then cut off (about 1cm2) gel for trypsin hydrolysis and collected and dried the peptide for MS analysis (Thermo Fisher Q Exactive).

2024-11-15 | PXD041556 | Pride

Resistant response of leaves of upland cotton line Im216 to Xanthomonas campestris pv. malvacearum race 1

Project description:Gene expression profiling of upland cotton line Im216 to inoculation with Xanthomonas campestris pv. malvacearum race 1. Fifth or sixth leaves of the bacterial blight-resistant cotton line Im216, which had been grown in a plant growth chamber, were infiltrated with a suspension of about 5x10^6 colony-forming units ml^-1 of Xanthomonas campestris pv. malvacearum race 1 in sterile saturated CaCO3 solution or were not inoculated (control). Keywords: Time-course

2006-01-01 | GSE2851 | GEO

mine drainage metagenome

Project description:AMD precipitates (18S data) Targeted Locus (Loci)

| PRJNA290280 | ENA

A simple and efficient approach for preparing cationic coating with tunable electroosmotic flow for capillary zone electrophoresis-mass spectrometry-based top-down proteomics

Project description:Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has become a valuable analytical technique in top-down proteomics (TDP) in recent years. CZE-MS/MS-based TDP typically employs separation capillaries with neutral coatings (i.e., linear polyacrylamide, LPA). However, issues related to separation resolution and reproducibility remain with the LPA-coated capillaries due to the unavoidable non-specific protein adsorption onto the capillary wall. Cationic coatings can be critical alternatives to LPA coating for CZE-MS/MS-based TDP due to the electrostatic repulsion between the positively charged capillary inner wall and proteoform molecules in the acidic separation buffer. Unfortunately, there are only very few studies using cationic coating-based CZE-MS/MS for TDP studies. In this work, we aimed to develop a simple and efficient approach for preparing separation capillaries with cationic coating, i.e., poly(acrylamide-co-(3-acrylamidopropyl)trimethylammonium chloride, PAMAPTAC for CZE-MS/MS-based TDP. The PAMAPTAC coating-based CZE-MS produced significantly better separation resolution of proteoforms compared to traditionally used LPA-coated approach. It achieved reproducible separation and measurement of simple proteoform mixture and a complex proteome sample (i.e., a yeast cell lysate) regarding migration time, proteoform intensity, and the number of proteoform identifications. The PAMAPTAC coating-based CZE-MS enabled the detection of large proteoforms (≥30 kDa) from the yeast cell lysate reproducibly without any size-based prefractionation. Interestingly, the electrophoretic mobility of proteoforms using the PAMAPTAC coating can be predicted accurately using a simple semiempirical model. The results render the PAMAPTAC coating as a valuable alternative to the LPA coating to advance CZE-MS-based TDP towards high-resolution separation and highly reproducible measurement of proteoforms in complex samples.

2024-10-15 | PXD051862 | Pride

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