Dataset Information

Degradation Parameters from Pulse-Chase Experiments.

ABSTRACT: Pulse-chase experiments are often used to study the degradation of macromolecules such as proteins or mRNA. Considerations for the choice of pulse length include the toxicity of the pulse to the cell and maximization of labeling. In the general case of non-exponential decay, varying the length of the pulse results in decay patterns that look different. Analysis of these patterns without consideration to pulse length would yield incorrect degradation parameters. Here we propose a method that constructively includes pulse length in the analysis of decay patterns and extracts the parameters of the underlying degradation process. We also show how to extract decay parameters reliably from measurements taken during the pulse phase.

SUBMITTER: Sin C

PROVIDER: S-EPMC4868333 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Degradation Parameters from Pulse-Chase Experiments.

Sin Celine C Chiarugi Davide D Valleriani Angelo A

PloS one 20160516 5

Pulse-chase experiments are often used to study the degradation of macromolecules such as proteins or mRNA. Considerations for the choice of pulse length include the toxicity of the pulse to the cell and maximization of labeling. In the general case of non-exponential decay, varying the length of the pulse results in decay patterns that look different. Analysis of these patterns without consideration to pulse length would yield incorrect degradation parameters. Here we propose a method that cons ...[more]

PMID: 27182698

Similar Datasets

Project description:Climatic fluctuations may significantly alter the taxonomic and biochemical composition of phytoplankton blooms and subsequently phytodetritus, the food source for the majority of deep-sea communities. To examine the response of abyssal benthic communities to different food resources we simulated a food sedimentation event containing diatoms and coccolithophorids at Station M in the NE Pacific. In one set of experiments we measured incorporation of diatomC and coccoN into the macrofauna using isotopically enriched (13)C-diatoms and (15)N-coccolithophores. In a second experiment we measured incorporation of C and N from dual-labelled ((13)C and (15)N) diatoms. The second experiment was repeated 2 months later to assess the effect of seasonality. The simulated food pulses represented additions of 650 - 800 mg C m(-2) and 120 mg N m(-2) to the seafloor. In all cases rapid incorporation of tracer was observed within 4 days, with between 20% and 52% of the macrofauna displaying evidence of enrichment. However, incorporation levels of both diatomC and coccoN were low (<0.05% and 0.005% of the added C and N). Incorporation of labelled diatoms was similar during both June and September suggesting that the community was not food limited during either period. We found no evidence for selective ingestion of the different food types in the metazoan fauna suggesting that macrofauna do not have strong preferences for diatom vs. coccolithophore dominated phytodetrital pulses. C?N ratios from both experiments suggest that the metazoan macrofauna community appear to have higher C demands and/or assimilation efficiencies compared to N. Concomitantly, the foraminifera preferentially selected for diatomN over coccoN, and we suggest that this may be related to foraminiferal requirements for intracellular nitrate. These experiments provide evidence that abyssal faunal feeding strategies are in part driven by an organism's internal stoichiometric budgets and biochemical requirements.

Project description:1. Human embryonic lung and skin fibroblasts were allowed to incorporate 32SO42- or 35SO42- and D-[1-3H]glucosamine. After removal of the medium the monolayer was subjected to sequential extractions by using EDTA, brief trypsin digestion, extraction with dithiothreitol ofllowed by freeze--thawing and extraction with trichloroacetic acid. The heparan sulphate and galactosaminoglycan contents of the various extracts were estimated after deaminative cleavage of the former component. Heparan sulphate was the major component of the trypsin digest, whereas galactosaminoglycans were the dominant component of other fractions. 2. Galactosaminoglycans of the various fractions were subjected to chemical (periodate oxidation/alkaline elimination) and enzymic (chondroitinase-AC and -ABC, as well as testicular hyaluronidase) degradations. Galactosaminoglycans from the insoluble cell fraction and the dithiothreitol extract contained larger amounts of L-iduronic acid than did those of other fractions. 3. Pulse-chase experiments were performed with and without replating of the cells at the start of the chase period. Radioactive glycans were isolated from the various extracts during the chase period. The half-lives of glycans of the insoluble cell fraction and the dithioreitol extract were shorter (5--8h) than were those of the trypsin digest and the EDTA extract (22h and 11h respectively). After replating of the cells in chase medium, radioactive cell-associated glycans were secreted from the cells and could be recovered in the trypsin digest, the EDTA extract and the medium. Furthermore, 35S/3H ratios of glycans from all these fractions decreased during the chase period. The following conclusions were reached. The insoluble cell fraction contains the synthesis pool and some structural material, whereas the soluble cell fraction is the storage and degradation pool. The dithiothreitol extract appears to contain the immediate precursors of secreted material. The trypsin-released glycans comprise structural components as well as material destined for pinocytosis or secretion into the medium. The EDTA extract is considered to consist of glycans en route to the medium. 4. The two presumptive precursor pools were preferentially depleted of L-iduronic acid-rich galactosaminoglycans during the chase. Glycans recovered from the trypsin digest, the EDTA extract and the medium during the chase contained larger amounts of periodate-resistant uronic acid residues (D-glucuronic acid and/or L-iduronic acid O-sulphate) than did their precursors. It is proposed that polymer-level modifications of secreted glycans are partly responsible for the results.

Dataset Information

Degradation Parameters from Pulse-Chase Experiments.

Publications

Degradation Parameters from Pulse-Chase Experiments.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets