Dataset Information

Effects of demineralization on the stable isotope analysis of bone samples.

ABSTRACT: RATIONALE:The sampling of sequential, annually formed bone growth layers for stable carbon (?(13)C values) and nitrogen (?(15)N values) isotope analysis (SIA) can provide a time series of foraging ecology data. To date, no standard protocol exists for the pre-SIA treatment of cortical samples taken from fresh, modern, bones. METHODS:Based on the SIA of historical bone, it is assumed that fresh bone samples must be pre-treated with acid prior to SIA. Using an elemental analyzer coupled to an isotope ratio mass spectrometer to measure stable carbon and nitrogen ratios, we tested the need to acidify cortical bone powder with 0.25 M HCl prior to SIA to isolate bone collagen for the determination of ?(13)C and ?(15)N values. We also examined the need for lipid extraction to remove potential biases related to ?(13)C analysis, based on a C:N ratio threshold of 3.5. RESULTS:It was found that acidification of micromilled cortical bone samples from marine turtles does not affect their ?(15)N values, and the small effect acidification has on ?(13)C values can be mathematically corrected for, thus eliminating the need for pre-SIA acidification of cortical bone. The lipid content of the cortical bone samples was low, as measured by their C:N ratios, indicating that lipid extracting cortical bone samples from modern marine turtles is unnecessary. CONCLUSIONS:We present a standard protocol for testing fresh, modern cortical bone samples prior to SIA, facilitating direct comparison of future studies. Based on the results obtained from marine turtle bones, pre-acidification and lipid removal of cortical bone are not recommended. This is especially useful as there is frequently not enough bone material removed via micromilling of sequential growth layers to accommodate both acid treatment and SIA.

SUBMITTER: Tomaszewicz CN

PROVIDER: S-EPMC4606465 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Effects of demineralization on the stable isotope analysis of bone samples.

Tomaszewicz Calandra N Turner CN Seminoff Jeffrey A JA Ramirez Matthew D MD Kurle Carolyn M CM

Rapid communications in mass spectrometry : RCM 20151001 20

<h4>Rationale</h4>The sampling of sequential, annually formed bone growth layers for stable carbon (δ(13)C values) and nitrogen (δ(15)N values) isotope analysis (SIA) can provide a time series of foraging ecology data. To date, no standard protocol exists for the pre-SIA treatment of cortical samples taken from fresh, modern, bones.<h4>Methods</h4>Based on the SIA of historical bone, it is assumed that fresh bone samples must be pre-treated with acid prior to SIA. Using an elemental analyzer cou ...[more]

PMID: 26411509

Similar Datasets

Project description:Despite the long-established therapeutic efficacy of lithium in the treatment of bipolar disorder (BPD), its molecular mechanism of action remains elusive. Newly developed stable isotope-resolved metabolomics (SIRM) is a powerful approach that can be used to elucidate systematically how lithium impacts glial and neuronal metabolic pathways and activities, leading ultimately to deciphering its molecular mechanism of action. The effect of lithium on the metabolism of three different (13)C-labeled precursors ([U-(13)C]-glucose, (13)C-3-lactate or (13)C-2,3-alanine) was analyzed in cultured rat astrocytes and neurons by nuclear magnetic resonance (NMR) spectroscopy and gas chromatography mass spectrometry (GC-MS). Using [U-(13)C]-glucose, lithium was shown to enhance glycolytic activity and part of the Krebs cycle activity in both astrocytes and neurons, particularly the anaplerotic pyruvate carboxylation (PC). The PC pathway was previously thought to be active in astrocytes but absent in neurons. Lithium also stimulated the extracellular release of (13)C labeled-lactate, -alanine (Ala), -citrate, and -glutamine (Gln) by astrocytes. Interrogation of neuronal pathways using (13)C-3-lactate or (13)C-2,3-Ala as tracers indicated a high capacity of neurons to utilize lactate and Ala in the Krebs cycle, particularly in the production of labeled Asp and Glu via PC and normal cycle activity. Prolonged lithium treatment enhanced lactate metabolism via PC but inhibited lactate oxidation via the normal Krebs cycle in neurons. Such lithium modulation of glycolytic, PC and Krebs cycle activity in astrocytes and neurons as well as release of fuel substrates by astrocytes should help replenish Krebs cycle substrates for Glu synthesis while meeting neuronal demands for energy. Further investigations into the molecular regulation of these metabolic traits should provide new insights into the pathophysiology of mood disorders and early diagnostic markers, as well as new target(s) for effective therapies.

Project description:The mineral component of fish otoliths (ear bones), which is aragonitic calcium carbonate (CaCO3), makes this structure the preferred sample choice for measuring biological carbon and oxygen-stable isotopes in order to address fundamental questions in fish ecology and fisheries science. The main drawback is that the removal of otoliths requires sacrificing the specimen, which is particularly impractical for endangered and commercially valuable species such as Atlantic bluefin tuna (Thunnus thynnus) (ABFT). This study explores the suitability of using the first dorsal fin spine bone of ABFT as a non-lethal alternative to otolith analysis or as a complementary hard structure. The fin spines of freshly caught ABFT were collected to identify carbonate ions within the mineral matrix (i.e., hydroxyapatite) and to determine the nature of the carbonate substitution within the crystal lattice, knowledge which is crucial for correct measurement and ecological interpretation of oxygen and carbon stable isotopes of carbonates. Fin spine sections were analyzed via X-ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy, and Fourier Transform InfraRed (FTIR). The XPS survey analysis showed signals of Ca, O, and P (three compositional elements that comprise hydroxyapatite). The Raman and FTIR techniques showed evidence of carbonate ions within the hydroxyapatite matrix, with the IR spectra being the most powerful for identifying the type B carbonate substitution as shown by the carbonate band in the v 2 CO3 2- domain at ∼872 cm-1. The results of this study confirmed the presence of carbonate ions within the mineral matrix of the fin spine bone of ABFT, showing the feasibility of using this calcified structure for analysis of stable isotopes. Overall, our findings will facilitate new approaches to safeguarding commercially valuable and endangered/protected fish species and will open new research avenues to improve fisheries management and species conservation strategies.

Project description:The response of natural microbial communities to environmental change can be assessed by determining DNA- or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a (13)C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with (13)C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA- and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.

Dataset Information

Effects of demineralization on the stable isotope analysis of bone samples.

Publications

Effects of demineralization on the stable isotope analysis of bone samples.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets