Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study

Hydroponic isotope labelling of entire plants (HILEP) is a cost-effective method enabling metabolic labelling of whole and mature plants with a stable isotope such as N-15. By utilising hydroponic media that contain N-15 inorganic salts as the sole nitrogen source, near to 100% N-15-labelling of proteins can be achieved. In this study, it is shown that HILEP, in combination with mass spectrometry, is suitable for relative protein quantitation of seven week-old Arabidopsis plants submitted to oxidative stress. Protein extracts from pooled N-14- and N-15-hydroponically grown plants were fractionated by SDS-PAGE, digested and analysed by liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS). Proteins were identified and the spectra of N-14/N-15 peptide pairs were extracted using their m/z chromatographic retention time, isotopic distributions, and the m/z difference between the N-14 and N-15 peptides. Relative amounts were calculated as the ratio of the sum of the peak areas of the two distinct N-14 and N-15 peptide isotope envelopes. Using Mascot and the open source trans-proteomic pipeline (TPP), the data processing was automated for global proteome quantitation down to the isoform level by extracting isoform specific peptides. With this combination of metabolic labelling and mass spectrometry it was possible to show differential protein expression in the apoplast of plants submitted to oxidative stress. Moreover, it was possible to discriminate between differentially expressed isoforms belonging to the same protein family, such as isoforms of xylanases and pathogen-related glucanases (PR 2). (C) 2008 Elsevier Ltd. All rights reserved.

Hydroponic isotope labeling of entire plants (HILEP) for quantitative plant proteomics

Quantitative analysis by mass spectrometry (MS) is a major challenge in proteomics as the correlation between analyte concentration and signal intensity is often poor due to varying ionisation efficiencies in the presence of molecular competitors. However, relative quantitation methods that utilise differential stable isotope labelling and mass spectrometric detection are available. Many drawbacks inherent to chemical labelling methods (ICAT, iTRAQ) can be overcome by metabolic labelling with amino acids containing stable isotopes (e.g. 13C and/or 15N) in methods such as Stable Isotope Labelling with Amino acids in Cell culture (SILAC). SILAC has also been used for labelling of proteins in plant cell cultures (1) but is not suitable for whole plant labelling. Plants are usually autotrophic (fixing carbon from atmospheric CO2) and, thus, labelling with carbon isotopes becomes impractical. In addition, SILAC is expensive. Recently, Arabidopsis cell cultures were labelled with 15N in a medium containing nitrate as sole nitrogen source. This was shown to be suitable for quantifying proteins and nitrogen-containing metabolites from this cell culture (2,3). Labelling whole plants, however, offers the advantage of studying quantitatively the response to stimulation or disease of a whole multicellular organism or multi-organism systems at the molecular level. Furthermore, plant metabolism enables the use of inexpensive labelling media without introducing additional stress to the organism. And finally, hydroponics is ideal to undertake metabolic labelling under extremely well-controlled conditions. We demonstrate the suitability of metabolic 15N hydroponic isotope labelling of entire plants (HILEP) for relative quantitative proteomic analysis by mass spectrometry. To evaluate this methodology, Arabidopsis plants were grown hydroponically in 14N and 15N media and subjected to oxidative stress.

An isotope dilution model for partitioning phenylalanine uptake by the liver of lactating dairy cows

An isotope dilution model for partitioning phenylalanine uptake by the liver of the lactating dairy cow was constructed and solved in the steady state. If assumptions are made, model solution permits calculation of the rate of phenylalanine uptake from portal vein and hepatic arterial blood supply, phenylalanine release into the hepatic vein, phenylalanine oxidation and synthesis, and degradation of hepatic constitutive and export proteins. The model requires the measurement of plasma fow rate through the liver in combination with phenylalanine concentrations and plateau isotopic enrichments in arterial, portal and hepatic plasma during a constant infusion of [1-13C]phenylalanine tracer. The model can be applied to other amino acids with similar metabolic fates and will provide a means for assessing the impact of hepatic metabolism on amino acid availability to peripheral tissues. This is of particular importance for the dairy cow when considering the requirements for milk protein synthesis and the negative environmental impact of excessive nitrogen excretion.

Carbon and nitrogen isotopic ratios of urine and faeces as novel nutritional biomarkers of meat and fish intake

Purpose Meat and fish consumption are associated with changes in the risk of chronic diseases. Intake is mainly assessed using self-reporting, as no true quantitative nutritional biomarker is available. The measurement of plasma fatty acids, often used as an alternative, is expensive and time-consuming. As meat and fish differ in their stable isotope ratios, δ13C and δ15N have been proposed as biomarkers. However, they have never been investigated in controlled human dietary intervention studies. Objective In a short-term feeding study, we investigated the suitability of δ13C and δ15N in blood, urine and faeces as biomarkers of meat and fish intake. Methods The dietary intervention study (n = 14) followed a randomised cross-over design with three eight-day dietary periods (meat, fish and half-meat–half-fish). In addition, 4 participants completed a vegetarian control period. At the end of each period, 24-h urine, fasting venous blood and faeces were collected and their δ13C and δ15N analysed. Results There was a significant difference between diets in isotope ratios in faeces and urine samples, but not in blood samples (Kruskal–Wallis test, p < 0.0001). In pairwise comparisons, δ13C and δ15N were significantly higher in urine and faecal samples following a fish diet when compared with all other diets, and significantly lower following a vegetarian diet. There was no significant difference in isotope ratio between meat and half-meat–half-fish diets for blood, urine or faecal samples. Conclusions The results of this study show that urinary and faecal δ13C and δ15N are suitable candidate biomarkers for short-term meat and fish intake.

Serum carbon and nitrogen stable isotopes as potential biomarkers of dietary intake and their relation with incident type 2 diabetes: the EPIC-Norfolk study

Background: Stable-isotope ratios of carbon (13C/12C, expressed as δ13C) and nitrogen (15N/14N, or δ15N) have been proposed as potential nutritional biomarkers to distinguish between meat, fish, and plant-based foods. Objective: The objective was to investigate dietary correlates of δ13C and δ15N and examine the association of these biomarkers with incident type 2 diabetes in a prospective study. Design: Serum δ13C and δ15N (‰) were measured by using isotope ratio mass spectrometry in a case-cohort study (n = 476 diabetes cases; n = 718 subcohort) nested within the European Prospective Investigation into Cancer and Nutrition (EPIC)–Norfolk population-based cohort. We examined dietary (food-frequency questionnaire) correlates of δ13C and δ15N in the subcohort. HRs and 95% CIs were estimated by using Prentice-weighted Cox regression. Results: Mean (±SD) δ13C and δ15N were −22.8 ± 0.4‰ and 10.2 ± 0.4‰, respectively, and δ13C (r = 0.22) and δ15N (r = 0.20) were positively correlated (P < 0.001) with fish protein intake. Animal protein was not correlated with δ13C but was significantly correlated with δ15N (dairy protein: r = 0.11; meat protein: r = 0.09; terrestrial animal protein: r = 0.12, P ≤ 0.013). δ13C was inversely associated with diabetes in adjusted analyses (HR per tertile: 0.74; 95% CI: 0.65, 0.83; P-trend < 0.001], whereas δ15N was positively associated (HR: 1.23; 95% CI: 1.09, 1.38; P-trend = 0.001). Conclusions: The isotope ratios δ13C and δ15N may both serve as potential biomarkers of fish protein intake, whereas only δ15N may reflect broader animal-source protein intake in a European population. The inverse association of δ13C but a positive association of δ15N with incident diabetes should be interpreted in the light of knowledge of dietary intake and may assist in identifying dietary components that are associated with health risks and benefits.

New-on-line method for water isotope analysis of speleothem fluid inclusions using laser absorption spectroscopy (WS-CRDS)

A new online method to analyse water isotopes of speleothem fluid inclusions using a wavelength scanned cavity ring down spectroscopy (WS-CRDS) instrument is presented. This novel technique allows us simultaneously to measure hydrogen and oxygen isotopes for a released aliquot of water. To do so, we designed a new simple line that allows the online water extraction and isotope analysis of speleothem samples. The specificity of the method lies in the fact that fluid inclusions release is made on a standard water background, which mainly improves the δ D robustness. To saturate the line, a peristaltic pump continuously injects standard water into the line that is permanently heated to 140 °C and flushed with dry nitrogen gas. This permits instantaneous and complete vaporisation of the standard water, resulting in an artificial water background with well-known δ D and δ18O values. The speleothem sample is placed in a copper tube, attached to the line, and after system stabilisation it is crushed using a simple hydraulic device to liberate speleothem fluid inclusions water. The released water is carried by the nitrogen/standard water gas stream directly to a Picarro L1102-i for isotope determination. To test the accuracy and reproducibility of the line and to measure standard water during speleothem measurements, a syringe injection unit was added to the line. Peak evaluation is done similarly as in gas chromatography to obtain &delta D; and δ18O isotopic compositions of measured water aliquots. Precision is better than 1.5 ‰ for δ D and 0.4 ‰ for δ18O for water measurements for an extended range (−210 to 0 ‰ for δ D and −27 to 0 ‰ for δ18O) primarily dependent on the amount of water released from speleothem fluid inclusions and secondarily on the isotopic composition of the sample. The results show that WS-CRDS technology is suitable for speleothem fluid inclusion measurements and gives results that are comparable to the isotope ratio mass spectrometry (IRMS) technique.

Diet and herding strategies in a changing environment: stable isotope analysis of Bronze Age and Late Antique skeletal remains from Ya'amūn, Jordan

Carbon and nitrogen stable isotope ratios of 45 human and 23 faunal bone collagen samples were measured to study human diet and the management of domestic herbivores in past Jordan, contrasting skeletal remains from the Middle and Late Bronze Age and the Late Roman and Byzantine periods from the site of Ya'amūn near Irbid. The isotope data demonstrate that the management of the sheep and goats changed over time, with the earlier animals consuming more plants from semi-arid habitats, possibly because of transhumant herding strategies. The isotope data for fish presented here are the first from archaeological contexts from the Southern Levant. Although fish of diverse provenance was available at the site, human diet was predominately based on terrestrial resources and there was little dietary variability within each time-period. Isotopic variation between humans from different time-periods can mostly be explained by ‘baseline shifts’ in the available food sources; however, it is suggested that legumes may have played a more significant role in Middle and Late Bronze Age diet than later on.

Stable carbon (delta(13)C) and nitrogen (delta(15)N) isotopes as natural indicators of live and dry food in Piaractus mesopotamicus (Holmberg, 1887) larval tissue

This study proposed the use of the stable isotope technique to track the type of food utilized by pacu Piaractus mesopotamicus larvae during their development, and to identify the moment when the larvae start using nutrients from the dry diet by retaining its carbon and nitrogen atoms in their body tissues. Five-day-old pacu larvae at the onset of exogenous feeding were fed Artemia nauplii or formulated diet exclusively; nauplii+formulated diet during the entire period; or were weaned from nauplii to a dry diet after 3, 6 or 12 days after the first feeding. delta(13)C and delta(15)N values for Artemia nauplii were -15.1 parts per thousand and 4.7 parts per thousand, respectively, and -25.0 parts per thousand and 7.4 parts per thousand for the dry diet. The initial isotopic composition of the larval tissue was -20.2 parts per thousand and 9.5 parts per thousand for delta(13)C and delta(15)N respectively. Later, at the end of a 42-day feeding period, larvae fed Artemia nauplii alone reached values of -12.7 parts per thousand and 7.0 parts per thousand for delta(13)C and delta(15)N respectively. Larvae that received the formulated diet alone showed values of -22.7 parts per thousand for delta(13)C and 9.6 parts per thousand for delta(15)N. The stable isotope technique was precise, and the time at which the larvae utilized Artemia nauplii, and later dry diet as a food source could be clearly defined.

The use of carbon and nitrogen stable isotopes for the detection of poultry offal meal in meat-type quail feeds

The objective of the present study was to trace the inclusion of poultry offal meal (POM) in the diet of meat-type quails reared for a long period using the technique of stable isotopes. A number of 320 quails were randomly distributed into eight treatments: vegetable diet (T1), and a diet containing 8% POM were fed until the end of the experimental period (T2) or replaced by the vegetable diet on day 42 (T3), 56 (T4), 70 (T5), 84 (T6), 98 (T7), and 112 (T8). Breast muscle samples were collected from four birds randomly selected per treatment every 14 days. The obtained isotope results were submitted to multivariate analysis of variance (MANOVA) with the aid of the GLM procedure of statistical SAS program. Treatments were different from T1 when birds were sacrificed at least two weeks after the diet was changed. T2 results were different from T1 in all evaluated periods. It was concluded that it is possible to trace poultry offal meal inclusion in a strictly vegetable diet after the diet was changed for at least 14 days.

Multivariate analysis of stable isotope data in the traceability process for birds

A análise isotópica tem se mostrado uma ferramenta de suma importância ao processo de rastreabilidade, no entanto, existem divergências nas análises estatísticas dos resultados, uma vez que os dados são dependentes e advindos de vários elementos químicos tais como Carbono, Hidrogênio, Oxigênio, Nitrogênio e Enxofre (CHON'S). Com o intuito de estabelecer a análise propícia para os dados de rastreabilidade em aves pela técnica de isótopos estáveis e avaliar a necessidade da análise conjunta das variáveis, foram usados dados de carbono-13 e de nitrogênio-15 de ovos (albúmen + gema) de poedeiras e músculo peitoral de frangos de corte, os quais foram submetidos à análise estatística univariada (Anova e complementada pelo teste de Tukey) e multivariada (Manova e Discriminante). Os dados foram analisados no software Minitab 16, e os resultados, consolidados na teoria, confirmam a necessidade de análise multivariada, mostrando também que a análise discriminante esclarece as dúvidas apresentadas nos resultados de outros métodos de análise comparados nesta pesquisa.

Effects of soil water deficit and nitrogen nutrition on water relations and photosynthesis of pot-grown Coffea canephora Pierre

Coffea canephora plants (clone INCAPER-99) were submitted to low N (LN) or high N (HN) applications and two watering regimes (daily irrigation and irrigation every 5 days for a month). Although water potential was not altered significantly by N, HN plants showed higher relative water content than did LN plants under water deficit. Only HN plants exhibited some ability for osmotic adjustment. Plants from both N treatments increased their cell wall rigidity under drought, with a more pronounced augmentation in HN plants. In well-watered plants, carbon assimilation rate increased with increasing N while stomatal conductance did not respond to N supply. Under drought conditions, carbon assimilation decreased by 68-80% compared to well-watered plants, whereas stomatal conductance and transpiration rate declined by 35% irrespective of the N applications. Stable carbon isotope analysis, combined with leaf gas exchange measurements, indicated that regardless of the watering treatments, N increased the long-term water use efficiency through changes in carbon assimilation with little or no effect on stomatal behaviour.

Nitrogen immobilization by Congo grass roots impairs cotton initial growth

In crop-livestock integration systems the presence of both grass roots in the soil and straw on the surface can temporarily immobilize nitrogen. This study examined the persistence of grass residues in the system as well as their effects on cotton response to N when grown after Congo grass (Brachiaria ruziziensis, Syn. Urochloa ruziziensis). Congo grass was grown in pots with soil. Next, cotton was grown in the same pots without residues, with whole plant residues (Congo grass roots and shoots) or root residues (grass roots) and fertilized with N as ammonium nitrate. Congo grass and cotton roots were separated using stable carbon isotope fractioning. Congo grass roots showed higher C/N ratio than shoots, losing 14% of its mass after 45 days and increasing soil N immobilization. The lower N availability resulted in N deficient and shorter cotton plants with lower dry matter yields. Nevertheless, the application of 80 to 120 mg kg-1 of N compensated the immobilization by the soil microorganisms, allowing cotton to show normal growth. When Congo grass is present in the cropping system, the effects of the decaying roots on soil N dynamics and availability are more important than those of the straw left on the soil surface.

Spatio-temporal variations in the diet and stable isotope composition of the Argentine hake Merluccius hubbsi Marini, 1933 of the continental shelf of southeastern Brazil

The feeding ecology of Merluccius hubbsi was investigated in 2 regions of SE Brazil. The major food sources for the hakes were fish, crustaceans, and squid. In the upwelling system of Cabo Frio, the diet was very similar in the summers of 2001/2002 and spring 2002; fish were the most important prey followed by crustaceans. In Ubatuba, euphausiids were an important prey during the winter 2001 (100 m), while in the summer 2002, fish and amphipods predominated in the diet in the shallower site (40 m) and squid in the deeper site (100 m). The hakes showed temporal differences in stable isotope signatures in both regions, while C:N ratios varied only in Cabo Frio. delta(15)N and delta(13)C (bulk and corrected for lipid content) increased with fish length, which seems to be related to the increasing importance of fish and decreasing importance of euphausiids and amphipods in the diet of larger hakes. The mean trophic level of 3.7 for M. hubbsi was estimated using delta(15)N of bivalves as baseline and the fractionation of 3.4aEuro degrees between trophic levels.

Stable isotope investigations of atmospheric nitrous oxide

ZusammenfassungDie Analyse von Isotopenverhältnissen ist von wachsender Bedeutung bei der Untersuchung von Quellen, Senken und chemischen Reaktionswegen atmosphärischer Spurengase. Distickstoffoxid (N2O) hat vier isotopisch einfach substituierte Spezies: 14N15N16O, 15N14N16O, 14N217O und 14N218O. In der vorliegenden Arbeit wurden massenspektrometrische Methoden entwickelt, die eine komplette Charakterisierung der Variationen im Vorkommen dieser Spezies ermöglichen. Es wird die bisher umfassendste Darstellung dieser Variationen in Troposphäre und Stratosphäre gegeben und mit Bezug auf eine Reihe von Laborexperimenten detailliert interpretiert.Die Laborexperimente machen einen großen Anteil dieser Doktorarbeit aus und konzentrieren sich auf die Isotopenfraktionierung in den stratosphärischen N2O-Senken, d. h. Photolyse und Reaktion mit elektronisch angeregten Sauerstoffatomen, O(1D). Diese Prozesse sind von dominantem Einfluß auf die Isotopenzusammensetzung von atmosphärischem N2O. Potentiell wichtige Parameter wie Temperatur- und Druckvariationen, aber auch Veränderungen der Wellenlänge im Fall der Photolyse wurden berücksichtigt. Photolyse bei stratosphärisch relevanten Wellenlängen > 190 nm zeigte immer Anreicherungen von 15N in beiden Stickstoffatomen des verbleibenden N2O wie auch in 17O und 18O. Die Anreicherungen waren am mittelständigen N-Atom signifikant höher als am endständigen N (mit mittleren Werten für 18O) und stiegen zu größeren Wellenlängen und niedrigeren Temperaturen hin an. Erstmalig wurden für 18O und 15N am endständigen N-Atom Isotopenabreicherungen bei 185 nm-Photolyse festgestellt. Im Gegensatz zur Photolyse waren die Isotopenanreicherungen bei der zweiten wichtigen N2O-Senke, Reaktion mit O(1D) vergleichsweise gering. Jedoch war das positionsabhängige Fraktionierungsmuster dem der Photolyse direkt entgegengesetzt und zeigte größere Anreicherungen am endständigen N-Atom. Demgemäß führen beiden Senkenprozesse zu charakteristischen Isotopensignaturen in stratosphärischem N2O. Weitere N2O-Photolyseexperimente zeigten, daß 15N216O in der Atmosphäre höchstwahrscheinlich mit der statistisch zu erwartenden Häufigkeit vorkommt.Kleine stratosphärische Proben erforderten die Anpassung der massenspektrometrischen Methoden an Permanentflußtechniken, die auch für Messungen an Firnluftproben von zwei antarktischen Stationen verwendet wurden. Das 'Firnluftarchiv' erlaubte es, den gegenwärtigen Trend und die präindustriellen Werte der troposphärischen N2O-Isotopensignatur zu bestimmen. Ein daraus konstruiertes globales N2O-Isotopenbudget ist im Einklang mit den besten Schätzungen der Gesamt-N2O-Emissionen aus Böden und Ozeanen.17O-Messungen bestätigten die Sauerstoffisotopenanomalie in atmosphärischem N2O, zeigten aber auch, daß N2O-Photolyse die Sauerstoffisotope gemäß einem massenabhängigen Fraktionierungsgesetz anreichert. Eine troposphärische Ursache für einen Teil des Exzeß-17O wurde vorgeschlagen, basierend auf der Reaktion von NH2 mit NO2, wodurch die Sauerstoffisotopenanomalie von O3 über NO2 an N2O übertragen wird.

Use of isotopes for studying nitrogen processes in a wetland within the Venice Lagoon watershed

The present study is based on the use of isotopes for evaluating the efficiency of nutrients removal of a wetland, in particular nitrogen and nitrates, also between the different habitats present in the wetland. Nutrients like nitrogen and phosphorus, normally distributed as fertilizers, are among the principal causes of diffuse pollution. This is particularly important in the Adriatic Sea, which is frequently subjected to eutrophication phenomena. So it is very crucial requalification of wetland, in which there are naturally depurative processes such as denitrification and plant uptake, which allow the reduction of pollutant loads that flow in water bodies. In this study nutrient reduction is analyzed in the wetland of the Comuna drain, which waters flow in the Venice lagoon. Chemical and isotopical analyses were performed on samples of water, vegetation, soil and sediments taken in the wetlands of the Comuna drain in four different periods of the year and on data of nitrogen and phosphorus concentration obtained by the LASA of the University of Padova. Values of total nitrogen and nitrates were obtained in order to evaluate the reduction within the different systems of the wetland. Instead, the isotopic values of nitrogen and carbon were used to evaluate which process influence more nitrogen reduction and to understand the origin of the nutrient, if it is from fertilizers, waste water or sewage. To conclude, the most important process in the wetland of the Comuna drain is plant uptake, in facts the bigger percentage of nitrogen reduction was in the period of vegetative growth. So it is important the study of isotopes in plant tissues and water residence time, whose increase would allow a greater reduction of nutrients.