SIMS microscopy: a tool to measure the intracellular concentration of carbon 14-labelled molecules.

Monolayer cultures of human fibroblasts were incubated for 24 h with 14C-arginine and observed by means of SIMS microscopy (ion microscopy). Carbon 14 imaging showed the intracellular distribution of labelled arginine which featured high nuclear incorporation. The local concentration of this amino acid in different cells and intracellular structures was assessed through local isotopic 14C/12C ratio measurement. This relates the signal intensity of the labelling isotope carbon 14 to that of the corresponding natural isotope (carbon 12) of known tissular concentration. Using this method we were able to measure minor variations in the molecular concentration of arginine (expressed as mumol/g of tissue) between different fibroblasts. Results of this study indicate that SIMS microscopy is well adapted to carbon 14 detection and can provide quantitative maps of the cellular and subcellular distribution of 14C-labelled molecules.     

Sample preparation of animal tissues and cell cultures for secondary ion mass spectrometry (SIMS) microscopy.

Sample preparation is a critical step in the elemental analysis of animal tissues and cell cultures with ion microscopy. Since live cells cannot be analyzed with ion microscopy, a careful sample fixation is necessary which preserves the native structural and chemical integrity of a specimen. The evaluation of morphological and chemical integrity of a fixed specimen is necessary before any physiological explanation of ion fluxes is interpreted based on ion microscopy. For diffusible ion localization studies, strict cryogenic procedures are recommended. Examples are shown for diffusible ion microanalysis in frozen-freeze-dried tissues and cell cultures. Ion microscopy studies of tightly bound elements/molecules may be conducted in chemically fixed and/or plastic embedded specimens. Since it is not generally known which elements/molecules are tightly bound to the tissue matrix, a confirmation of elemental distribution with cryogenic procedures is desirable. A recent approach of combining laser scanning confocal fluorescence microscopy and ion microscopy on the same frozen freeze-dried cell is also discussed for recognizing smaller cytoplasmic structures in ion microscopy images.     

土壤剖面碳氮稳定同位素自然丰度的垂直分布模式及其影响机制

土壤碳、氮稳定同位素自然丰度(δ13C和δ15N)随土壤深度变化的研究,对揭示碳、氮元素生物地球化学循环机制具有重要意义.本文在概述土壤剖面δ13C和δ15N垂直分布特征的基础上,重点介绍了土壤δ13C和δ15N垂直分布模式的影响机制.土壤剖面δ13C垂直分布模式的影响机制主要有3种:1)植被δ13C值的历史变化;2)...     

Mapping of intracellular halogenous molecules by low and high resolution SIMS microscopy.

The subcellular distribution of halogenous molecules has been studied by SIMS microscopy in cultured cells of a human breast carcinoma (MCF-7 cell line). Two instruments of microanalysis were used. A low lateral resolution ion microscope (SMI 300 CAMECA) and a prototype scanning ion microscope equipped with a cesium gun that gives high lateral resolution images. This apparatus has been developed by G Slodzian, in Onera Laboratories (Office National d'Etudes et de Recherches Aérospatiales). Molecules studied by low lateral resolution ion microscope were halogenous steroids: fluorometholone, triamcinolone, bromocriptine and bromoandrosterone. Analytical images show that the first two compounds are mainly localized in the nuclear structure of MCF-7 cells whereas the last two molecules are localized in cytoplasm of these cells. Images were obtained with a resolution of 1 micron. With the scanning ion microscope, it is now possible to obtain images at the ultrastructural level. Four analytical images can be simultaneously obtained by a single scan of the imaged area, corresponding to a depth of erosion of the section of ten nm. The intranuclear distributions of three pyrimidine analogs, 5-bromo-2'-deoxyuridine, 5-iodo-2'-deoxyuridine and 5-fluorouracil have been studied in phase S and M of MCF-7 cells and these images have been compared to the distribution of sulfur, nitrogen and phosphorus. All these images have been obtained with a lateral resolution better than 100 nm.     

Imaging the distribution of the stable isotopes of nitrogen 14N and 15N in biological samples by "secondary-ion emission microscopy"

Thanks to the "secondary-ion emission microscope" (CAMECA IMS 300), we have been able to image the distribution of the stable isotopes of nitrogen 14N and 15N in sections of plant roots (spatial resolution better than 1 micron), as well as to estimate the relative concentrations of these isotopes. The plants used (Lupinus spec.) originated from seeds with natural (i.e., 14N) nitrogen and had been fed for a few days with [15N]-nitrate before sampling. We have found in root sections of 6-day-old plants (prepared at 5 mm from the root tip) a clear-cut regionalization of the distribution of 15N between the vascular cylinder and the cortex. The latter contained approximately 5% 15N (of total nitrogen), whereas the relative concentration of the heavy isotope in the vascular cylinder was significantly lower. The observed concentration difference is probably due to the Casparian strip, which is a barrier for the apoplastic diffusion of solutes from the cortex to the vascular cylinder.     

Carbon isotopes in functional soil ecology

Soil is an integral part of terrestrial ecosystems. Many soil ecologists interested in soil ecosystem functioning rely, to some degree, on stable isotope methodologies. The study of the natural abundance of carbon isotopes, especially (13)C but also (14)C, in the environment and the use of stable carbon isotope tracers have proved very useful in investigating the soil carbon cycle and soil trophic relationships. Recent methodological and technical advances have greatly extended the possibilities for the application of stable carbon isotopes to terrestrial ecology and have vastly improved our knowledge of belowground ecosystem functioning and will continue to do so. A better understanding of soil processes is invaluable in predicting the future impacts of global environmental change on terrestrial ecosystems.     

Ultrasensitive radioisotope,stable-isotope,and trace-element analysis in the biological sciences using tandem accelerator mass spectrometry

The new technique of tandem accelerator mass spectrometry (TAMS) has improved the sensitivity for measurement of several long-lived radioisotopes and certain stable isotopes by many orders of magnitude. Nuclear physics tandems and new small dedicated accelerators are now able to measure¹⁴C,¹⁰Be,²⁶Al,³²Si,³⁶Cl,⁴¹Ca, and¹²⁹I in natural materials. Sensitivities down to 10⁵ atoms per sample can be achieved in favorable cases. By accelerating ions to MeV energies, one can eliminate molecules and uniquely identify the atomic numbers below 20. Although most applications to date have been in the earth sciences, the opportunity now exists for important new applications in biology and toxicology. Trace elements can be measured at the parts per billion (10⁹) level using a secondary ion mass spectrometry (SIMS) ion source. Radioactive tracer measurements can be made for elements, such as aluminum, for which there are no isotopes with suitable half-lives for conventional decay counting methods. For¹⁴C, counting times become much shorter and dose levels can be reduced.     

山西乡宁内阳垣遗址先民食物结构分析

本文应用C、N稳定同位素分析方法,对山西乡宁内阳垣遗址先民的食物结构进行了分析,旨在揭示该遗址先民的生活方式及社会经济状况,探索戎狄对该遗址先民的影响。分析表明,该遗址先民的δ13C平均值为-8.27‰,δ15N平均值为9.54‰,由此推测他们主要的经济模式应为畜牧业。考古学证据显示该遗址主体文化为晋,但食物结构分析却反映,先民的经济模式主要为畜牧业,明显受到了游牧民族(戎狄)的影响。样品XNM50具有异常的δ13C值(-15.36‰)和较高的δ15N值(9.88‰),当与其从事狩猎活动有关。δ13C和δ15N的统计分析表明,不同性别的先民在食物结构上无明显差异,而不同规格的墓葬却差异明显。     

SIMS microscopy in the biomedical field.

We attempted to indicate the requirements for biomedical applications of SIMS microscopy. Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue. Furthermore, it is often necessary to correlate ionic and light microscope images. This implies a common methodological approach to sample preparation for both microscopes. The use of low or high mass resolution depends on the elements studied and their concentrations. To improve the acquisition and processing of images, digital imaging systems have to be designed and require both ionic and optical image superimposition. However, the images do not accurately reflect element concentration; a relative quantitative approach is possible by measuring secondary ion beam intensity. Using an internal reference element (carbon) and standard curves the results are expressed in micrograms/mg of tissue. Despite their limited lateral resolution (0.5 microns) the actual SIMS microscopes are very suitable for the resolution of biomedical problems posed by action modes and drug localization in human pathology. SIMS microscopy should provide a new tool for metabolic radiotherapy by facilitating dose evaluation. The advent of high lateral resolution SIMS imaging (less than 0.1 microns) should open up new fields in biomedical investigation.     

Application of high-precision isotope ratio monitoring mass spectrometry to identify the biosynthetic origins of proteins

Isotope ratio monitoring (IRM) mass spectrometry was used to measure the relative abundance of stable isotopes in several samples of adult human hemoglobin expressed in E. coli, yeast, and human blood. The results showed significant differences in the distribution of (15)N and (13)C isotopes among hemoglobin samples produced in these organisms. This indicates that IRM mass spectrometry can be used in forensic protein chemistry to identify the origin of protein expression.     

Stable isotopes of carbon and nitrogen in soil ecological studies

The development of stable isotope techniques is one of the main methodological advances in ecology of the last decades of the 20th century. Many biogeochemical processes are accompanied by changes in the ratio between stable isotopes of carbon and nitrogen (¹²C/¹³C and ¹⁴N/¹⁵N), which allows different ecosystem components and different ecosystems to be distinguished by their isotopic composition. Analysis of isotopic composition makes it possible to trace matter and energy flows through biological systems and to evaluate the rate of many ecological processes. The main concepts and methods of stable isotope ecology and patterns of stable isotope fractionation during organic matter decomposition are considered with special emphasis on the fractionation of isotopes in food chains and the use of stable isotope studies of trophic relationships between soil animals in the field.     

Deconvolving single-molecule intensity distributions for quantitative microscopy measurements

In fluorescence microscopy, images often contain puncta in which the fluorescent molecules are spatially clustered. This article describes a method that uses single-molecule intensity distributions to deconvolve the number of fluorophores present in fluorescent puncta as a way to "count" protein number. This method requires a determination of the correct statistical relationship between the single-molecule and single-puncta intensity distributions. Once the correct relationship has been determined, basis histograms can be generated from the single-molecule intensity distribution to fit the puncta distribution. Simulated data were used to demonstrate procedures to determine this relationship, and to test the methodology. This method has the advantages of single-molecule measurements, providing both the mean and variation in molecules per puncta. This methodology has been tested with the avidin-biocytin binding system for which the best-fit distribution of biocytins in the sample puncta was in good agreement with a bulk determination of the avidin-biocytin binding ratio.     

Lipid biomarkers and carbon isotope signatures of a microbial (Beggiatoa) mat associated with gas hydrates in the gulf of Mexico

White and orange mats are ubiquitous on surface sediments associated with gas hydrates and cold seeps in the Gulf of Mexico. The goal of this study was to determine the predominant pathways for carbon cycling within an orange mat in Green Canyon (GC) block GC 234 in the Gulf of Mexico. Our approach incorporated laser-scanning confocal microscopy, lipid biomarkers, stable carbon isotopes, and 16S rRNA gene sequencing. Confocal microscopy showed the predominance of filamentous microorganisms (4 to 5 mum in diameter) in the mat sample, which are characteristic of Beggiatoa. The phospholipid fatty acids extracted from the mat sample were dominated by 16:1omega7c/t (67%), 18:1omega7c (17%), and 16:0 (8%), which are consistent with lipid profiles of known sulfur-oxidizing bacteria, including Beggiatoa. These results are supported by the 16S rRNA gene analysis of the mat material, which yielded sequences that are all related to the vacuolated sulfur-oxidizing bacteria, including Beggiatoa, Thioploca, and Thiomargarita. The delta13C value of total biomass was -28.6 per thousand; those of individual fatty acids were -29.4 to -33.7 per thousand. These values suggested heterotrophic growth of Beggiatoa on organic substrates that may have delta13C values characteristic of crude oil or on their by-products from microbial degradation. This study demonstrated that integrating lipid biomarkers, stable isotopes, and molecular DNA could enhance our understanding of the metabolic functions of Beggiatoa mats in sulfide-rich marine sediments associated with gas hydrates in the Gulf of Mexico and other locations.     

A simple and effective sample preparation method for atomic force microscopy visualization of individual DNA molecules in situ

A simple, controllable and effective sample preparation method was established for atomic force microscopy (AFM) imaging of individual DNA molecules in aqueous solution. Firstly, magnesium ion (Mg²⁺) at a concentration of 5.0–10.0 mM as a positively charged bridge was transferred onto mica to immobilize DNA molecules. Then Mg²⁺-modified mica was used to investigate DNA molecules in any buffer without magnesium ion by AFM. AFM images demonstrated that DNA molecules can be successfully observed in solution with good resolution, reproducibility, and stability. Further, this DNA sample preparation method makes AFM successful to investigate DNA molecular interaction in situ and DNA/chitosan complex in gene delivery.     

Distribution of the heavy isotope of carbon (13C) in biological systems

Causes conditioning fractionation of carbon isotopes in biological systems are considered. Concepts of E. M. Galimov are discussed. According to these concepts distribution of carbon isotopes between biomolecules and their fragments is quaziequilibrium, i. e. it differs from the equilibrium one by a constant multiplier, which is the same for all the biomolecules of an organism but different for various organisms. These concepts have no theoretical grounds and do not agree with the experimental evidence available. An analysis of experimental data, as well as theoretical considerations, indicate that the observed differences in isotope composition of metabolytes and their fragments in the living organisms are conditioned by the kinetic isotope effects of carbon at the stages of their enzymic transformations and by the portion of substances participating in the reaction. It means that these differences do not depend directly on the constants characterizing the equilibrium distribution of carbon isotopes between corresponding compounds and between different groups inside their molecules.     

Status and diet in precontact highland ecuador

Excavation at the Ecuadorian highland site of La Florida in suburban Quito revealed six deep shaft tombs yielding high-status individuals (n = 9) as well as apparent sacrifices and other low-status individuals (n = 23). Determination of sex and age at death of the recovered skeletal remains resulted in a sample of 32 individuals aged from approximately 7 to 50 years of age. The sample of 18 individuals over the age of 18 years included 14 females and 4 males. Temporally, the remains are assigned to the Chaupicruz Phase (circa 100 to 450 AD) of the Regional Developmental Period. In this study, we analyze stable isotopes of carbon and nitrogen from human bone in order to compare the diets of the high- and low-status individuals. Stable carbon isotope analyses were carried out on preserved protein and biological apatite (bioapatite), and stable nitrogen isotope analyses were carried out on preserved protein. There is a statistically significant difference in δ¹³C between the two groups for both protein and mineral sources of carbon with evidence for the greater consumption of maize in the high-status group. There is no significant difference in δ¹⁵N between the two groups, nor is there a significant difference in the spacing between protein and mineral δ¹³C values between the two groups. Ethnohistorical evidence for the 16th century AD provides the expectation that the only dietary difference was the higher consumption of animal protein by the elite. There is no evidence for this based on the bone chemistry data from La Florida. Instead, the isotope data, along with the archaeological evidence, indicate that the major dietary difference during the Chaupicruz Phase was the greater intake of maize by the elite, probably in the form of beer (chicha). © 1995 Wiley-Liss, Inc.     

Advantages of the scanning ion microscopy for mapping halogen corticoids in normal and transformed cells in culture

Summary— The intra-cellular distribution of eight halogen glucocorticoids was investigated by ion microscopy in two cellular varieties of cultured non-cancer cells (fibroblast 3T3) and cancer cells (human breast tumor cells MCF-7). Two types of ion microscopy helped to determine this distribution, a direct imaging ion microscope (SMI 300) with low spatial resolution, and a scanning ion microscope (IMS4F), featuring high resolution, serving to obtain maps representing the intra-cellular distribution of the fluorine elements and drugs present in these monolayer cultured cells. The fluorine images representative of the drugs containing fluorine showed that these drugs are essentially concentrated in the cell nuclei. In these nuclei, the distribution of these drugs is different from that of heterochromatin and of the nucleolus.     

Cell-surface receptors and proteins on platelet membranes imaged by scanning force microscopy using immunogold contrast enhancement.

High resolution scanning force microscope (SFM) images of fibrinogen-exposed platelet membranes are presented. Using ultrasharp carbon tips, we are able to obtain submolecular scale resolution of membrane surface features. Corroboration of SFM results is achieved using low voltage, high resolution scanning electron microscopy (LVHRSEM) to image the same protein molecule that is seen in the SFM. We obtain accurate height dimensions by SFM complemented by accurate lateral dimensions obtained by LVHRSEM. The use of 14- and 5-nm gold labels to identify specific membrane-bound biomolecules and to provide contrast enhancement with the SFM is explored as a useful adjunct to observation of unlabeled material. It is shown that the labels are useful for locating specific protein molecules on platelet membrane surfaces and for assessing the distribution of these molecules using the SFM. Fourteen nm labels are shown to be visible over the membrane corrugation, whereas 5-nm labels appear difficult to resolve using the present SFM instrumental configuration. When using the 5-nm labels, collateral use of LVHRSEM allows one to examine SFM images at submolecular resolution and associate function with the structures imaged after the SFM experiment is completed.     

The Use of ToF-SIMS for Analysis of Bioorganic Samples

The technique for the preparation of biological tissue sections developed for Electron Probe Microanalysis has been adapted for ToF-SIMS analysis of mouse GV stage oocytes. GV-oocyte sample preparation involves the following steps: plunge freezing, freeze drying, impregnation in an embedding medium, and section cutting. Molecule-specific images of the distribution of molecules in a single oocyte have been obtained with the described technique and ToF-SIMS analysis. The ToF-SIMS analysis data show that the efficient lateral image resolution is approximately 1 μm. Hence, ToF-SIMS enables us to study the distribution of chemical substances in relation to the morphological data obtained by scanning electron microscopy or conventional light microscopy.     

Effects of elemental composition on the incorporation of dietary nitrogen and carbon isotopic signatures in an omnivorous songbird

The use of stable isotopes to infer diet requires quantifying the relationship between diet and tissues and, in particular, knowing of how quickly isotopes turnover in different tissues and how isotopic concentrations of different food components change (discriminate) when incorporated into consumer tissues. We used feeding trials with wild-caught yellow-rumped warblers (Dendroica coronata) to determine delta15N and delta13C turnover rates for blood, delta15N and delta13C diet-tissue discrimination factors, and diet-tissue relationships for blood and feathers. After 3 weeks on a common diet, 36 warblers were assigned to one of four diets differing in the relative proportion of fruit and insects. Plasma half-life estimates ranged from 0.4 to 0.7 days for delta13C and from 0.5 to 1.7 days for delta15N . Half-life did not differ among diets. Whole blood half-life for delta13C ranged from 3.9 to 6.1 days. Yellow-rumped warbler tissues were enriched relative to diet by 1.7-3.6% for nitrogen isotopes and by -1.2 to 4.3% for carbon isotopes, depending on tissue and diet. Consistent with previous studies, feathers were the most enriched and whole blood and plasma were the least enriched or, in the case of carbon, slightly depleted relative to diet. In general, tissues were more enriched relative to diet for birds on diets with high percentages of insects. For all tissues, carbon and nitrogen isotope discrimination factors increased with carbon and nitrogen concentrations of diets. The isotopic signature of plasma increased linearly with the sum of the isotopic signature of the diet and the discrimination factor. Because the isotopic signature of tissues depends on both elemental concentration and isotopic signature of the diet, attempts to reconstruct diet from stable isotope signatures require use of mixing models that incorporate elemental concentration.