Development of Imaging Mass Spectrometry Analysis of Lipids in Biological and Clinically Relevant Applications

La spectrométrie de masse mesure la masse des ions selon leur rapport masse sur charge. Cette technique est employée dans plusieurs domaines et peut analyser des mélanges complexes. L’imagerie par spectrométrie de masse (Imaging Mass Spectrometry en anglais, IMS), une branche de la spectrométrie de masse, permet l’analyse des ions sur une surface, tout en conservant l’organisation spatiale des ions détectés. Jusqu’à présent, les échantillons les plus étudiés en IMS sont des sections tissulaires végétales ou animales. Parmi les molécules couramment analysées par l’IMS, les lipides ont suscité beaucoup d'intérêt. Les lipides sont impliqués dans les maladies et le fonctionnement normal des cellules; ils forment la membrane cellulaire et ont plusieurs rôles, comme celui de réguler des événements cellulaires. Considérant l’implication des lipides dans la biologie et la capacité du MALDI IMS à les analyser, nous avons développé des stratégies analytiques pour la manipulation des échantillons et l’analyse de larges ensembles de données lipidiques. La dégradation des lipides est très importante dans l’industrie alimentaire. De la même façon, les lipides des sections tissulaires risquent de se dégrader. Leurs produits de dégradation peuvent donc introduire des artefacts dans l’analyse IMS ainsi que la perte d’espèces lipidiques pouvant nuire à la précision des mesures d’abondance. Puisque les lipides oxydés sont aussi des médiateurs importants dans le développement de plusieurs maladies, leur réelle préservation devient donc critique. Dans les études multi-institutionnelles où les échantillons sont souvent transportés d’un emplacement à l’autre, des protocoles adaptés et validés, et des mesures de dégradation sont nécessaires. Nos principaux résultats sont les suivants : un accroissement en fonction du temps des phospholipides oxydés et des lysophospholipides dans des conditions ambiantes, une diminution de la présence des lipides ayant des acides gras insaturés et un effet inhibitoire sur ses phénomènes de la conservation des sections au froid sous N2. A température et atmosphère ambiantes, les phospholipides sont oxydés sur une échelle de temps typique d’une préparation IMS normale (~30 minutes). Les phospholipides sont aussi décomposés en lysophospholipides sur une échelle de temps de plusieurs jours. La validation d’une méthode de manipulation d’échantillon est d’autant plus importante lorsqu’il s’agit d’analyser un plus grand nombre d’échantillons. L’athérosclérose est une maladie cardiovasculaire induite par l’accumulation de matériel cellulaire sur la paroi artérielle. Puisque l’athérosclérose est un phénomène en trois dimension (3D), l'IMS 3D en série devient donc utile, d'une part, car elle a la capacité à localiser les molécules sur la longueur totale d’une plaque athéromateuse et, d'autre part, car elle peut identifier des mécanismes moléculaires du développement ou de la rupture des plaques. l'IMS 3D en série fait face à certains défis spécifiques, dont beaucoup se rapportent simplement à la reconstruction en 3D et à l’interprétation de la reconstruction moléculaire en temps réel. En tenant compte de ces objectifs et en utilisant l’IMS des lipides pour l’étude des plaques d’athérosclérose d’une carotide humaine et d’un modèle murin d’athérosclérose, nous avons élaboré des méthodes «open-source» pour la reconstruction des données de l’IMS en 3D. Notre méthodologie fournit un moyen d’obtenir des visualisations de haute qualité et démontre une stratégie pour l’interprétation rapide des données de l’IMS 3D par la segmentation multivariée. L’analyse d’aortes d’un modèle murin a été le point de départ pour le développement des méthodes car ce sont des échantillons mieux contrôlés. En corrélant les données acquises en mode d’ionisation positive et négative, l’IMS en 3D a permis de démontrer une accumulation des phospholipides dans les sinus aortiques. De plus, l’IMS par AgLDI a mis en évidence une localisation différentielle des acides gras libres, du cholestérol, des esters du cholestérol et des triglycérides. La segmentation multivariée des signaux lipidiques suite à l’analyse par IMS d’une carotide humaine démontre une histologie moléculaire corrélée avec le degré de sténose de l’artère. Ces recherches aident à mieux comprendre la complexité biologique de l’athérosclérose et peuvent possiblement prédire le développement de certains cas cliniques. La métastase au foie du cancer colorectal (Colorectal cancer liver metastasis en anglais, CRCLM) est la maladie métastatique du cancer colorectal primaire, un des cancers le plus fréquent au monde. L’évaluation et le pronostic des tumeurs CRCLM sont effectués avec l’histopathologie avec une marge d’erreur. Nous avons utilisé l’IMS des lipides pour identifier les compartiments histologiques du CRCLM et extraire leurs signatures lipidiques. En exploitant ces signatures moléculaires, nous avons pu déterminer un score histopathologique quantitatif et objectif et qui corrèle avec le pronostic. De plus, par la dissection des signatures lipidiques, nous avons identifié des espèces lipidiques individuelles qui sont discriminants des différentes histologies du CRCLM et qui peuvent potentiellement être utilisées comme des biomarqueurs pour la détermination de la réponse à la thérapie. Plus spécifiquement, nous avons trouvé une série de plasmalogènes et sphingolipides qui permettent de distinguer deux différents types de nécrose (infarct-like necrosis et usual necrosis en anglais, ILN et UN, respectivement). L’ILN est associé avec la réponse aux traitements chimiothérapiques, alors que l’UN est associé au fonctionnement normal de la tumeur.

Fenóis voláteis em vinhos tintos

As leveduras Dekkera/Brettanomyces são responsáveis pela formação de fenóis voláteis em vinhos tintos, tornando-se numa grande preocupação para a produção enológica a nível mundial, devido à dificuldade em controlá-las. Os fenóis voláteis são responsáveis por aromas desagradáveis nos vinhos tintos, diminuindo a sua qualidade e resultando em grandes perdas económicas. Este trabalho teve como principal objectivo estudar um método de preparação de amostra e um método cromatográfico para analisar e quantificar os principais fenóis voláteis (4-etilfenol, 4-etilguaiacol, 4-etilcatecol, 4-vinilfenol e o 4-vinilguaiacol), em meio sintético e em vinhos tintos comerciais. A preparação de amostras foi efectuada através do método de extracção líquido-líquido e a separação dos compostos foi efectuada por cromatografia gasosa com detector de ionização de chama (GC-FID). Os resultados obtidos permitem concluir que é possível detectar e quantificar os fenóis voláteis com este método, incluindo o 4-etilcatecol. O 4-etilfenol foi o composto mais abundante nos vinhos tintos comerciais estudados. ABSTRACT: The yeasts Dekkera I Brettanomyces are responsible for the formation of volatile phenols in red wine, becoming a major concern for the enological production worldwide because of the difficulty in controlling them. The volatile phenols are responsible for unpleasant aromas in red wines, reducing its quality and resulting in great economic lasses. The main objective of this work was to study a sample preparation and a chromatographic method to analyze main volatile phenols (4-ethylphenol, 4-ethylguaiacol, 4-ethylcatechol, 4-vinylphenol and 4-vinylguaiacol) in synthetic wine and red wines. Sample preparation was done by liquid-liquid extraction and compounds separation was achieved by gas chromatography with flame ionization detector (GC­ FID) Results showed that it is possible to detect and quantified volatile phenols with the methodology proposed, including 4-ethylcatechol. 4-ethylphenol was the main compound found in commercial red wines.

Unravelling the nanostructure of strawberry fruit pectins by atomic force microscopy

Atomic force microscopy (AFM) allows the analysis of individual polymers at nanostructural level with a minimal sample preparation. This technique has been used to analyse the pectin disassembly process during the ripening and postharvest storage of several fleshy fruits. In general, pectins analysed by AFM are usually visualized as isolated chains, unbranched or with a low number of branchs and, occasionally, as large aggregates. However, the exact nature of these structures is unknown. It has been suggested that pectin aggregates represent a mixture of rhamnonogalacturonan I and homogalacturonan, while isolated chains and their branches are mainly composed by polygalacturonic acid. In order to gain insight into the nature of these structures, sodium carbonate soluble pectins from ripe strawberry (Fragaria x ananassa, Duch.) fruits were subjected to enzymatic digestion with endo-Polygalacturonase M2 from Aspergillus aculeatus, and the samples visualized by AFM at different time intervals. Pectins isolated from control, non-transformed plants, and two transgenic genotypes with low level of expression of ripening-induced pectinase genes encoding a polygalacturonase (APG) or a pectate lyase (APEL) were also included in this study. Before digestion, isolated pectin chains from control were shorter than those from transgenic fruits, showing number-average (LN) contour length values of 73.2 nm vs. 95.9 nm and 91.4 nm in APG and APEL, respectively. The percentage of branched polymers was significantly higher in APG polyuronides than in the remaining genotypes, 33% in APG vs. 6% in control and APEL. As a result of the endo-PG treatment, a gradual decrease in the main backbone length of isolated chains was observed in the three samples. The minimum LN value was reached after 8 h of digestion, being similar in the three genotypes, 22 nm. By contrast, the branches were not visible after 1.5-2 h of digestion. LN values were plotted against digestion time and the data fitted to a first-order exponential decay curve, obtaining R2 values higher than 0.9. The half digestion time calculated with these equations were similar for control and APG pectins, 1.7 h, but significantly higher in APEL, 2.5 h, indicating that these polymer chains were more resistant to endo-PG digestion. Regarding the pectin aggregates, their volumes were estimated and used to calculate LN molecular weights. Before digestion, control and APEL samples showed complexes of similar molecular weights, 1722 kDa, and slightly higher than those observed in APG samples. After endo-PG digestion, size of complexes diminished significantly, reaching similar values in the three pectin samples, around 650 kDa. These results suggest that isolated polymer chains visualized by AFM are formed by a HG domain linked to a shorter polymer resistant to endo-PG digestion, maybe xylogalacturonan or RG-I. The silencing of the pectate lyase gene slightly modified the structure and/or chemical composition of polymer chains making these polyuronides more resistant to enzymatic degradation. Similarly, polygalacturonic acid is one of the main component of the aggregates.

Influence of shade, curing mode, and aging on the color stability of resin cements

The color stability of resin cements is essential for aesthetic restorations. Aim: To evaluate the influence of shade and aging time on the color stability of two light-cured and two dual-cured resin cements. Methods: The CIE-Lab color parameters (n=6) were measured immediately after sample preparation and at 7, 30 and 90 days of aging in distilled water. The color difference (ΔE) was calculated and then analyzed by three-way ANOVA for repeated measures and Tukey’s HSD test (α=0.05). Results: ΔE was higher for transparent resin colors, followed by dark and light colors. The mean values of ΔE were lower for both light-cured resin cements compared to the dual-cured cements. As the aging time increased, ΔE values increased. Conclusions: The light-cured resin cements showed greater color stability. The lighter shades of luting were more likely to display a greater color change.

Desenvolvimento de método para discriminação entre marcas de uísque e identificação de adulteração por espectroscopia UV-Vis e PLS-DA

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2015.

Photochemistry of 4-chlorophenol on cellulose and silica

The photochemistry of 4-chlorophenol (4-CP) was studied on silica and cellulose, using time-resolved diffuse reflectance techniques and product degradation analysis. The results have shown that the photochemistry of 4-CP depends on the support, on the concentration, and also on the sample preparation method. Transient absorption and photoproduct results can be understood by assuming the formation of the carbene 4-oxocyclohexa-2,5-dienylidene in both supports. On cellulose, at concentrations lower than 10 mumol g(-1), the carbene leads to the unsubstituted phenoxyl radical, and phenol is the main degradation product. At higher concentrations a new transient resulting from phenoxyl radicals coupling was also observed, and dihydroxybiphenyls are also formed. The reaction of the carbene with ground-state 4-CP was also detected through the formation of 5-chloro-2,4'-dihydroxybiphenyl. 4-Chlorophenoxyl radical and degradations products resulting from its coupling were also detected. Oxygen has little effect on the photochemistry of 4-CP on cellulose. On silica the transient benzoquinone O-oxide was formed in the presence of oxygen. Benzoquinone and hydroquinone are the main degradation products. In well-dried samples the formation of hydroquinone is reduced. At higher concentrations the same products as detected on cellulose were observed. 4-CP undergoes slow photochemical decomposition under solar radiation in both supports. The same main degradation products were observed in these conditions.

Libs in cultural heritage: recognition and identification of objects in an underwater archaeological shipwreck

Nowadays, one of the most important areas of interest in archeology is the characterization of the submersed cultural heritage. Mediterranean Sea is rich in archaeological findings due to storms, accidents and naval battles since prehistoric times. Chemical analysis of submerged materials is an extremely valuable source of information on the origin and precedence of the wrecks, and also the raw materials employed during the manufacturing of the objects found in these sites. Nevertheless, sometimes it is not possible to extract the archaeological material from the marine environment due to size of the sample, the legislation or preservation purposes. In these cases, the in-situ analysis turns into the only alternative for obtaining information. In spite of this demand, no analytical techniques are available for the in-situ chemical characterization of underwater materials. The versatility of laser-induced breakdown spectroscopy (LIBS) has been successfully tested in oceanography 1. Advantages such as rapid and in situ analysis with no sample preparation make LIBS a suitable alternative for field measurements. To further exploit the inherent advantages of the technology, a mobile fiber-based LIBS platform capable of performing remote measurements up to 50 meters range has been designed for the recognition and identification of artworks in underwater archaeological shipwrecks. The LIBS prototype featured both single-pulse (SP-LIBS) and multi-pulse excitation (MP-LIBS) 2. The use of multi-pulse excitation allowed an increased laser beam energy (up to 95 mJ) transmitted through the optical fiber. This excitation mode results in an improved performance of the equipment in terms of extended range of analysis (to a depth of 50 m) and a broader variety of samples to be analyzed (i.e., rocks, marble, ceramics and concrete). In the present work, the design and construction considerations of the instrument are reported and its performance is discussed on the basis of the spectral response, the remote irradiance achieved upon the range of analysis and its influence on plasma properties, as well as the effect of the laser pulse duration and purge gas to the LIBS signal. Also, to check the reliability and reproducibility of the instrument for field analysis several robustness tests were performed outside the lab. Finally, the capability of this instrument was successfully demonstrated in an underwater archaeological shipwreck (San Pedro de Alcántara, Malaga).

BARIUM CONCENTRATIONS IN ROCK SALT BY LASER INDUCED BREAKDOWN SPECTROSCOPY

Time-REsolved Laser Induced Breakdown Spectroscopy (TRELIBS) was used to determine the elemental concentration of barium in Texas Dome rock salt. TRELIBS allows for an efficient and in situ concentration analysis technique that detects a wide range of elements with no sample preparation. TRELIBS measurements were made in the 545nm to 594nm wavelength range. The proximity of a strong barium emission line (553.5481 nm) to the sodium doublet (588.9950 nm and 589.5924 nm) allowed for measurement within a single frame of the spectrograph. This barium emission line was compared to the sodium doublet for relative intensity. A homemade calibration sample containing known amounts of barium and sodium was used to determine the relative concentrations. By approximating the sodium content in the rock salt as 50%, we determined the absolute concentration of barium in the salt to be (0.13±0.03)%.

Elemental Analysis and Forensic Comparison of Soils by Laser-Induced Breakdown Spectroscopy (LIBS) and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS)

The elemental analysis of soil is useful in forensic and environmental sciences. Methods were developed and optimized for two laser-based multi-element analysis techniques: laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser-induced breakdown spectroscopy (LIBS). This work represents the first use of a 266 nm laser for forensic soil analysis by LIBS. Sample preparation methods were developed and optimized for a variety of sample types, including pellets for large bulk soil specimens (470 mg) and sediment-laden filters (47 mg), and tape-mounting for small transfer evidence specimens (10 mg). Analytical performance for sediment filter pellets and tape-mounted soils was similar to that achieved with bulk pellets. An inter-laboratory comparison exercise was designed to evaluate the performance of the LA-ICP-MS and LIBS methods, as well as for micro X-ray fluorescence (μXRF), across multiple laboratories. Limits of detection (LODs) were 0.01-23 ppm for LA-ICP-MS, 0.25-574 ppm for LIBS, 16-4400 ppm for µXRF, and well below the levels normally seen in soils. Good intra-laboratory precision (≤ 6 % relative standard deviation (RSD) for LA-ICP-MS; ≤ 8 % for µXRF; ≤ 17 % for LIBS) and inter-laboratory precision (≤ 19 % for LA-ICP-MS; ≤ 25 % for µXRF) were achieved for most elements, which is encouraging for a first inter-laboratory exercise. While LIBS generally has higher LODs and RSDs than LA-ICP-MS, both were capable of generating good quality multi-element data sufficient for discrimination purposes. Multivariate methods using principal components analysis (PCA) and linear discriminant analysis (LDA) were developed for discriminations of soils from different sources. Specimens from different sites that were indistinguishable by color alone were discriminated by elemental analysis. Correct classification rates of 94.5 % or better were achieved in a simulated forensic discrimination of three similar sites for both LIBS and LA-ICP-MS. Results for tape-mounted specimens were nearly identical to those achieved with pellets. Methods were tested on soils from USA, Canada and Tanzania. Within-site heterogeneity was site-specific. Elemental differences were greatest for specimens separated by large distances, even within the same lithology. Elemental profiles can be used to discriminate soils from different locations and narrow down locations even when mineralogy is similar.

Environmental scanning electron microscope imaging of vesicle systems

The structural characteristics of liposomes have been widely investigated and there is certainly a strong understanding of their morphological characteristics. Imaging of these systems, using techniques such as freeze-fracturing methods, transmission electron microscopy, and cryo-electron imaging, has allowed us to appreciate their bilayer structures and factors which can influence this. However, there are few methods which all us to study these systems in their natural hydrated state; commonly the liposomes are visualized after drying, staining, and/or fixation of the vesicles. Environmental Scanning Electron Microscopy (ESEM) offers the ability to image a liposome in its hydrated state without the need for prior sample preparation. Within our studies we were the first to use ESEM to study liposomes and niosomes and we have been able to dynamically follow the hydration of lipid films and changes in liposome suspensions as water condenses on to, or evaporates from, the sample in real time. This provides insight into the resistance of liposomes to coalescence during dehydration, thereby providing an alternative assay of liposome formulation and stability.

Automated flow-injection method for cadmium determination with pre-concentration and reagent preparation on-line

The spectrophotometric determination of Cd(II) using a flow injection system provided with a solid-phase reactor for cadmium preconcentration and on-line reagent preparation, is described. It is based on the formation of a dithizone-Cd complex in basic medium. The calibration curve is linear between 6 and 300 µg L-1 Cd(II), with a detection limit of 5.4 µg L-1, an RSD of 3.7% (10 replicates in duplicate) and a sample frequency of 11.4 h-1. The proposed method was satisfactorily applied to the determination of Cd(II) in surface, well and drinking waters.

Investigation of resins suitable for the preparation of biological sample for 3-D electron microscopy.

In the last two decades, the third-dimension has become a focus of attention in electron microscopy to better understand the interactions within subcellular compartments. Initially, transmission electron tomography (TEM tomography) was introduced to image the cell volume in semi-thin sections (∼500nm). With the introduction of the focused ion beam scanning electron microscope, a new tool, FIB-SEM tomography, became available to image much larger volumes. During TEM tomography and FIB-SEM tomography, the resin section is exposed to a high electron/ion dose such that the stability of the resin embedded biological sample becomes an important issue. The shrinkage of a resin section in each dimension, especially in depth, is a well-known phenomenon. To ensure the dimensional integrity of the final volume of the cell, it is important to assess the properties of the different resins and determine the formulation which has the best stability in the electron/ion beam. Here, eight different resin formulations were examined. The effects of radiation damage were evaluated after different times of TEM irradiation. To get additional information on mass-loss and the physical properties of the resins (stiffness and adhesion), the topography of the irradiated areas was analysed with atomic force microscopy (AFM). Further, the behaviour of the resins was analysed after ion milling of the surface of the sample with different ion currents. In conclusion, two resin formulations, Hard Plus and the mixture of Durcupan/Epon, emerged that were considerably less affected and reasonably stable in the electron/ion beam and thus suitable for the 3-D investigation of biological samples.

Preparation of a blood culture pellet for rapid bacterial identification and antibiotic susceptibility testing.

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections.

Ethyl Carbamate Analysis in German Fruit Spirits and Brazilian Sugarcane Spirits (Cachaca): Improved Sample Cleanup with Automated Parallel Evaporation

The analysis of alcoholic beverages for the important carcinogenic contaminant ethyl carbamate is very time-consuming and expensive. Due to possible matrix interferences, sample cleanup using diatomaceous earth (Extrelut) column is required prior to gas chromatographic and mass spectrometric measurement. A limiting step in this process is the rotary evaporation of the eluate containing the analyte in organic solvents, which is currently conducted manually and requires approximately 20-30 min per sample. This paper introduces the use of a parallel evaporation device for ethyl carbamate analysis, which allows for the simultaneous evaporation of 12 samples to a specified residual volume without manual intervention. A more efficient and, less expensive analysis is therefore possible. The method validation showed no differences between the fully-automated parallel evaporation and the manual operation. The applicability was proven by analyzing authentic spirit samples from Germany, Canada and Brazil. It is interesting to note that Brazilian cachacas had a relatively high incidence for ethyl carbamate contamination (55% of all samples were above 0.15 mg/l), which may be of public health relevance and requires further evaluation.

Cone-beam computed tomography analysis of the apical third of curved roots after mechanical preparation with different automated systems

The present study evaluated by cone-beam computed tomography (CBCT) the apical canal transportation and centralizing ability of different automated systems after root canal preparation. The mesiobuccal canals of maxillary first molars (n=10 per group) were prepared with: GI - reciprocating system with K-Flexofile; GII - reciprocating system with NiTiFlex files; GIII - rotary system with K3 instruments; GIV - rotary system with RaCe instruments. CBCT scans were taken before and after biomechanical preparation up to a #40.02 diameter. Canal transportation was determined by measuring the smallest distance between the inner canal walls and the mesial and distal sides of the root. The centralization ability corresponded to the difference between the measurements from transportation evaluation, using the linear voxel to voxel method of analysis. The mean transportation was 0.06 ± 0.14 mm, with a tendency to deviate to the mesial side of the root (n=22), with no statistically significant difference among the groups (p=0.4153). The mean centralization index was 0.15 ± 0.65 also without statistically significant difference among the groups (p=0.0881). It may be concluded that apical canal transportation and centralization ability were not influenced by the type of mechanical movement and instruments used.