Advances in microbial diagnosis: using mass spectrometry for proteomics and genomics applications

Since the last two decades mass spectrometry (MS) has been applied to analyse the chemical cellular components of microorganisms, providing rapid and discriminatory proteomic profiles for their species identification and, in some cases, subtyping. The application of MS for the microbial diagnosis is currently well-established. The remarkable reproducibility and objectivity of this method is based on the measurement of constantly expressed and highly abundant proteins, mainly important conservative ribosomal proteins, which are used as markers to generate a cellular fingerprint. Mass spectrometry based on matrix-assisted laser desorption ionization-time of flight (MALDI- TOF) technique has been an important tool for the microbial diagnostic. However, some technical limitation concerning both MALDI-TOF and its used protocols for sample preparation have fostered the research of new mass spectrometry systems (e.g. LC MS/MS). LC MS/MS is able to generate online mass spectra of specific ions with further online sequencing of these ions, which include both specific proteins and DNA fragments. In this work a set of data for yeasts and filamentous fungi diagnostic obtained through an international collaboration project involving partners from Argentina, Brazil, Chile and Portugal will be presented and discussed.

Titanium oxide adhesion layer for high temperature annealed Si/Si3N4/TiOx/Pt/LiCoO2 battery structures

This work describes the influence of a high annealing temperature of about 700C on the Si(substrate)/Si3N4/TiOx/Pt/LiCoO2 multilayer system for the fabrication of all-solid-state lithium ion thin film microbatteries. Such microbatteries typically utilize lithium cobalt oxide (LiCoO2) as cathode material with a platinum (Pt) current collector. Silicon nitride (Si3N4) is used to act as a barrier against Li diffusion into the substrate. For a good adherence between Si3N4 and Pt, commonly titanium (Ti) is used as intermediate layer. However, to achieve crystalline LiCoO2 the multilayer system has to be annealed at high temperature. This post-treatment initiates Ti diffusion into the Pt-collector and an oxidation to TiOx, leading to volume expansion and adhesion failures. To solve this adhesion problem, we introduce titanium oxide (TiOx) as an adhesion layer, avoiding the diffusion during the annealing process. LiCoO2, Pt and Si3N4 layers were deposited by magnetron sputtering and the TiOx layer by thermal oxidation of Ti layers deposited by e-beam technique. Asdeposited and annealed multilayer systems using various TiOx layer thicknesses were studied by scanning electron microscopy (SEM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) and x-ray photoelectron spectroscopy (XPS). The results revealed that an annealing process at temperature of 700C leads to different interactions of Ti atoms between the layers, for various TiOx layer thicknesses (25–45 nm).

New insights in carbohydrate-deficient transferrin analysis with capillary electrophoresis-mass spectrometry

Capillary zone electrophoresis (CZE) with UV detection has been widely used for the determination of carbohydrate-deficient transferrin (CDT), an indirect marker of the chronic alcohol consumption (≥60-80g/day). A commercially available method (CEofix? CDT kit), containing a bilayer anionic coating, allows for the analysis of CDT with a high resolution between transferrin (Tf) glycoforms with reduced protein adsorption onto the capillary wall. Although widely used in routine analysis, this procedure presents some limitations in terms of selectivity and sensitivity which may be overcome with mass spectrometry (MS). However, the available method is not MS-compatible due to the non-volatile coating as well as the phosphate and borate buffers present in the background electrolyte (BGE). This study firstly consisted in developing MS-compatible separation conditions, i.e., coating and BGE compositions. Numerous cationic, neutral, and anionic coatings were evaluated in combination with BGEs covering a broad range of pH values. A bilayer coating composed of a cationic layer of 10% polybrene (m/v) and an anionic layer of 10% dextran sulfate (m/v) combined with a BGE composed of 20mM ammonium acetate at pH 8.5 provided the best results in terms of glycoforms' resolution, efficiency, adsorption reduction, migration times' repeatability, and coating stability. The method was then transferred to CZE-MS after investigations of the electrospray ionization (ESI) source, equipped with a sheath-flow interface, and the time-of-flight (TOF/MS) parameters. A successful MS detection of tetrasialo-Tf was obtained during infusion, while the experiments highlighted the challenges and issues encountered with intact glycoprotein analysis by CZE-ESI-MS.

Pairing in a two-component ultracold Fermi gas: Phases with broken-space symmetries

We explore the phase diagram of a two-component ultracold atomic Fermi gas interacting with zero-range forces in the limit of weak coupling. We focus on the dependence of the pairing gap and the free energy on the variations in the number densities of the two species while the total density of the system is held fixed. As the density asymmetry is increased, the system exhibits a transition from a homogenous Bardeen-Cooper-Schrieffer (BCS) phase to phases with spontaneously broken global space symmetries. One such realization is the deformed Fermi surface superfluidity (DFS) which exploits the possibility of deforming the Fermi surfaces of the species into ellipsoidal form at zero total momentum of Cooper pairs. The critical asymmetries at which the transition from DFS to the unpaired state occurs are larger than those for the BCS phase. In this precritical region the DFS phase lowers the pairing energy of the asymmetric BCS state. We compare quantitatively the DFS phase to another realization of superconducting phases with broken translational symmetry: the single-plane-wave Larkin-Ovchinnikov-Fulde-Ferrell phase, which is characterized by a nonvanishing center-of-mass momentum of the Cooper pairs. The possibility of the detection of the DFS phase in the time-of-flight experiments is discussed and quantified for the case of 6Li atoms trapped in two different hyperfine states.

A steroidomic approach for biomarkers discovery in doping control.

Anti-doping authorities have high expectations of the athlete steroidal passport (ASP) for anabolic-androgenic steroids misuse detection. However, it is still limited to the monitoring of known well-established compounds and might greatly benefit from the discovery of new relevant biomarkers candidates. In this context, steroidomics opens the way to the untargeted simultaneous evaluation of a high number of compounds. Analytical platforms associating the performance of ultra-high pressure liquid chromatography (UHPLC) and the high mass-resolving power of quadrupole time-of-flight (QTOF) mass spectrometers are particularly adapted for such purpose. An untargeted steroidomic approach was proposed to analyse urine samples from a clinical trial for the discovery of relevant biomarkers of testosterone undecanoate oral intake. Automatic peak detection was performed and a filter of reference steroid metabolites mass-to-charge ratio (m/z) values was applied to the raw data to ensure the selection of a subset of steroid-related features. Chemometric tools were applied for the filtering and the analysis of UHPLC-QTOF-MS(E) data. Time kinetics could be assessed with N-way projections to latent structures discriminant analysis (N-PLS-DA) and a detection window was confirmed. Orthogonal projections to latent structures discriminant analysis (O-PLS-DA) classification models were evaluated in a second step to assess the predictive power of both known metabolites and unknown compounds. A shared and unique structure plot (SUS-plot) analysis was performed to select the most promising unknown candidates and receiver operating characteristic (ROC) curves were computed to assess specificity criteria applied in routine doping control. This approach underlined the pertinence to monitor both glucuronide and sulphate steroid conjugates and include them in the athletes passport, while promising biomarkers were also highlighted.

SARM-S4 and metabolites detection in sports drug testing: a case report.

Recently, pharmaceutical industry developed a new class of therapeutics called Selective Androgen Receptor Modulator (SARM) to substitute the synthetic anabolic drugs used in medical treatments. Since the beginning of the anti-doping testing in sports in the 1970s, steroids have been the most frequently detected drugs mainly used for their anabolic properties. The major advantage of SARMs is the reduced androgenic activities which are the main source of side effects following anabolic agents' administration. In 2010, the Swiss laboratory for doping analyses reported the first case of SARMs abuse during in-competition testing. The analytical steps leading to this finding are described in this paper. Screening and confirmation results were obtained based on liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses. Additional information regarding the SARM S-4 metabolism was investigated by ultra high-pressure liquid chromatography coupled to quadrupole time-of-flight mass spectrometer (UHPLC-QTOF-MS).

A simple, robust and rapid approach to detect carbapenemases in Gram-negative isolates by MALDI-TOF mass spectrometry: validation with triple quadripole tandem mass spectrometry, microarray and PCR.

Carbapenemases should be accurately and rapidly detected, given their possible epidemiological spread and their impact on treatment options. Here, we developed a simple, easy and rapid matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)-based assay to detect carbapenemases and compared this innovative test with four other diagnostic approaches on 47 clinical isolates. Tandem mass spectrometry (MS-MS) was also used to determine accurately the amount of antibiotic present in the supernatant after 1 h of incubation and both MALDI-TOF and MS-MS approaches exhibited a 100% sensitivity and a 100% specificity. By comparison, molecular genetic techniques (Check-MDR Carba PCR and Check-MDR CT103 microarray) showed a 90.5% sensitivity and a 100% specificity, as two strains of Aeromonas were not detected because their chromosomal carbapenemase is not targeted by probes used in both kits. Altogether, this innovative MALDI-TOF-based approach that uses a stable 10-μg disk of ertapenem was highly efficient in detecting carbapenemase, with a sensitivity higher than that of PCR and microarray.

Interhospital aeromedical transfers: need for a specific training

Introduction: The interhospital aeromedical transfers concern mainly unstable patients presenting with multiple organ failure and among whom the intensity, as well as the difficulty of care are often underestimated. Material and method: Retrospective analysis of 2094 interhospital transfers made by the Rega helicopter of Lausanne between 2003 and 2008, with description of the pathologies, the demographic characteristics, as well as the medical and technical difficulties. Results: Male patient are overrepresented (65 vs 35%), their age being 40-80 years old. On the other hand, we note an important number (10%) of patients less than 10 years. The average time of flight is 13 minutes, with a high rate of night transfers (34%). In 73% of the cases, the transfers concern medical, especially cardiovascular and neurological situations. Trauma and surgical situations account for less than 20%. The transferred patients often require mechanical ventilation (27%), as well as invasive measure of blood pressure (11%), particularly in cases of neurological, pulmonary or cardiac diseases. In 6% of the cases, we note a haemodynamic instability, requiring the use of catecholamines. In 1% a cardiopulmonary resuscitation was initiated during the flight. The overall mortality at 48 hours is about 5%. Conclusions: In spite of relatively brief flights, the complexity and the variety of the pathologies require a specific training for the medical teams involved in the transfers, concerning the aspects of resuscitation, mechanical ventilation, and the knowledge of advanced life support in paediatrics, traumatology and cardiopulmonary intensive care.

Angiografia por ressonância magnética: aspectos técnicos de um método de estudo vascular não-invasivo

As primeiras técnicas de angiografia por ressonância magnética (angio-RM) utilizavam seqüências sensíveis ao fluxo sanguíneo para estabelecimento do contraste vascular. Há três técnicas fundamentadas neste princípio: contraste de fase ("phase-contrast"), TOF ("time-of-flight") e as técnicas de sangue escuro ("black blood"). Estas seqüências, de aquisição demorada, são mais suscetíveis a artefatos de movimento, perda de sinal em áreas de estenoses ou turbilhonamento de fluxo, e apresentam ainda baixa sensibilidade à detecção do fluxo lento. O uso do contraste paramagnético para estudos angiográficos pela ressonância magnética ofereceu um método simples, rápido e de excelente detalhamento vascular, baseando o contraste da imagem no realce do sinal vascular em oposição à supressão dos demais tecidos. Metodologias modernas que priorizam a obtenção do espaço k central, responsável pelo contraste da imagem, e o aperfeiçoamento das técnicas de planejamento do intervalo temporal para aquisição dos dados foram fatores fundamentais para o aprimoramento técnico da angio-RM. O papel atual da angio-RM como ferramenta diagnóstica merece destaque na avaliação de anomalias anatômicas, estenoses, oclusões e complicações vasculares pós-cirúrgicas, principalmente nos casos de transplantes de órgãos. Suas principais vantagens estão na não utilização do contraste iodado ou radiação ionizante, rapidez e fácil execução, mínima invasividade e possibilidade de avaliar complementarmente o parênquima de órgãos adjacentes de interesse diagnóstico.

Avaliação da aterosclerose carotídea por intermédio de ultra-sonografia e ressonância magnética

OBJETIVO: Identificar ateromas carotídeos em coronariopatas com indicação de terapia cirúrgica. Avaliar o grau de estenose das artérias carótidas internas por meio de ultra-sonografia com Doppler colorido (UDC) e angiografia por ressonância magnética (ARM). Comparar a ecogenicidade das placas visualizadas pela ultra-sonografia (US), com a intensidade de sinal nos exames de ressonância magnética (RM). Avaliar a qualidade de imagens e confiabilidade interobservadores nos exames de RM. MATERIAIS E MÉTODOS: Estudo prospectivo em 50 pacientes. Utilizamos US e RM em seqüências ponderadas em T1 e T2, ambas pelas técnicas "black-blood" (BB) e "fat sat black-blood" (FSBB), e ARM 3D TOF ("time-of-flight'') com e sem contraste paramagnético. RESULTADOS: Do total de 100 segmentos, 81% apresentaram estenose pela US. Em 72 placas com ecogenicidade tipo 4 houve aumento da intensidade de sinal em 59,7% em T1-BB, 65,3% em T1-FSBB, 62,5% em T2-BB e 66,7% em T2-FSBB. Nas placas tipo 2 houve aumento da intensidade de sinal em 71,4% em T1-BB e T1-FSBB, 85,7% em T2-BB e 71,4% em T2-FSBB. Nas placas tipo 1 houve aumento da intensidade de sinal em 50,0% em T1 e T2. Em 19 segmentos a US foi considerada normal. Quando estes segmentos foram avaliados pela RM, houve aumento da intensidade de sinal em 47,4% em T1-BB, 57,9% em T1-FSBB e 52,6% em T2-BB e T2-FSBB. CONCLUSÃO: Houve alta incidência de aterosclerose carotídea. Houve reprodutibilidade marginal na associação entre o grau de estenose visualizado pela UDC e ARM. Não houve correlação entre os tipos de ecogenicidade das placas visualizadas pela US com as alterações de intensidade de sinal pela RM. A qualidade de imagens dos exames de RM foi considerada ótima em T1 e T2 e muito boa em 3D TOF (axial). A qualidade de imagem dos exames de ARM foi excelente. Notou-se ótima reprodutibilidade interobservadores, com valores de índice kappa acima de 0,71.

Agenesia da artéria carótida interna: relato de caso

Relata-se, aqui, caso de uma adolescente de 14 anos de idade que apresentou episódio isolado de síncope, sem outros sintomas. No exame de ressonância magnética observou-se, nos cortes nos planos axial e coronal ponderados em T2, ausência do flow void da artéria carótida interna direita na sua porção intracavernosa. Realizou-se, então, angiorressonância magnética técnica time-of-flight, que mostrou ausência da artéria carótida interna direita, o que foi comprovado com a angiorressonância magnética de vasos cervicais e com angiotomografia computadorizada, que mostrou, nos cortes axiais, agenesia do canal carotídeo direito. Tal achado é relatado na literatura, em associação com outras anomalias, como encefaloceles transesfenoidais e aneurismas do polígono de Willis. No presente caso, não foram observadas tais associações. A paciente permaneceu assintomática.

Fragmentação de moléculas pela luz síncrotron e por elétrons rápidos. I. O caso do halotano, C2F3HClBr

The photofragmentation of a core-excited halogenated compound, Halotane (C2F3HClBr), generally used as anesthetic by inhalation, has been studied using high energy photons and electrons near C 1s ionization edge (~ 300 eV), using time-of-flight mass spectrometry in multicoincidence mode. We observe strong differences between the molecular fragmentation induced by photons and electron impact.

Um espectômetro de massas de tempo-de-vôo para o estudo da ionização de amostras gasosas por elétrons rápidos (0,5 - 1,0 keV)

A simple and inexpensive time-of-flight mass spectrometer, dedicated to the study of gas-phase ionization processes induced by high energy electrons (0.5 - 3.0 keV), is described. The spectrometer design is based on the Wiley-McLaren principle, with a total length of about 18 cm. As a demonstration of the performance of the apparatus, mass spectra for Ar, CH4, CO2, and SF6, obtained at 1 keV electron energy, are presented.

Irradiação de polímeros com feixe de elétrons: caracterização de íons positivos através da técnica de tempo-de-vôo

With the aim of studying the interaction of fast electrons with solid surfaces we have developed an experimental set-up based on electron stimulated desorption (ESD) coupled to time-of-flight (TOF) mass spectrometry. Poly(methyl methacrylate) and poly(vynil chloride) samples have been irradiated by a pulsed electron beam of 1.2 keV and 0.18 µs FWHM. The results show that H+ is the main ionic species to desorb after electron bombardment. In addition, other ionic fragments were also observed and assigned. These results show the potentiality of this technique in the study of ESD of polymers.