The sample processing time interval as an influential factor in flow cytometry analysis of lymphocyte subsets

The objective of this paper is to propose a protocol to analyze blood samples in yellow fever 17DD vaccinated which developed serious adverse events. We investigated whether or not the time between sample collection and sample processing could interfere in lymphocyte subset percentage, for it is often impossible to analyze blood samples immediately after collection due to transport delay from collection places to the flow cytometry facility. CD4+CD38+ T, CD8+CD38+ T, CD3+ T, CD19+ B lymphocyte subsets were analyzed by flow cytometry in nine healthy volunteers immediately after blood collection and after intervals of 24 and 48 h. The whole blood lysis method and gradient sedimentation by Histopaque were applied to isolate peripheral blood mononuclear cells for flow cytometry analyses. With the lysis method, there was no significant change in lymphocyte subset percentage between the two time intervals (24 and 48 h). In contrast, when blood samples were processed by Histopaque gradient sedimentation, time intervals for sample processing influenced the percentage in T lymphocyte subsets but not in B cells. From the results obtained, we could conclude that the whole blood lysis method is more appropriate than gradient sedimentation by Histopaque for immunophenotyping of blood samples collected after serious adverse events, due to less variation in the lymphocyte subset levels with respect to the time factor.

Influence of sample processing on the analysis of carotenoids in maize

We performed a number of tests with the aim to develop an effective extraction method for the analysis of carotenoid content in maize seed. Mixtures of methanol–ethyl acetate (6:4, v/v) and methanol–tetrahydrofuran (1:1, v/v) were the most effective solvent systems for carotenoid extraction from maize endosperm under the conditions assayed. In addition, we also addressed sample preparation prior to the analysis of carotenoids by liquid chromatography (LC). The LC response of extracted carotenoids and standards in several solvents was evaluated and results were related to the degree of solubility of these pigments. Three key factors were found to be important when selecting a suitable injection solvent: compatibility between the mobile phase and injection solvent, carotenoid polarity and content in the matrix.

Evaluation of sample processing methods for the polar contaminant analysis of sewage sludge using liquid chromatography - mass spectrometry (LC/MS)

Monitoring of sewage sludge has proved the presence of many polar anthropogenic pollutants since LC/MS techniques came into routine use. While advanced techniques may improve characterizations, flawed sample processing procedures, however, may disturb or disguise the presence and fate of many target compounds present in this type of complex matrix before analytical process starts. Freeze-drying or oven-drying, in combination with centrifugation or filtration as sample processing techniques were performed followed by visual pattern recognition of target compounds for assessment of pretreatment processes. The results shown that oven-drying affected the sludge characterization, while freeze-drying led to less analytical misinterpretations.

From Sample Processing to Quantification: A Full Electrochemical Approach for Neutral Analyte Derivatization, Capillary Electrophoresis Separation, and Contactless Conductivity Detection

A thin-layer electrochemical flow cell coupled to capillary electrophoresis with contactless conductivity detection (EC-CE-(CD)-D-4) was applied for the first time to the derivatization and quantification of neutral species using aliphatic alcohols as model compounds. The simultaneous electrooxidation of four alcohols (ethanol, 1-propanol, 1-butanol, and 1-pentanol) to the corresponding carboxylates was carried out on a platinum working electrode in acid medium. The derivatization step required 1 min at 1.6 V vs. Ag/AgCl under stopped flow conditions, which was preceded by a 10 s activation at 0 V. The solution close to the electrode surface was then hydrodynamically injected into the capillary, and a 2.5 min electrophoretic separation was carried out. The fully automated flow system operated at a frequency of 12 analyses per hour. Simultaneous determination of the four alcohols presented detection limits of about 5 x 10(-5) mol As a practical application with a complex matrix, ethanol concentrations were determined in diluted pale lager beer and in nonalcoholic beer. No statistically significant difference was observed between the EC-CE-(CD)-D-4 and gas chromatography with flame ionization detection (GC-FID) results for these samples. The derivatization efficiency remained constant over several hours of continuous operation with lager beer samples (n = 40).

Use of selective medium for Burkholderia cepacia isolation in respiratory samples from cystic fibrosis patients

Burkholderia cepacia colonizes cystic fibrosis (CF) patients. We evaluated the impact of the use of a selective medium in the rate of B. cepacia recovery from respiratory samples of CF patients. During a 6-month period, respiratory samples were collected from 106 CF patients and cultivated on selective media including a B. cepacia selective medium. Confirmation of the identity of B. cepacia isolates was carried out by species specific PCR and determination of genomovar status performed by a sequential PCR approach. Results of B. cepacia isolation during this period were compared to the preceding two years, when the sample processing was identical except for the lack of the B. cepacia selective medium. B. cepacia was isolated in 11/257 (4.2%) of the samples using the selective medium, in contrast with the preceding two years, when it was isolated in 6/1029 samples (0.58%), p < 0.0001. Identity of all 11 isolates was confirmed by PCR and genomovar determination was accomplished in all but one isolate. These results suggest that the use of a selective medium increases recovery rate of B. cepacia from respiratory samples.

Recommendations for the detection of Leptospira in urine by PCR

In the present study PCR was applied to detect leptospires in human urine. Several approaches for sample processing were evaluated to optimize the detection of leptospires in urine mixed with this bacterium. Furthermore, some changes in the composition of the reaction mix were studied. No amplification was observed in acidic urine, therefore neutralization of the sample immediately after collection is strongly recommended. PBS gave better results than Tris or NaOH as neutralizing reagents. Freezing and thawing of samples before processing yielded negative results. Elimination of epithelial cells, leukocytes and crystals by centrifugation at 3,000 rpm at room temperature increased sensitivity. In addition, both the washing step after collecting leptospires by centrifugation and the inclusion of 0.1% bovine serum albumin in the reaction mix minimized the interference of other inhibitory compounds. These modifications were useful to improve the detection of Leptospira in urine by PCR.

Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.

Evaluation of four molecular methods for the diagnosis of tuberculosis in pulmonary and blood samples from immunocompromised patients

The present study analysed the concordance among four different molecular diagnostic methods for tuberculosis (TB) in pulmonary and blood samples from immunocompromised patients. A total of 165 blood and 194 sputum samples were collected from 181 human immunodeficiency virus (HIV)-infected patients with upper respiratory complaints, regardless of suspicious for TB. The samples were submitted for smear microscopy, culture and molecular tests: a laboratory-developed conventional polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR) and the Gen-Probe and Detect-TB Ampligenix kits. The samples were handled blindly by all the technicians involved, from sample processing to results analysis. For sputum, the sensitivity and specificity were 100% and 96.7% for qPCR, 81.8% and 94.5% for Gen-Probe and 100% and 66.3% for Detect-TB, respectively. qPCR presented the best concordance with sputum culture [kappa (k) = 0.864)], followed by Gen-Probe (k = 0.682). For blood samples, qPCR showed 100% sensitivity and 92.3% specificity, with a substantial correlation with sputum culture (k = 0.754) and with the qPCR results obtained from sputum of the corresponding patient (k = 0.630). Conventional PCR demonstrated the worst results for sputa and blood, with a sensitivity of 100% vs. 88.9% and a specificity of 46.3% vs. 32%, respectively. Commercial or laboratory-developed molecular assays can overcome the difficulties in the diagnosis of TB in paucibacillary patients using conventional methods available in most laboratories.

Simultaneous detection of the C282Y, H63D and S65C mutations in the hemochromatosis gene using quenched-FRET real-time PCR

Hereditary hemochromatosis (HH) is a common autosomal disorder of iron metabolism mainly affecting Caucasian populations. Three recurrent disease-associated mutations have been detected in the hemochromatosis gene (HFE): C282Y, H63D, and S65C. Although HH phenotype has been associated with all three mutations, C282Y is considered the most relevant mutation responsible for hemochromatosis. Clinical complications of HH include cirrhosis of the liver, congestive cardiac failure and cardiac arrhythmias, endocrine pancreatic disease, which can be prevented by early diagnosis and treatment. Therefore, a reliable genotyping method is required for presymptomatic diagnosis. We describe the simultaneous detection of the C282Y, H63D and S65C mutations in the hemochromatosis gene by real-time PCR followed by melting curve analysis using fluorescence resonance energy transfer (FRET) probes. The acceptor fluorophore may be replaced by a quencher, increasing multiplex possibilities. Real-time PCR results were compared to the results of sequencing and conventional PCR followed by restriction digestion and detection by agarose gel electrophoresis (PCR-RFLP). Genotypes from 80 individuals obtained both by the conventional PCR-RFLP method and quenched-FRET real-time PCR were in full agreement. Sequencing also confirmed the results obtained by the new method, which proved to be an accurate, rapid and cost-effective diagnostic assay. Our findings demonstrate the usefulness of real-time PCR for the simultaneous detection of mutations in the HFE gene, which allows a reduction of a significant amount of time in sample processing compared to the PCR-RFLP method, eliminates the use of toxic reagents, reduces the risk of contamination in the laboratory, and enables full process automation.

Analyse par spectrométrie de masse des antibiotiques vétérinaires liés à l’élevage porcin

L’élevage des porcs représente une source importante de déversement d’antibiotiques dans l’environnement par l’intermédiaire de l’épandage du lisier qui contient une grande quantité de ces molécules sur les champs agricoles. Il a été prouvé que ces molécules biologiquement actives peuvent avoir un impact toxique sur l’écosystème. Par ailleurs, elles sont aussi suspectées d’engendrer des problèmes sanitaires et de contribuer à la résistance bactérienne pouvant mener à des infections difficilement traitables chez les humains. Le contrôle de ces substances dans l’environnement est donc nécessaire. De nombreuses méthodes analytiques sont proposées dans la littérature scientifique pour recenser ces composés dans plusieurs types de matrice. Cependant, peu de ces méthodes permettent l’analyse de ces contaminants dans des matrices issues de l’élevage agricole intensif. Par ailleurs, les méthodes analytiques disponibles sont souvent sujettes à des faux positifs compte tenu de la complexité des matrices étudiées et du matériel utilisé et ne prennent souvent pas en compte les métabolites et produits de dégradation. Enfin, les niveaux d’analyse atteints avec ces méthodes ne sont parfois plus à jour étant donné l’évolution de la chimie analytique et de la spectrométrie de masse. Dans cette optique, de nouvelles méthodes d’analyses ont été développées pour rechercher et quantifier les antibiotiques dans des matrices dérivées de l’élevage intensif des porcs en essayant de proposer des approches alternatives sensibles, sélectives et robustes pour quantifier ces molécules. Une première méthode d’analyse basée sur une technique d’introduction d’échantillon alternative à l’aide d’une interface fonctionnant à l’aide d’une désorption thermique par diode laser munie d’une source à ionisation à pression atmosphérique, couplée à la spectrométrie de masse en tandem a été développée. L’objectif est de proposer une analyse plus rapide tout en atteignant des niveaux de concentration adaptés à la matrice étudiée. Cette technique d’analyse couplée à un traitement d’échantillon efficace a permis l’analyse de plusieurs antibiotiques vétérinaires de différentes classes dans des échantillons de lisier avec des temps d’analyse courts. Les limites de détection atteintes sont comprises entre 2,5 et 8,3 µg kg-1 et sont comparables avec celles pouvant être obtenues avec la chromatographie liquide dans une matrice similaire. En vue d’analyser simultanément une série de tétracyclines, une deuxième méthode d’analyse utilisant la chromatographie liquide couplée à la spectrométrie de masse à haute résolution (HRMS) a été proposée. L’utilisation de la HRMS a été motivée par le fait que cette technique d’analyse est moins sensible aux faux positifs que le triple quadripôle traditionnel. Des limites de détection comprises entre 1,5 et 3,6 µg kg-1 ont été atteintes dans des échantillons de lisier en utilisant un mode d’analyse par fragmentation. L’utilisation de méthodes de quantifications ciblées est une démarche intéressante lorsque la présence de contaminants est suspectée dans un échantillon. Toutefois, les contaminants non intégrés à cette méthode d’analyse ciblée ne peuvent être détectés même à de fortes concentrations. Dans ce contexte, une méthode d’analyse non ciblée a été développée pour la recherche de pharmaceutiques vétérinaires dans des effluents agricoles en utilisant la spectrométrie de masse à haute résolution et une cartouche SPE polymérique polyvalente. Cette méthode a permis l’identification d’antibiotiques et de pharmaceutiques couramment utilisés dans l’élevage porcin. La plupart des méthodes d’analyse disponibles dans la littérature se concentrent sur l’analyse des composés parents, mais pas sur les sous-produits de dégradation. L’approche utilisée dans la deuxième méthode d’analyse a donc été étendue et appliquée à d’autres classes d’antibiotiques pour mesurer les concentrations de plusieurs résidus d’antibiotiques dans les sols et les eaux de drainage d’un champ agricole expérimental. Les sols du champ renfermaient un mélange d’antibiotiques ainsi que leurs produits de dégradation relatifs à des concentrations mesurées jusqu’à 1020 µg kg-1. Une partie de ces composés ont voyagé par l’intermédiaire des eaux de drainage du champ ou des concentrations pouvant atteindre 3200 ng L-1 ont pu être relevées.

Multiplexed quantitative proteomics using differential metabolic 15N-labeling

There are several advantages of using metabolic labeling in quantitative proteomics. The early pooling of samples compared to post-labeling methods eliminates errors from different sample processing, protein extraction and enzymatic digestion. Metabolic labeling is also highly efficient and relatively inexpensive compared to commercial labeling reagents. However, methods for multiplexed quantitation in the MS-domain (or ‘non-isobaric’ methods), suffer from signal dilution at higher degrees of multiplexing, as the MS/MS signal for peptide identification is lower given the same amount of peptide loaded onto the column or injected into the mass spectrometer. This may partly be overcome by mixing the samples at non-uniform ratios, for instance by increasing the fraction of unlabeled proteins. We have developed an algorithm for arbitrary degrees of nonisobaric multiplexing for relative protein abundance measurements. We have used metabolic labeling with different levels of 15N, but the algorithm is in principle applicable to any isotope or combination of isotopes. Ion trap mass spectrometers are fast and suitable for LC-MS/MS and peptide identification. However, they cannot resolve overlapping isotopic envelopes from different peptides, which makes them less suitable for MS-based quantitation. Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry is less suitable for LC-MS/MS, but provides the resolving power required to resolve overlapping isotopic envelopes. We therefore combined ion trap LC-MS/MS for peptide identification with FTICR LC-MS for quantitation using chromatographic alignment. We applied the method in a heat shock study in a plant model system (A. thaliana) and compared the results with gene expression data from similar experiments in literature.

Identification of the nuclear factor kappa-beta (NF-kB) in cortical of mice Wistar using Technovit 7200 VCR (R)

Objective: this study aimed to develop a nondecalcified bone sample processing technique enabling immunohistochemical labeling of proteins by kappa-beta nuclear factor (NF-kB) utilizing the Technovit 7200 VCR (R) in adult male Wistar rats. Study Method: A 1.8 mm diameter defect was performed 0.5mm from the femur proximal joint by means of a round bur. Experimental groups were divided according to fixing solution prior to histologic processing: Group 1- ethanol 70%; Group 2-10% buffered formalin; and Group 3- Glycerol diluted in 70% ethanol at a 70/30 ratio + 10% buffered formalin. The post-surgical periods ranged from 01 to 24 hours. Control groups included a nonsurgical procedure group (NSPG) and surgical procedures where bone exposure was performed (SPBE) without drilling. Prostate carcinoma was the positive control (PC) and samples subjected to incomplete immunohistochemistry protocol were the negative control (NC). Following euthanization, all samples were kept at 4 degrees C for 7 days, and were dehydrated in a series of alcohols at -20 degrees C. The polymer embedding procedure was performed at ethanol/polymer ratios of 70%-30%, 50%-50%, 30%-70%, 100%, and 100% for 72 hours at -20 degrees C. Polymerization followed the manufacturer`s recommendation. The samples were grounded and polished to 10-15 mu m thickness, and were deacrylated. The sections were rehydrated and were submitted to the primary polyclonal antibody anti-NF-kB on a 1:75 dilution for 12 hours at room temperature. Results: Microscopy showed that the Group 2 presented positive reaction to NF-kB, diffuse reactions for NSPG and SPBE, and no reaction for the NC group. Conclusion: The results obtained support the feasibility of the developed immunohistochemistry technique.

Ultrastructural morphology and morphometry of the normal corneal endothelium of adult crossbred pig

O endotélio corneal é uma monocamada de células poligonais. A integridade e saúde dessa camada são essenciais para a manutenção da transparência corneal normal. Este estudo reportou pela primeira vez, de forma detalhada, a morfologia ultra-estrutural e a morfometria do endotélio corneal de suínos adultos mestiços à microscopia eletrônica de varredura (MEV). A superfície endothelial corneal apresentou um padrão regular de células poligonais, com predomínio da forma hexagonal e de bordas celulares nítidas. O núcleo foi observado como protuberância arredondada no centro da célula. Também foram observados os cílios (2-4) em apenas algumas células da região periférica da córnea, as aberturas das vesículas pinocitóticas na proximidade dos cílios, as microvilosidades, as varas da borda e as bordas celulares em formato de zigzag. A área celular média foi significativamente maior (P<0,05) no centro da córnea do que na periferia, com um coeficiente de variação menor no centro da córnea. A densidade celular média foi significativamente maior na periferia (P<0,05) e 43,9% maior que os dados reportados por outros autores na microscopia especular, o que demonstra o efeito da retração celular durante o processamento das amostras. O valor médio do número de lados das células (pleomorfismo) foi de 5,9, o que evidencia um predomínio do formato hexagonal. A percentagem de células hexagonais foi significativamente maior no centro (P<0,001). Os parâmetros obtidos nesta pesquisa servirão de base para estudos futuros sobre o efeito de medicamentos, cirurgias intracamerulares ou soluções para armazenamento de córneas para transplantes no endotélio corneal do suíno.

Evaluation of different protocols for anatomical studies in Parmeliaceae (lichenized Ascomycota)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo morfológico e imunológico da encefalite induzida pelo vírus juruaçá em modelo murino

Muitos estudos têm sido realizados para o entendimento da neuropatogênese das encefalites virais a partir de trabalhos experimentais, porém, nenhum estudo experimental foi dedicado à compreensão da neuropatogênese de membros da família Picornaviridae isolados de morcegos na região amazônica. O vírus Juruaçá, um desses agentes, parcialmente caracterizado como membro da família Picornaviridae por Araújo e colaboradores (2006), causou lesões no encéfalo de camundongos neonatos com presença de gliose reativa, apesar de não provocar efeito citopático (ECP) em cultivos primários de células do sistema nervoso central (SNC), sugerindo que este agente viral seja responsável pela morte dos animais devido a uma intensa resposta imune. O objetivo desse trabalho foi investigar a resposta imune no SNC e alterações celulares causadas pelo vírus Juruaçá em camundongos albinos da linhagem BALB/c neonatos a partir de análises histopatológicas, de ativação microglial e da expressão de citocinas, óxido nítrico (NO) e espécies reativas de oxigênio (ROS). Para tanto, foram realizados processamento de amostras para histopatologia, ensaios imunoenzimáticos, imunohistoquímicos e de imunofluorescência, além de testes para quantificação de NO e ROS e análises estatísticas. Nossos resultados demonstraram que o vírus Juruaçá induz lesões por todo o encéfalo, com maior intensidade no parênquima cortical. Os testes imunohistoquímicos demonstraram a presença de antígenos virais e de micróglias reativas distribuídos por todo o encéfalo e região anterior da medula espinhal. Micróglias com aspecto ameboide, demonstrando intensa ativação, foram observadas principalmente no córtex cerebral, bulbo olfatório, núcleo olfatório anterior, prosencéfalo e diencéfalo próximo ao ventrículo lateral. A produção das citocinas anti-inflamatórias (IL-10, IL-4) diminuiu ao longo do tempo, enquanto que as pró-inflamatórias (IL-12, IL-6, IL-1β, TNF-α, IFN-γ) aumentaram significativamente a partir do 8º dia. Os ensaios para detecção de ROS demonstraram grande produção de radicais superóxido desde o 4º dia, já a produção de NO foi sempre menor nos animais infectados. Provavelmente, a ativação das células gliais, principalmente micróglias, e consequente produção de citocinas pró-inflamatórias e ROS promoveram uma ação devastadora sobre as células do SNC, que coincide com a intensificação dos sinais clínicos. Diante do exposto, ficou evidente que os nossos resultados indicam que o vírus Juruaçá é responsável por uma doença de cunho inflamatório que leva a óbito 100% de camundongos neonatos infectados.