A green-footprint approach for parallel multiclass analysis of contaminants in roasted coffee via LC-HRMS.

The development and validation of a simple, comprehensive, and environment-friendly procedure to determine pesticide residues, naturally occurring and processing contaminants in roasted coffee is presented. A solid-liquid extraction of pesticides and mycotoxins with ethyl acetate and the concurrent partition of acrylamide to an aqueous phase follows a parallel analytical strategy that requires a single analytical portion to determine contaminants that are typically analyzed by dedicated single residue methods. The partition rules the lipids out of the aqueous extract before an "in-tube" dispersive solid phase microextraction (dSPME) for acrylamide retention. This is followed by the elution with buffer prior to injection. This extract is independently introduced into the system front end followed by the injection of the compounds from the organic phase, yet all spotted in the same run. A novel liquid chromatography high-resolution mass spectrometry (LC-HRMS) method setup enables the quantification of 186 compounds at 10 µg/kg, 226 at 5 µg/kg, and the acrylamide at 200 µg/kg for a total of 414 molecules, with acceptable recoveries (70-120%) and precision (RSD < 20%) making this strategy significantly faster and cost-effective than the dedicated single residue methods. Even though the presence of chlorpyrifos, acrylamide, and ochratoxin A was confirmed on samples of different origins, the findings were below the limit of quantification. During the storage of raw coffee, no proof of masking of OTA was found; however, condensation with glucose was evidenced during thermal processing experiments with sucrose by using stable isotope labeling (SIL). No detected conjugates were found in roasted nor in commercial sugar-added torrefacto samples, an industrial processing usually carried out above the decomposition temperature of the disaccharide.

Proteomic analysis reveals stage-specific reprogramed metabolism for the primary breast cancer cell lines MGSO-3 and MACL-1.

Breast cancer is the most prevalent cancer in women worldwide. Its molecular subtypes are based on the presence/absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). MACL-1 and MGSO-3 are cell lines derived from primary tumor sites of patients diagnosed with luminal A subtype carcinoma (ER+/PR+/HER2-) and ductal carcinoma in situ (ER-/PR-/HER2+), respectively. However, these cell lines lost the expression of these markers over cell culturing, and both have triple-negative phenotypes (ER-/PR-/HER2-), which has the poorest prognosis. Here, we sought to study the proteome signature of MGSO-3 and MACL-1, comparing them with the epithelial cell line MCF-10A and the well-established metastatic-derived breast cancer cell line MDA-MB-231. Our results showed that proteins associated with the tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS) were upregulated in MGSO-3 and MACL-1 cells. These cell lines also showed upregulation of pro-apoptotic proteins when compared with MDA-MB-231. The molecular differences highlighted in this study may clarify the molecular basis behind cancer cells functioning and may reveal novel signatures across the breast cancer cell models.

Engineering Posttranslational Regulation of Glutamine Synthetase for Controllable Ammonia Production in the Plant Symbiont Azospirillum brasilense.

Nitrogen requirements for modern agriculture far exceed the levels of bioavailable nitrogen in most arable soils. As a result, the addition of nitrogen fertilizer is necessary to sustain productivity and yields, especially for cereal crops, the planet's major calorie suppliers. Given the unsustainability of industrial fertilizer production and application, engineering biological nitrogen fixation directly at the roots of plants has been a grand challenge for biotechnology. Here, we designed and tested a potentially broadly applicable metabolic engineering strategy for the overproduction of ammonia in the diazotrophic symbiont Azospirillum brasilense. Our approach is based on an engineered unidirectional adenylyltransferase (uAT) that posttranslationally modifies and deactivates glutamine synthetase (GS), a key regulator of nitrogen metabolism in the cell. We show that this circuit can be controlled inducibly, and we leveraged the inherent self-contained nature of our posttranslational approach to demonstrate that multicopy redundancy can improve strain evolutionary stability. uAT-engineered Azospirillum is capable of producing ammonia at rates of up to 500 µM h-1 unit of OD600 (optical density at 600 nm)-1. We demonstrated that when grown in coculture with the model monocot Setaria viridis, these strains increase the biomass and chlorophyll content of plants up to 54% and 71%, respectively, relative to the wild type (WT). Furthermore, we rigorously demonstrated direct transfer of atmospheric nitrogen to extracellular ammonia and then plant biomass using isotopic labeling: after 14 days of cocultivation with engineered uAT strains, 9% of chlorophyll nitrogen in Setaria seedlings was derived from diazotrophically fixed dinitrogen, whereas no nitrogen was incorporated in plants cocultivated with WT controls. This rational design for tunable ammonia overproduction is modular and flexible, and we envision that it could be deployable in a consortium of nitrogen-fixing symbiotic diazotrophs for plant fertilization. IMPORTANCE Nitrogen is the most limiting nutrient in modern agriculture. Free-living diazotrophs, such as Azospirillum, are common colonizers of cereal grasses and have the ability to fix nitrogen but natively do not release excess ammonia. Here, we used a rational engineering approach to generate ammonia-excreting strains of Azospirillum. Our design features posttranslational control of highly conserved central metabolism, enabling tunability and flexibility of circuit placement. We found that our strains promote the growth and health of the model grass S. viridis and rigorously demonstrated that in comparison to WT controls, our engineered strains can transfer nitrogen from 15N2 gas to plant biomass. Unlike previously reported ammonia-producing mutants, our rationally designed approach easily lends itself to further engineering opportunities and has the potential to be broadly deployable.

Quantitative gingival crevicular fluid proteome in type 2 diabetes mellitus and chronic periodontitis.

OBJECTIVE: The aim of this study was to investigate the proteome of the gingival crevicular fluid comparing the relative abundance of proteins from type 2 diabetes mellitus (2DM) individuals and chronic periodontitis (CP) affected sites, subjects affected by both conditions and healthy individuals. MATERIAL AND METHODS: Twenty individuals were equally allocated in four groups, 2DM with CP, 2DM periodontally healthy, CP without 2DM, and periodontally healthy without 2DM. The relative quantification of proteins was accessed with iTRAQ labeling and mass spectrometry. RESULTS AND CONCLUSION: A total of 104 proteins showed significant differences in abundance in pairwise comparisons. Some presented different levels in all diseased groups as compared to control, either increasing (rap guanine nucleotide exchange factor, S100A8, S100A9, and immunoglobulins) or decreasing (actins, myristoylated alanine-rich C-kinase substrate, and glutathione S-transferase). Other differences were specific for a given condition: Titin, neutrophil elastase, and myeloperoxidase levels were higher in the DP group, cathelicidin antimicrobial peptide decreased in CP, and annexin decreased in DH. These differences in the proteome can provide clues for further studies that will validate the variation in their levels and their role in both diseases.

A Guide to Mass Spectrometry-Based Quantitative Proteomics.

Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.

iTRAQ-Based Shotgun Proteomics Approach for Relative Protein Quantification.

Shotgun proteomics has a key role in quantitative estimation of proteins from biological systems under different conditions, which is crucial in the understanding of their functional roles. Isobaric tagging for relative and absolute quantitation (iTRAQ) mass spectrometry is based on pre-labeling of peptides with mass tags which allows the multiplex analysis of up to eight proteomes simultaneously. We describe here a detailed protocol for sample preparation and iTRAQ 4-plex labeling for relative quantification of multiple samples from human and plant tissues. We also present two strategies for peptide fractionation after the iTRAQ labeling protocol.

Galactose oxidation using 13C in healthy and galactosemic children

Galactosemia is an inborn error of galactose metabolism that occurs mainly as the outcome of galactose-1-phosphate uridyltransferase (GALT) deficiency. The ability to assess galactose oxidation following administration of a galactose-labeled isotope (1-13C-galactose) allows the determination of galactose metabolism in a practical manner. We aimed to assess the level of galactose oxidation in both healthy and galactosemic Brazilian children. Twenty-one healthy children and seven children with galactosemia ranging from 1 to 7 years of age were studied. A breath test was used to quantitate 13CO2 enrichment in exhaled air before and at 30, 60, and 120 min after the oral administration of 7 mg/kg of an aqueous solution of 1-13C-galactose to all children. The molar ratios of 13CO2 and 12CO2 were quantified by the mass/charge ratio (m/z) of stable isotopes in each air sample by gas-isotope-ratio mass spectrometry. In sick children, the cumulative percentage of 13C from labeled galactose (CUMPCD) in the exhaled air ranged from 0.03% at 30 min to 1.67% at 120 min. In contrast, healthy subjects showed a much broader range in CUMPCD, with values from 0.4% at 30 min to 5.58% at 120 min. The study found a significant difference in galactose oxidation between children with and without galactosemia, demonstrating that the breath test is useful in discriminating children with GALT deficiencies.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

Comparação de aspectos anatomopatológicos entre ROLL e carvão / Comparison of anatomopathological aspects between ROLL and Carbon localization

Objetivo: Vários métodos são descritos para a localização pré-operatória de lesões de mama clinicamente ocultas que necessitam de estudo histológico. A marcação com ROLL (localização radioguiada de lesões ocultas) utiliza injeção de radiofármaco na lesão oculta e localização intra-operatória com sonda de captação de radiação. A técnica de marcação com carvão consiste na injeção de solução de carvão ativado na lesão e localização visual. Ambas apresentam vantagens e desvantagens. O objetivo desse estudo foi comparar a eficácia entre as técnicas de carvão e ROLL para localização de lesões não palpáveis em relação aos aspectos anatomopatológicos, considerando as variáveis: peso e volume dos espécimes cirúrgicos excisados e alterações morfológicas quanto à resposta inflamatória. Método: Foram avaliados 84 casos mediante revisão retrospectiva de laudos anatomopatológicos e suas respectivas lâminas, 42 casos marcados com técnica ROLL e 42 com a técnica de carvão. As variáveis acima descritas foram comparadas por meio de testes estatísticos, assumindo nível de significância estatística de 5%. Resultados: Peso e volume dos espécimes cirúrgicos foram significativamente menores com a técnica do carvão (p=0,002 para peso e p<0,001 para volume). Quanto à reação inflamatória, observou-se presença de reação inflamatória aguda ou crônica na totalidade dos casos do grupo carvão, enquanto que em um caso do grupo ROLL foi demonstrada infiltração linfocítica (p<0,001). Conclusão: O carvãomostrou-se um marcador eficaz para localização de lesões não palpáveis da mama. Na comparação com a técnica do ROLL permitiu obtenção de espécimes cirúrgicos de menor peso e volume, estando associado à maior reação inflamatória.

Objective: Several methods are described for the preoperatively localization of clinically occult breast lesions that need to be defined histologically. The ROLL technique (radioguided occult lesion localization) uses radiotracer injection in hidden lesion and intraoperative localization with a gamma probe. The carbon marking is the injection of activated carbon in the lesion and visual localization. Both methods have advantages and disadvantages. The objective was to compare the efficacy of carbon marking and ROLL for locating non-palpable lesions by pathological aspects, considering the following variables: weight and volume of surgical specimens and morphological changes as the inflammatory response. Methods: 84 cases were assessed by a retrospective review of pathology reports and their histological H/E stained slides, 42 cases with ROLL and 42 with carbon marking. The variables described above were compared with Fisher exact test and Mann-Whitney test, assuming significance level of 5 %. Results: Weight and volume of surgical specimens were significantly lower with carbon marking (p=0.002 for weight and p<0.001 for volume). In relation of the inflammatory reaction, the presence of acute or chronic inflammatory reaction was observed in all cases of the carbon group, while in only one case of the ROLL group was demonstrated lymphocytic infiltration. Conclusion: The carbon marking is effective marker for locating nonpalpable breast lesions. In comparison with ROLL, allowed obtaining surgical specimens of lower weight and volume, but is associated with the presence of inflammatory reaction.

Comparación de oos técnicas como herramienta dignóstica de la deficiencia de ccarnitina acilcarnitina translocasa / Comparison of woo techniques as carnitine acylarnitine translocase deficiencyy diagnosis tools

Objetivo: comparar dos técnicas como herramientas para el diagnóstico por laboratorio de la deficiencia de carnitina acilcarnitina translocasa, desorden poco frecuente de herencia autosómico recesiva en la oxidación de ácidos grasos. Materiales y métodos: los fibroblastos de pacientes y controles fueron incubados con sustratos tritiados y sustratos deuterados. Resultados: la oxidación de los sustratos tritiados se encontró muy deprimida en los fibroblastos de pacientes con esta enfermedad; sin embargo, no fue posible establecer un perfil característico para el diagnóstico de la enfermedad utilizando sustratos deuterados. Conclusión: la incubación de fibroblastos en presencia de sustratos tritiados constituye una buena herramienta para el diagnóstico por laboratorio de pacientes afectados por la deficiencia de carnitina acilcarnitina translocasa, no así la incubación con sustratos deuterados.

Objective: to compare two laboratory diagnosis techniques for carnitine acylcarnitine translocase deficiency, a rare inherited autosomal recessive disorder in fatty acid oxidation. Materials and methods: fibroblasts of patients and controls were incubated with tritiated substrates and deuterated substrates. Results: a severe depression for oxidizing the tritiated substrates was observed for the fibroblasts of patients with this disease; however it was not possible to establish a characteristic profile for the diagnosis of the disease using deuterated substrates. Conclusion: the incubation of fibroblasts using tritiated substrates constitutes a good tool for laboratory diagnosis of patients suffering carnitine-acylcarnitine translocase deficiency, in contrast, incubation with deuterated substrates does not.

Neovascularization after ischemic injury: evaluation with 99mTc-HYNIC-RGD / Neovascularizacao apos lesao isquemica: avaliacao com 99mTc-HYNIC-RGD

Purpose: Angiogenesis involves many mediators including integrins, and the tripeptide RGD is a target amino acid recognition sequence for many of them. Hindlimb ischemia is a simple and convenient animal model however standardization of the injection procedures in the devascularized and control limb is lacking, thus rendering difficult the interpretation of results. The aim of this investigations was to evaluate neovascularization in a hindlimb murine model by means of 99mTc-HYNIC-ß-Ala-RGD. Methods: 99mTc-HYNIC-RGD analog was prepared using coligands. Ischemia was induced in Wistar rats by double- ligation of the common femoral artery. Radiolabeled RGD was injected after 2h, as well as 1, 3, 5, 7, 10 and 14 days. Uptake was evaluated by planar imaging and biodistribution studies. Results: The highest ratio between ischemia and control was achieved at the 7th day (2.62 ± 0.95), with substantial decrease by the 14th day. For pertechnetate the 7th day ratio was 0.87 ± 0.23. Scintigraphic image confirmed different uptakes. Conclusion: 99mTc-HYNIC-RGD analog concentrated in ischemic tissue by the time of widespread angiogenesis and pertechnetate confirmed reduction in blood flow. In this sense, the protocol can be recommended for ischemic models. (AU)

Objetivo: A angiogênese em resposta a fenômenos isquêmicos envolve vários mediadores como as integrinas, sendo que o tripeptídeo RGD possui uma seqüência de aminoácidos com reconhecimento para este alvo. O modelo animal de isquemia de pata traseira é simples e conveniente, porém não há uma padronização do procedimento de injeção e controle radioisotópico em membro desvascularizado, dificultando, portanto a interpretação de resultados. O objetivo deste estudo foi avaliar a neovascularização em modelo murino de isquemia de pata traseira através do radiotraçador 99mTc-HYNIC-ß-Ala-RGD. Métodos: O análogo 99mTc-HYNIC-RGD foi preparado usando coligantes. A isquemia foi induzida em ratos Wistar por dupla-ligação da artéria femoral comum na prega inguinal. Peptídeo RGD radiomarcado foi injetado após 2h, assim como 1, 3, 5, 7, 10 e 14 dias. A captação foi avaliada por imagem planar e estudos de biodistribuição. Resultados: A maior diferença de captação entre isquemia e pata controle foi obtida no 7o dia (2,62 ± 0,95), com decréscimo acentuado no 14o dia. Para o pertecnetato a razão no 7o dia foi 0,87 ± 0,23. A imagem cintilográfica confirmou as diferentes captações. Conclusões: O análogo 99mTc-HYNIC-RGD concentrou-se no tecido isquêmico na etapa em que a angiogênese é mais acentuada, e o estudo do pertecnetato confirmou a redução no fluxo sanguíneo. Desta maneira, este protocolo diagnóstico pode ser recomendado para modelos isquêmicos. (AU)

Neovascularization after ischemic injury: evaluation with 99mTc-HYNIC-RGD / Neovascularização após lesão isquêmica: avaliação com 99mTc-HYNIC-RGD

Purpose: Angiogenesis involves many mediators including integrins, and the tripeptide RGD is a target amino acid recognition sequence for many of them. Hindlimb ischemia is a simple and convenient animal model however standardization of the injection procedures in the devascularized and control limb is lacking, thus rendering difficult the interpretation of results. The aim of this investigations was to evaluate neovascularization in a hindlimb murine model by means of 99mTc-HYNIC-ß-Ala-RGD. Methods: 99mTc-HYNIC-RGD analog was prepared using coligands. Ischemia was induced in Wistar rats by double- ligation of the common femoral artery. Radiolabeled RGD was injected after 2h, as well as 1, 3, 5, 7, 10 and 14 days. Uptake was evaluated by planar imaging and biodistribution studies. Results: The highest ratio between ischemia and control was achieved at the 7th day (2.62 ± 0.95), with substantial decrease by the 14th day. For pertechnetate the 7th day ratio was 0.87 ± 0.23. Scintigraphic image confirmed different uptakes. Conclusion: 99mTc-HYNIC-RGD analog concentrated in ischemic tissue by the time of widespread angiogenesis and pertechnetate confirmed reduction in blood flow. In this sense, the protocol can be recommended for ischemic models.

Objetivo: A angiogênese em resposta a fenômenos isquêmicos envolve vários mediadores como as integrinas, sendo que o tripeptídeo RGD possui uma seqüência de aminoácidos com reconhecimento para este alvo. O modelo animal de isquemia de pata traseira é simples e conveniente, porém não há uma padronização do procedimento de injeção e controle radioisotópico em membro desvascularizado, dificultando, portanto a interpretação de resultados. O objetivo deste estudo foi avaliar a neovascularização em modelo murino de isquemia de pata traseira através do radiotraçador 99mTc-HYNIC-ß-Ala-RGD. Métodos: O análogo 99mTc-HYNIC-RGD foi preparado usando coligantes. A isquemia foi induzida em ratos Wistar por dupla-ligação da artéria femoral comum na prega inguinal. Peptídeo RGD radiomarcado foi injetado após 2h, assim como 1, 3, 5, 7, 10 e 14 dias. A captação foi avaliada por imagem planar e estudos de biodistribuição. Resultados: A maior diferença de captação entre isquemia e pata controle foi obtida no 7º dia (2,62 ± 0,95), com decréscimo acentuado no 14º dia. Para o pertecnetato a razão no 7º dia foi 0,87 ± 0,23. A imagem cintilográfica confirmou as diferentes captações. Conclusões: O análogo 99mTc-HYNIC-RGD concentrou-se no tecido isquêmico na etapa em que a angiogênese é mais acentuada, e o estudo do pertecnetato confirmou a redução no fluxo sanguíneo. Desta maneira, este protocolo diagnóstico pode ser recomendado para modelos isquêmicos.

Estudio in vitro de las enfermedades por deficiencias enzimáticas del sistema de transporte de la carnitina / In vitro studie of the diseases caused by enzymatic deficiencies of carnitine transport system

Los errores innatos del metabolismo constituyen un grupo de enfermedades por deficiencias enzimáticas, las que incluyen a las deficiencias de las enzimas necesarias para el paso de los ácidos grasos de cadena larga desde el citoplasma al interior de la mitocondria, como paso necesario para la obtención de energía en los estados de ayuno y ejercicio prolongado. El presente trabajo muestra la utilidad de la incubación de fibroblastos con sustratos tritiados para su diagnóstico. Fue encontrada severamente deprimida la oxidación de estos sustratos en los pacientes con estas enfermedades. Sin embargo no fue posible diferenciar entre las tres deficiencias enzimáticas estudiadas.

The inherited inborn metabolic errors are a group of diseases caused by enzymatic deficiencies, including deficiencies of the enzymes used for the income of long-chain fatty acids into the mitochondria, as a necessary step for obtaining energy during endurance exercise and fasting. The present work shows the utility of incubating fibroblasts with tritiated substrates for the diagnosis of these diseases. A severe depression for oxidizing these substrates was observed for these patients. However, it was not possible to differentiate between the three enzymatic deficiencies studied.