pinecone/core-2020-05-10-deduplication huggingface dataset:
(1)H-NMR-based metabolomic analysis of the effect of moderate wine consumption on subjects with cardiovascular risk factors

Moderate wine consumption is associated with health-promoting activities. An H-NMR-based metabolomic approach was used to identify urinary metabolomic differences of moderate wine intake in the setting of a prospective, randomized, crossover, and controlled trial. Sixty-one male volunteers with high cardiovascular risk factors followed three dietary interventions (28 days): dealcoholized red wine (RWD) (272mL/day, polyphenol control), alcoholized red wine (RWA) (272mL/day) and gin (GIN) (100mL/day, alcohol control). After each period, 24-h urine samples were collected and analyzed by (1) H-NMR. According to the results of a one-way ANOVA, significant markers were grouped in four categories: alcohol-related markers (ethanol); gin-related markers; wine-related markers; and gut microbiota markers (hippurate and 4-hydroxphenylacetic acid). Wine metabolites were classified into two groups; first, metabolites of food metabolome: tartrate (RWA and RWD), ethanol, and mannitol (RWA); and second, biomarkers that relates to endogenous modifications after wine consumption, comprising branched-chain amino acid (BCAA) metabolite (3-methyl-oxovalerate). Additionally, a possible interaction between alcohol and gut-related biomarkers has been identified. To our knowledge, this is the first time that this approach has been applied in a nutritional intervention with red wine. The results show the capacity of this approach to obtain a comprehensive metabolome picture including food metabolome and endogenous biomarkers of moderate wine intake
SpectraBank: An open access tool for rapid microorganism identification by MALDI-TOF MS fingerprinting

13 páginas, 3 figurasMatrix-assisted laser desorption/ionisation (MALDI) time-of-flight (TOF) mass spectrometry (MS) has proved to be an accurate, rapid and cost-effective technique for microbial identification in which the spectral fingerprint of an unknown strain can be compared to a database of spectra from reference strains. Most of the existing databases are private and often costly to access, and little spectral information is shared among researchers. The objective of the present communication is to introduce the SpectraBank database (http://www.spectrabank.org), which provides open access MALDI-TOF mass spectra from a variety of microorganisms. This work aims to familiarise readers with the SpectraBank database, from the sample preparation, data collection, and data analysis to how the spectral reference data can be used for microbial species identification. The database currently includes more than 200 MALDI-TOF MS spectra from more than 70 bacterial species and links to the freely available web-based application SPECLUST (http://bioinfo.thep.lu.se/speclust.html) to allow comparisons of the obtained peak mass lists and evaluate phyloproteomic relationships. The SpectraBank database is intended to be expanded by the addition of new spectra from microbial strains, obtained in our laboratory and by other researchers.This work was funded by project 10PXIB261045PR from Xunta de Galicia and by project AGL2010-\ud
19646 from the Spanish Ministry of Science and Technology.Peer reviewe
Neoglycoproteins as carbohydrate antigens : synthesis, analysis, and polyclonal antibody response

The analysis and polyclonal antibody response for newly synthesized maltose-BSA conjugate neoglycoproteins is described. In this first proof of concept study, a simple carbohydrate antigen, maltose, was linked to BSA by reductive amination. An aglycone spacer was utilized to conserve the intact annular maltose structure and to promote the accessibility of the carbohydrate immunogen hapten during immunization. The neoglycoproteins were investigated by CGE and the number of conjugated maltose residues was determined by MALDI-TOF MS. The neoglycoproteins were then evaluated by immunization of BALB/c mice and the polyclonal antibody response was tested by ELISA as evidence for the presence of sugar-containing epitope-specific antibodies. Selective antibody binding was demonstrated to the synthesized neoglycoproteins with different (low and high) glycosylation degrees suggesting the possible use of this approach to generate antibodies. Moreover, the polyclonal antibody response was not inhibited by maltose or other simple carbohydrates to confirm presence of the neoglycoprotein-specific antibodies
iMole, a web based image retrieval system from biomedical literature

iMole is a platform that automatically extracts images and captions from biomedical literature. Images are tagged with terms contained in figure captions by means of a sophisticate text-mining tool. Moreover, iMole allows the user to upload directly their own images within the database and manually tag images by curated dictionary. Using iMole the researchers can develop a proper biomedical image database, storing the images extracted from paper of interest, image found on the web repositories, and their own experimental images. In order to show the functioning of the platform, we used iMole to build a 2DE database. Briefly, tagged 2DE gel images were collected and stored in a searchable 2DE gel database, available to users through an interactive web interface. Images were obtained by automatically parsing 16,608 proteomic publications, which yielded more than 16,500 images. The database can be further expanded by users with images of interest trough a manual uploading process. iMole is available with a preloaded set of 2DE gel data at http://imole.biodigitalvalley.co
Discrimination of glycoproteins via two-color laser-induced fluorescence detection coupled with postcolumn derivatization in capillary electrophoresis

Here, we report a novel method consisting of capillary electrophoretic separation followed by two-color LIF detection with postcolumn derivatization. The method can be used to discriminate glycoproteins in a protein mixture containing both glycosylated and unglycosylated proteins. The detector permitted simultaneous measurements of two electropherograms obtained by 450 nm (diode laser) and 532 nm (Nd:YAG laser) lasers excited native proteins following postcolumn derivatization with naphthalene-2,3-dicarboxaldehyde and concanavalin A (Con A) labeled with tetramethylrhodamine (rhodamine-labeled Con A), respectively. So, a protein can be assigned as glycosylated if it shows a peak at the same migration time in both electropherograms. According to the proposed principle, in a single run we discriminated a glycosylated protein (thyroglobulin) from an unglycosylated protein (albumin) in the presence of rhodamine-labeled Con A. Because the methodology permits the simultaneous detection of native proteins and their complexes with a fluorescently labeled probe, it should have broad applicability to binding assays
Recent advances in the application of capillary electromigration methods for food analysis and Foodomics

In this work, the analysis of foods and food components using capillary electromigration methods is reviewed. The present work presents and discusses the main CE applications performed in Food Science and Technology including the new field of Foodomics, reviewing recent results on food quality and safety, nutritional value, storage, bioactivity, as well as applications of CE for monitoring food interactions and food processing. The CE analysis of a large variety of food-related molecules with different chemical properties, including amino acids, peptides, proteins, phenolic compounds, carbohydrates, DNA fragments, vitamins, toxins, pesticides, additives, and other minor compounds is described. The use of microchips, CE-MS, and chiral-CE in food analysis is also discussed as well as other current and foreseen trends in this area of research. Following the previous review by Castro-Puyana et al. (Electrophoresis, 2012, 33, 147-167), the current review covers the papers that were published from February 2011 to February 2013. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.Funded by: Ministerio de Economia y Competitividad, Spain. Grant Number: AGL2011-29857-C03-01 and Programa CONSOLIDER, Ministerio de Educacion y Ciencia, Spain. Grant Number: CSD2007-00063 FUN-C-FOOD. M.C-P. thanks the Ministerio de Ciencia e Innovación for her Juan de la Cierva contract (JCI-2009-05297).Peer Reviewe
Speciation analysis of mercury in water samples by dispersive liquid-liquid microextraction coupled to capillary electrophoresis

In this study, a method of pretreatment and speciation analysis of mercury by dispersive liquid-liquid microextraction along with CE was developed. The method was based on the fact that mercury species including methylmercury (MeHg), ethylmercury (EtHg), phenylmercury (PhHg), and Hg(II) were complexed with 1-(2-pyridylazo)-2-naphthol to form hydrophobic chelates and l-cysteine could displace 1-(2-pyridylazo)-2-naphthol to form hydrophilic chelates with the four mercury species. Factors affecting complex formation and extraction efficiency, such as pH value, type, and volume of extractive solvent and disperser solvent, concentration of the chelating agent, ultrasonic time, and buffer solution were investigated. Under the optimal conditions, the enrichment factors were 102, 118, 547, and 46, and the LODs were 1.79, 1.62, 0.23, and 1.50 g/L for MeHg, EtHg, PhHg, and Hg(II), respectively. Method precisions (RSD, n = 5) were in the range of 0.29-0.54% for migration time, and 3.08-7.80% for peak area. Satisfactory recoveries ranging from 82.38 to 98.76% were obtained with seawater, lake, and tap water samples spiked at three concentration levels, respectively, with RSD (n = 5) of 1.98-7.18%. This method was demonstrated to be simple, convenient, rapid, cost-effective, and environmentally benign, and could be used as an ideal alternative to existing methods for analyzing trace residues of mercury species in water samples.In this study, a method of pretreatment and speciation analysis of mercury by dispersive liquid-liquid microextraction along with CE was developed. The method was based on the fact that mercury species including methylmercury (MeHg), ethylmercury (EtHg), phenylmercury (PhHg), and Hg(II) were complexed with 1-(2-pyridylazo)-2-naphthol to form hydrophobic chelates and l-cysteine could displace 1-(2-pyridylazo)-2-naphthol to form hydrophilic chelates with the four mercury species. Factors affecting complex formation and extraction efficiency, such as pH value, type, and volume of extractive solvent and disperser solvent, concentration of the chelating agent, ultrasonic time, and buffer solution were investigated. Under the optimal conditions, the enrichment factors were 102, 118, 547, and 46, and the LODs were 1.79, 1.62, 0.23, and 1.50 g/L for MeHg, EtHg, PhHg, and Hg(II), respectively. Method precisions (RSD, n = 5) were in the range of 0.29-0.54% for migration time, and 3.08-7.80% for peak area. Satisfactory recoveries ranging from 82.38 to 98.76% were obtained with seawater, lake, and tap water samples spiked at three concentration levels, respectively, with RSD (n = 5) of 1.98-7.18%. This method was demonstrated to be simple, convenient, rapid, cost-effective, and environmentally benign, and could be used as an ideal alternative to existing methods for analyzing trace residues of mercury species in water samples
In silico detection of phylogenetic informative Y-chromosomal SNPs from WGS data

A state-of-the-art phylogeny of the human Y-chromosome is an essential tool for forensic genetics. The explosion of whole genome sequencing (WGS) data due to the rapid progress of next generation sequencing facilities is useful to optimize and to increase the resolution of the phylogenetic Y-chromosomal tree. The most interesting Y-chromosomal variants to increase the phylogeny are single nucleotide polymorphisms (Y-SNPs) especially since the software to call them in WGS data and to genotype them in forensic assays has been optimized over the past years. The PENNY software presented here detects potentially phylogenetic interesting Y-SNPs in silico based on SNP calling data files and classifies them into different types according their position in the currently used Y-chromosomal tree. The software utilized 790 available male WGS samples and in total 1,269 Y-SNPs potentially capable of increasing the resolution of the Y-chromosomal phylogenetic tree were detected with PENNY. Based on a test-panel we could prove that these newly added Y-SNPs indeed increased the resolution of the phylogenetic Y-chromosomal analysis substantially. Finally, we performed a second run with PENNY whereby all samples including those of the test-panel are used and this resulted in 509 additional phylogenetic promising Y-SNPs. By including these additional Y-SNPs a final update of the present phylogenetic Y-chromosomal tree which is useful for forensic applications was generated. In order to find more convincing forensic interesting Y-SNPs with this PENNY software, the number of samples and variety of the haplogroups to which these samples belong needs to increase.status: publishe
Separation and characterization of phlorotannins from brown algae Cystoseira abies-marina by comprehensive two-dimensional liquid chromatography

Phlorotannins are an important class of polyphenolic compounds only found in brown algae. The chemical analysis of these bioactive polyphenols is rather difficult due to the great chemical variability and complexity of the natural composition of these components in algae, forming large phloroglucinol polymers. In the present work, a new approach based on the use of comprehensive 2D LC (LC × LC) is shown to analyze this complex family of compounds. The developed LC × LC methodology is based on the coupling of a hydrophilic-interaction LC (HILIC)-based separation in the first dimension and an RP-based separation in the second dimension. The employment of this online coupling together with DAD and MS/MS allowed the separation and identification of more than 50 compounds in a Cystoseira abies-marina brown alga extract. Phlorotannins containing from 5 to 17 phloroglucinol units were identified in this sample by HILIC × RP-DAD-MS/MS. Besides, using the 2,4-dimethoxybenzaldehyde assay, it was possible to determine that the total amount of phlorotannins present in the extract was 40.2 mg phloroglucinol equivalents per gram of extract. To our knowledge, this work is the first demonstration of the usefulness of HILIC × RP-DAD-MS/MS for the determination of phlorotannins. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.Funded by: BEA (Banco Español de Algas, Las Palmas de Gran Canaria, Spain). Grant Number: AGL2011-29857-C03-01 and ALIBIRD. Grant Number: S2009/AGR-1469.Peer Reviewe
The molecular characterisation of a depurinated trial dna sample can be a model to understand the reliability of the results in forensic genetics.

The role of DNA damage in PCR processivity/fidelity is a relevant topic in molecular investigation of aged/forensic samples. In order to reproduce one of the most common lesions occurring in post mortem tissues, a new protocol based on aqueous hydrolysis of the DNA was developed in vitro. Twenty five forensic laboratories were then provided with 3.0 μg of a trial sample (TS) exhibiting, in mean, the loss of 1 base out of 20, and a molecular weight below 300 bp. Each participating laboratory could freely choose any combination of methods, leading to the quantification and to the definition of the STR profile of the TS, through the documentation of each step of the analytical approaches selected. The results of the TS quantification by qPCR showed significant differences in the amount of DNA recorded by the participating laboratories using different commercial kits. This data shows that only DNA quantification "relative" to the used kit (probe) is possible, being the "absolute" amount of DNA inversely related to the length of the target region (r2 = 0.891). In addition, our results indicate that the absence of a shared stable and certified reference quantitative standard is also likely involved. STR profiling was carried out selecting five different commercial kits and amplifying the TS for a total number of 212 multiplex PCRs, thus representing an interesting overview of the different analytical protocols used by the participating laboratories. Nine laboratories decided to characterise the TS using a single kit, with a number of amplifications varying from 2 to 12, obtaining only partial STR profiles. Most of the participants determined partial or full profiles using a combination of two or more kits, and a number of amplifications varying from 2 to 27. The performance of each laboratory was described in terms of number of correctly characterised loci, dropped out markers, unreliable genotypes and incorrect results. The incidence of unreliable and incorrect genotypes was found to be higher for participants carrying out a limited number of amplifications, insufficient to define the correct genotypes from damaged DNA samples such as the TS. Finally, from a dataset containing about 4,500 amplicons, the frequency of PCR artefacts (allele drop out, allele drop in and allelic imbalance) was calculated for each kit showing that the new chemistry of the kits is not able to overcome the concern of template-related factors. The results of this collaborative exercise emphasize the advantages of using a standardized degraded DNA sample in the definition of which analytical parameters are critical for the outcome of the STR profiles
Global properties and propensity to dimerization of the amyloid-beta (12-28) peptide fragment through the modeling of its monomer and dimer diffusion coefficients and electrophoretic mobilities

Neuronal activity loss may be due to toxicity caused mainly by amyloid-beta (1–40) and (1–42) peptides forming soluble oligomers. Here the amyloid-beta (12–28) peptide fragment (monomer) and its dimer are characterized at low pH through the modeling of their diffusion coefficients and effective electrophoretic mobilities. Translational diffusion coefficient experimental values of monomer and dimer analogs of this peptide fragment and monomer and dimer mixtures at thermodynamic equilibrium are used as reported in the literature for different monomer initial concentrations. The resulting electrokinetic and hydrodynamic global properties are employed to evaluate the amyloid-beta (12–28) peptide fragment propensity to dimerization through a thermodynamic theoretical framework. Therefore equilibrium constants are considered at pH 2.9 to elucidate one of the amyloidogenic mechanisms involving the central hydrophobic region LVFFA of the peptide spanning residues 17–21 associated with phenylalanine at positions 19 and 20 in the amino acid sequence of amyloid-beta peptides. An analysis demonstrating that peptide aggregation is a concentration-dependent process is provided, where both pair and intraparticle charge regulation phenomena become relevant. It is shown that the modeling of the effective electrophoretic mobility of the amyloid-beta (12–28) peptide fragment is crucial to understand the effect of hydrophobic region LVFFA in the amyloidogenic process.Fil: Deiber, Julio Alcides. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química (i); ArgentinaFil: Peirotti, Marta Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química (i); ArgentinaFil: Piaggio, María. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentin
Combined dielectrophoretic and impedance system for on-chip controlled bacteria concentration: Application to Escherichia coli

The present paper reports a bacteria autonomous controlled concentrator prototype with a user-friendly interface for bench-top applications. It is based on a micro-fluidic lab-on-a-chip and its associated custom instrumentation, which consists in a dielectrophoretic actuator, to pre-concentrate the sample, and an impedance analyser, to measure concentrated bacteria levels. The system is composed by a single micro-fluidic chamber with interdigitated electrodes and a instrumentation with custom electronics. The prototype is supported by a real-time platform connected to a remote computer, which automatically controls the system and displays impedance data used to monitor the status of bacteria accumulation on-chip. The system automates the whole concentrating operation. Performance has been studied for controlled volumes of Escherichia coli (E. coli) samples injected into the micro-fluidic chip at constant flow rate of 10 μL/min. A media conductivity correcting protocol has been developed, as the preliminary results showed distortion of the impedance analyser measurement produced by bacterial media conductivity variations through time. With the correcting protocol, the measured impedance values were related to the quantity of bacteria concentrated with a correlation of 0.988 and a coefficient of variation of 3.1%. Feasibility of E. coli on-chip automated concentration, using the miniaturized system, has been demonstrated. Furthermore, the impedance monitoring protocol had been adjusted and optimized, to handle changes in the electrical properties of the bacteria media over time
Phenolic and microbial-targeted metabolomics to discovering and evaluating wine intake biomarkers in human urine and plasma

The discovery of biomarkers of intake in nutritional epidemiological studies is essential in establishing an association between dietary intake (considering their bioavailability) and diet-related risk factors for diseases. The aim is to study urine and plasma phenolic and microbial profile by targeted metabolomics approach in a wine intervention clinical trial for discovering and evaluating food intake biomarkers. High-risk male volunteers (n = 36) were included in a randomized, crossover intervention clinical trial. After a washout period, subjects received red wine or gin, or dealcoholized red wine over four weeks. Fasting plasma and 24-h urine were collected at baseline and after each intervention period. A targeted metabolomic analysis of 70 host and microbial phenolic metabolites was performed using ultra performance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS). Metabolites were subjected to stepwise logistic regression to establish prediction models and received operation curves were performed to evaluate biomarkers. Prediction models based mainly on gallic acid metabolites, obtained sensitivity, specificity and area under the curve (AUC) for the training and validation sets of between 91 and 98% for urine and between 74 and 91% for plasma. Resveratrol, ethylgallate and gallic acid metabolite groups in urine samples also resulted in being good predictors of wine intake (AUC>87%). However, lower values for metabolites were obtained in plasma samples. The highest correlations between fasting plasma and urine were obtained for the prediction model score (r = 0.6, P<0.001), followed by gallic acid metabolites (r = 0.5-0.6, P<0.001). This study provides new insights into the discovery of food biomarkers in different biological samples
Feedback-amplified electrochemical dual-plate boron-doped diamond microtrench detector for flow injection analysis

An electrochemical flow cell with a boron-doped diamond dual-plate microtrench electrode has been developed and demonstrated for hydroquinone flow injection electroanalysis in phosphate buffer pH 7. Using the electrochemical generator-collector feedback detector improves the sensitivity by one order of magnitude (when compared to a single working electrode detector). The diffusion process is switched from an analyte consuming "external" process to an analyte regenerating "internal" process with benefits in selectivity and sensitivity