Peptide fingerprinting of the neurotoxic fractions isolated from the secretions of sea anemones Stichodactyla helianthus and Bunodosoma granulifera. New members of the APETx-like family identified by a 454 pyrosequencing approach

Sea anemones are known to contain a wide diversity of biologically active peptides, mostly unexplored according to recent peptidomic and transcriptomic studies. In the present work, the neurotoxic fractions from the exudates of Stichodactyla helianthus and Bunodosoma granulifera were analyzed by reversed-phase chromatography and mass spectrometry. The first peptide fingerprints of these sea anemones were assessed, revealing the largest number of peptide components (156) so far found in sea anemone species, as well as the richer peptide diversity of B. granulifera in relation to S. helianthus. The transcriptomic analysis of B. granulifera, performed by massive cDNA sequencing with 454 pyrosequencing approach allowed the discovery of five new APETx-like peptides (U-AITX-Bg1a-e - including the full sequences of their precursors for four of them), which together with type 1 sea anemone sodium channel toxins constitute a very distinguishable feature of studied sea anemone species belonging to genus Bunodosoma. The molecular modeling of these new APETx-like peptides showed a distribution of positively charged and aromatic residues in putative contact surfaces as observed in other animal toxins. On the other hand, they also showed variable electrostatic potentials, thus suggesting a docking onto their targeted channels in different spatial orientations. Moreover several crab paralyzing toxins (other than U-AITX-Bg1a-e), which induce a variety of symptoms in crabs, were isolated. Some of them presumably belong to new classes of crab-paralyzing peptide toxins, especially those with molecular masses below 2 kDa, which represent the smallest peptide toxins found in sea anemones. (C) 2011 Elsevier Inc. All rights reserved.

Electrospray Ionization Mass Spectrometry Fingerprinting of Extracts of the Leaves of Arrabidaea chica

Arrabidaea chica (crajiru) is an important Amazonian plant. Its extracts are used as red pigments, antimicrobial agents and astringents. Three different varieties of this species are cultivated in the Amazon region. In this work, direct infusions of A. chica extracts from these three varieties were analyzed via electrospray ionization mass spectrometry (ESI(+)-MS) fingerprinting. Derived data from the spectra were classified by using a multivariate method (PLS-DA, partial least squares-discriminant analysis). The direct method that is herein presented relies on extraction of dry, powdered leaves with acidified methanol/water solution with no further sample preparation. The resulting supernatants were analyzed by direct infusion ESI(+)-MS, which provides characteristic fingerprints of the sample composition. 3-Deoxyanthocyanidins are important substances in A. chica, their ions were used as markers in the PLS-DA data treatment. PLS-DA was able to differentiate the three varieties. ESI(+)-MS fingerprinting works as a simple and fast method to differentiate varieties of A. chica.

Nonculture-based identification of bacteria in milk by protein fingerprinting

Traditional methods for bacterial identification include Gram staining, culturing, and biochemical assays for phenotypic characterization of the causative organism. These methods can be time-consuming because they require in vitro cultivation of the microorganisms. Recently, however, it has become possible to obtain chemical profiles for lipids, peptides, and proteins that are present in an intact organism, particularly now that new developments have been made for the efficient ionization of biomolecules. MS has therefore become the state-of-the-art technology for microorganism identification in microbiological clinical diagnosis. Here, we introduce an innovative sample preparation method for nonculture-based identification of bacteria in milk. The technique detects characteristic profiles of intact proteins (mostly ribosomal) with the recently introduced MALDI SepsityperTM Kit followed by MALDI-MS. In combination with a dedicated bioinformatics software tool for databank matching, the method allows for almost real-time and reliable genus and species identification. We demonstrate the sensitivity of this protocol by experimentally contaminating pasteurized and homogenized whole milk samples with bacterial loads of 10(3)-10(8) colony-forming units (cfu) of laboratory strains of Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus. For milk samples contaminated with a lower bacterial load (104 cfu mL-1), bacterial identification could be performed after initial incubation at 37 degrees C for 4 h. The sensitivity of the method may be influenced by the bacterial species and count, and therefore, it must be optimized for the specific application. The proposed use of protein markers for nonculture-based bacterial identification allows for high-throughput detection of pathogens present in milk samples. This method could therefore be useful in the veterinary practice and in the dairy industry, such as for the diagnosis of subclinical mastitis and for the sanitary monitoring of raw and processed milk products.

Lipid fingerprinting in women with early-onset preeclampsia: A first look

Objectives: The aim of this preliminary study was to characterize the plasma lipid profiling of women with preeclampsia. Design and methods: Plasma samples of 8 pregnant women with early-onset preeclampsia and 8 normal pregnant women were evaluated. Lipids were extracted from plasma using the Bligh-Dyer protocol. The extracts were subjected to MALDI-MS. Data matrix was exported for partial least squares discriminant analysis (PLS-DA) and a parameter VIP was employed to reflect the variable importance in the discriminant analysis. The major discriminant variables were selected and underwent to Mann-Whitney U test. Results: A total of 1290 ions were initially identified and twelve m/z signals were highlighted as the most important lipids for the discrimination of patients with preeclampsia. The identification of these differential lipids was carried out through Lipid Database Search. Conclusions: The main classes identified were glycerophosphocholines [GP01], glycerophosphoserines [GP03], glycerophosphoglycerols [GP04], glycosyldiradylglycerols [GL05] and glycerophosphates [GP10]. (C) 2012 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Studio e valutazione sperimentale di tecniche di radio fingerprinting per navigazione indoor con dispositivi mobili Android

Lo studio effettuato raccoglie informazioni al fine di svolgere un’analisi globale delle tecniche attualmente in uso, o in fase di studio, nel campo della localizzazione di dispositivi all’interno di un ambiente chiuso, ovvero laddove non è possibile sfruttare la copertura del sistema GPS. La panoramica è frutto dell’analisi e dello studio di paper tecnici pubblicati dai collaboratori dell’IEEE, fruibili all’interno del portale IEEE Xplore. A corredo di questo studio è stata sviluppata una applicazione per dispositivi Android basata sulla tecnica del Wi-Fi fingerprint; l’applicazione, che rappresenta un primo approccio alle tecniche di localizzazione, è a tutti gli effetti un sistema standalone per la localizzazione, consente cioè di costruire sia la mappa per la localizzazione, partendo da un ambiente sconosciuto, sia di ottenere la posizione dell’utente all’interno di una mappa conosciuta. La tesi si conclude con una analisi dei risultati e delle performance ottenute dall’applicazione in un uso comune, al fine di poter valutare l’efficacia della tecnica presa in considerazione. I possibili sviluppi futuri sono analizzati in un capitolo a parte e trovano spazio in ambienti nei quali si vogliono offrire servizi "context-based", ovvero basati sulla posizione esatta dell’utente.

Progettazione e implementazione di una piattaforma per la localizzazione indoor basata su tecniche di radio fingerprinting e data-crowdsourcing

Questa tesi ha come scopo principale l'analisi delle diverse tecnologie di localizzazione in ambito indoor, analizzando in particolare l'utilizzo del Wifi RSS Fingerprinting. La tecnica del Wifi RSS Fingerprinting è una tecnica per la localizzazione all'interno di ambienti chiusi, che consiste nella definizione di un 'impronta'(fingerprint) in un punto preciso dell'ambiente(definito reference point), andando a inserire in un database i valori di potenza del segnale ricevuto(RSS) da ogni access point rilevato all'interno di quel determinato reference point. Per l'implementazione di questa tecnica è stato sviluppato un applicativo con un architettura client-server. Il client è stato sviluppato in ambiente Android, realizzando una applicazione per la gestione della fase di salvataggio di nuovi fingerprint e per la fase di localizzazione della posizione corrente, tramite l'utilizzo dei vari fingerprint precedentemente inseriti all'interno del DB. Il server, sviluppato in Node.js(framework Javascript), gestirà le diverse richieste ricevute dal client tramite delle chiamate AJAX, prelevando le informazioni richieste direttamente dal database. All'interno delle applicativo sono stati implementati diversi algoritmi per la localizzazione indoor, in modo da poter verificare l'applicabilità di questo sistema in un ambito reale. Questi algoritmi sono stati in seguito testati per valutare l'accuratezza e la precisione di ciascuno, andando ad individuare gli algoritmi migliori da utilizzare in base a scenari diversi.

Improved impurity fingerprinting of heparin by high resolution (1)H NMR spectroscopy

For improving the identification of potential heparin impurities such as oversulfated chondroitin sulfate (OSCS) the standard 2D (1)H-(1)H NMR NOESY was applied. Taking advantage of spin diffusion and adjusting the experimental parameters accordingly additional contaminant-specific signals of the corresponding sugar ring protons can easily be detected. These are usually hidden by the more intense heparin signals. Compared to the current 1D (1)H procedure proposed for screening commercial unfractionated heparin samples and focusing on the contaminants acetyl signals more informative and unique fingerprints may be obtained. Correspondingly measured (1)H fingerprints of a few potential impurities are given and their identification in two contaminated commercial heparin samples is demonstrated. The proposed 2D NOESY method is not intended to replace the current 1D method for detecting and quantifying heparin impurities but may be regarded as a valuable supplement for an improved and more reliable identification of these contaminants.

Enzyme Assays: High-throughput Screening, Genetic Selection and Fingerprinting

Edited by one of the leading experts in the field, this book fills the need for a book presenting the most important methods for high-throughput screenings and functional characterization of enzymes. It adopts an interdisciplinary approach, making it indispensable for all those involved in this expanding field, and reflects the major advances made over the past few years. For biochemists, analytical, organic and catalytic chemists, and biotechnologists.