An Easy and efficient method for native and immunoreactive <i>Echinococcus granulosus</i> antigen 5 enrichment from hydatid cyst fluid

Background:Currently, the serodiagnosis of cystic echinococcosis relies mostly on crude Echinococcus granulosus hydatid cyst fluid as the antigen. Consequently, available immunodiagnostic tests lack standardization of the target antigen and, in turn, this is reflected on poor sensitivity and specificity of the serological diagnosis. Methodology/Principal Findings: Here, a chromatographic method enabling the generation of highly enriched Antigen 5 (Ag5) is described. The procedure is very easy, efficient and reproducible, since different hydatid cyst fluid (HCF) sources produced very similar chromatograms, notwithstanding the clearly evident and extreme heterogeneity of the starting material. In addition, the performance of the antigen preparation in immunological assays was preliminarily assessed by western immunoblotting and ELISA on a limited panel of cystic echinococcosis patients and healthy controls. Following western immunoblotting and ELISA experiments, a high reactivity of patient sera was seen, with unambiguous and highly specific results. Conclusions/Significance: The methods and results reported open interesting perspectives for the development of sensitive diagnostic tools to enable the timely and unambiguous detection of cystic echinococcosis antibodies in patient sera

Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture

Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and reliability of metaproteomic results. Specifically, the use of iterative searches and of suitable filters for taxonomic assignments is proposed with the aim of increasing coverage and trustworthiness of metaproteomic data.</br

Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics

Background: The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Results: Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin. Conclusions: This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests.Pubblicat

Cytoprotective, antioxidant, and anti-migratory activity of Pistacia lentiscus L. supercritical carbon dioxide extract on primary human endothelial cells

Green chemistry is a useful tool for producing valuable chemicals from biomass. However, extracted compounds need to be tested for safety and efficacy before their use in humans. Here we investigate the chemical composition and biological effects of a leaves Pistacia lentiscus L. supercritical carbon dioxide (SCCO2) extract. Terpenes represented the main extract fraction, with Germacrene D (11.18%), delta-cadinene (10.54%), and alpha-pinene (8.7%) the most abundant molecules. Challenged with endothelial cells (ECs), increasing extract concentrations failed to affect cell proliferation or promote cell toxicity. ROS assessment in unstressed and H2O2-treated ECs revealed an extract dose-dependent antioxidant activity. Exposition of H2O2-treated ECs to increasing extract concentrations dose-dependently counteracted H2O2-induced cell impairments. The extract significantly counteracted fetal calf serum-induced ECs migration. For the first time, we report that a SCCO2 extract obtained from PL leaves is safe on ECs and may be a useful source of valuable compounds with vasculoprotective properties.Open Access funding was provided by the Qatar National Library

An Easy and Efficient Method for Native and Immunoreactive Echinococcus granulosus Antigen 5 Enrichment from Hydatid Cyst Fluid

Background: Currently, the serodiagnosis of cystic echinococcosis relies mostly on crude Echinococcus granulosus hydatid cyst fluid as the antigen. Consequently, available immunodiagnostic tests lack standardization of the target antigen and, in turn, this is reflected on poor sensitivity and specificity of the serological diagnosis. Methodology/Principal Findings: Here, a chromatographic method enabling the generation of highly enriched Antigen 5 (Ag5) is described. The procedure is very easy, efficient and reproducible, since different hydatid cyst fluid (HCF) sources produced very similar chromatograms, notwithstanding the clearly evident and extreme heterogeneity of the starting material. In addition, the performance of the antigen preparation in immunological assays was preliminarily assessed by western immunoblotting and ELISA on a limited panel of cystic echinococcosis patients and healthy controls. Following western immunoblotting and ELISA experiments, a high reactivity of patient sera was seen, with unambiguous and highly specific results. Conclusions/Significance: The methods and results reported open interesting perspectives for the development of sensitive diagnostic tools to enable the timely and unambiguous detection of cystic echinococcosis antibodies in patient sera.This work was supported by Regione Autonoma della Sardegna (http://www.regione.sardegna.it/)Pubblicat

Chemical Waves

In our paper we try to describe the basic concepts of chemical waves and spatial pattern formation in a simple way. We pay particular attention to self-organisation phenomena in extended excitable systems. These result in the appearance of travelling waves, spiral waves, target patterns, Turing structures or more complicated structures called scroll waves, which are three-dimensional systems. We describe the most famous oscillating reaction, the Belousov-Zhabotinsky (BZ) reaction, in greater detail. This is because it is of great interest in both physical chemistry and in studies on the evolution and sustenance of self-organising biological systems

A Ternary nonequilibrium phase diagram for a closed unstirred Belousov-Zhabotinsky system

In order to analyze the fields of existence of the chaotic region as a function of initial concentration in a closed unstirred cerium catalyzed Belousov-Zhabotinsky system, a large number of experiments were carried out, varying the relative quantities of the three principal reactants (malonic acid, potassium bromate and cerium(IV)). A ternary bifurcation diagram is shown as a function of the percentage in volume of the three initial concentrations of reactants. Chaotic, quasi-periodic, periodic and no oscillations regions are clearly demonstrated

A human proteomic dataset from untreated and depleted/enriched serum samples

We present a proteomic dataset generated from a human serum sample and the enriched/depleted fractions obtained by seven commercial products. This report is related to the research article entitled “Comparative evaluation of seven commercial products for human serum enrichment/depletion by shotgun proteomics” [1]. All samples were analyzed by LC-MS/MS, label free quantitation using the spectral counting approach, and Gene Ontology (GO) annotation. Protein relative abundances and functions were reported

Macroscopic dynamics as reporter of mesoscopic organization: the Belousov-Zhabotinsky reaction in aqueous layers of DPPC lamellar phases

The propagation of traveling chemical waves in the excitable Belousov-Zhabotinsky (BZ) system when performed in the presence of 1,2-dipalmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) bilayers responds sensitively to the phospholipid content. The characteristic features of wave propagation, such as spiral pitch, rotation period, and size of the spiral core region, show two regions of different behavior, one below and the other above a DPPC content of 12.5% (w/w) thus suggesting a transition in the organization of the lipid domains at a DPPC content of ∼12.5% (w/w). This transition is supported by small-angle X-ray scattering data, which show pronounced changes in the coherence lengths of the lyotropic smectic domains. Thus, the dynamics of the chemical system occurring at a macroscopic length scale reflects the organization of the water/lipid domains which extend over mesoscopic lengths. These findings indicate that in the BZ/DPPC system, there is an interaction between processes that occurs at length scales differing by as much as 3 orders of magnitude

Comparison of blood serum peptide enrichment methods by Tricine SDS-PAGE and mass spectrometry

Characterisation of blood serum peptides can provide valuable information on physiological and pathological processes. However, the analysis of raw serum samples by MS results in the identification of a limited number of peptides. In order to improve sensitivity, many peptide enrichment methods have been proposed during the last ten years. Here, we present a comparison of fractionation methods aimed to simplify analysis of small proteins and peptides in blood serum, one of the most promising sources of putative biomarkers. Specifically, three methods based on ultrafiltration, differential precipitation, and peptide ligand libraries (ProteoMiner) were evaluated for the enrichment of peptides and low molecular weight proteins, as demonstrated by Tricine SDS-PAGE and subsequent LC-MS/MS (GeLC-MS/MS). As a result, differential solubilisation (DS) allowed the identification of the highest number of peptides. Moreover, the DS method enabled also the quantitative comparison of samples, producing fundamental information in biomarker discovery approaches