Lower miR-21/ROS/HNE levels associate with lower glycemia after habit-intervention: DIAPASON study 1-year later.

Background: The prevalence of prediabetes is increasing in the global population and its metabolic derangements may expose to a higher risk to develop type 2 diabetes (T2D) and its cardiovascular burden. Lifestyle modifications might have considerable benefits on ameliorating metabolic status. Alternative biomarkers, such as circulating miR-21, has been recently discovered associated with dysglycemia.

A case of personalized and precision medicine: Pharmacometabolomic applications to rare cancer, microbiological investigation, and therapy.

Rationale: Advances in metabolomics, together with consolidated genetic approaches, have opened the way for investigating the health of patients using a large number of molecules simultaneously, thus providing firm scientific evidence for personalized medicine and consequent interventions. Metabolomics is an ideal approach for investigating specific biochemical alterations occurring in rare clinical situations, such as those caused by rare associations between comorbidities and immunosuppression.

Methods: Metabolomic database matching enables clear identification of molecular factors associated with a metabolic disorder and can provide a rationale for elaborating personalized therapeutic protocols.

Detection of familial hypercholesterolemia in patients from a general practice database.

Objectives: Familial hypercholesterolemia (FH) is the most common monogenic lipid disorder associated with premature coronary heart disease. Early cholesterol-lowering therapy could effectively reduce cardiovascular disease morbidity and mortality in these patients. However, the majority of people with FH are undiagnosed, also due to low awareness and knowledge of FH in general practice, despite the high number of contacts GPs have with most of their patients which allows a systematic and effective approach to the detection of this condition.

SANIST: optimization of a technology for compound identification based on the European Union directive with applications in forensic, pharmaceutical and food analyses.

Electrospray Ionization and collision induced dissociation tandem mass spectrometry are usually employed to obtain compound identification through a mass spectra match. Different algorithms have been developed for this purpose (for example the nist match algorithm). These approaches compare the tandem mass spectra of the unknown analyte with the tandem mass spectra spectra of known compounds inserted in a database.

Sieve-based device for MALDI sample preparation. II. Instrumental parameterization.

A simple device effective for matrix-assisted laser desorption/ionization (MALDI) sample preparation, based on the spraying of matrix/sample solution through a stainless steel sieve (sieve-based device, SBD), has been employed for the preparation of MALDI samples of peptides, polysaccharides and high molecular weight proteins. The instrumental parameters, mainly the sprayer voltage, solution and auxiliary gas flows, and distances between sprayer-sieve and sieve-MALDI sample holder have been optimized. The MALDI spectra obtained by laser irradiation of the microspots so obtained, exhibit resolution and sensitivity higher than those achieved by the commonly employed dried droplets (DD) method.

A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.

Background: The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of "unconventional" transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort.

Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

Background: A new priority in genome research is large-scale resequencing of genes to understand the molecular basis of hereditary disease and cancer. We assessed the ability of massively parallel pyrosequencing to identify sequence variants in pools. From a large collection of human PCR samples we selected 343 PCR products belonging to 16 disease genes and including a large spectrum of sequence variations previously identified by Sanger sequencing.

Sieve-based device for MALDI sample preparation. I. Influence of sample deposition conditions in oligonucleotide analysis to achieve significant increases in both sensitivity and resolution.

Spraying of oligonucleotide-matrix solutions through a stainless steel (ss) sieve (38 microm, 450 mesh) leads to the formation, on the matrix-assisted laser desorption/ionization (MALDI) sample holder, of uniformly distributed microcrystals, well separated from each other. When the resulting sample holder surface is irradiated by laser, abundant molecular species form, with a clear increase in both intensity and resolution with respect to values obtained by 'Dried Droplet', 'Double Layer', and 'Sandwich' deposition methods. In addition, unlike the usual situation, the sample is perfectly homogeneous, and identical spectra are obtained by irradiating different areas.

Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays.

Background: The Saccharopolyspora erythraea genome sequence, recently published, presents considerable divergence from those of streptomycetes in gene organization and function, confirming the remarkable potential of S. erythraea for producing many other secondary metabolites in addition to erythromycin. In order to investigate, at whole transcriptome level, how S.

Surface-activated chemical ionization ion trap mass spectrometry for the analysis of cocaine and benzoylecgonine in hair after extraction and sample dilution.

Surface-activated chemical ionization (SACI) was employed for the analysis of cocaine and its metabolite, benzoylecgonine, extracted from hair. Following decontamination and acid hydrolysis procedures on the hair sample, the sample solution was diluted (1:10) and directly analyzed by liquid chromatography/surface-activated chemical ionization multiple collisional stage single reaction monitoring mass spectrometry (LC/SACI-MS(3)-SRM) without solid-phase extraction (SPE) pre-purification and concentration procedures. To increase the selectivity of the method, MS(3) was chosen instead of the less selective MS/MS.

Development and applications of surface-activated chemical ionization.

This review regards the recently developed ionization source named surface-activated chemical ionization (SACI) that employs an interaction with a surface placed at low voltage for the activation of the ionization of sample molecules to increase the sensitivity in the analysis of various compounds of biological and clinical interest. These results are due to the strong chemical noise decrease and the increase of ionization efficiency. This ionization source has been employed for the analysis of various compounds of different molecular mass and polarity (addicted and pharmaceutical drugs, amino acids, steroids, peptides, and proteins).

Identification of the sites of deoxyhaemoglobin PEGylation.

The 2-iminothiolane reaction with protein amino groups adds a spacer arm ending with a thiol group, which can be further treated with molecules carrying a maleimido ring. This approach is currently used for the preparation of a candidate 'blood substitute' in which human Hb (haemoglobin) is conjugated with long chains of PEG [poly(ethylene glycol)]. To identify the thiolation sites by MS, we have carried out the reaction using deoxyHb bound to inositol hexaphosphate to protect some of the residues crucial for function and NEM (N-ethylmaleimide) to block and stabilize the thiol groups prior to enzymatic digestion by trypsin and pepsin.

Surface-activated chemical ionization and high-flow gradient chromatography to reduce matrix effect.

The new atmospheric pressure chemical ionization source, named surface-activated chemical ionization (SACI), has been used in conjunction with high-flow gradient chromatography to reduce the matrix effect. This high-flow gradient chromatography approach avoids the co-elution of analyte and biological matrix compounds that leads to a reduction in quantitation errors due to matrix effect. However, this approach cannot be employed with the classical electrospray ionization (ESI) source that usually works at low eluent flow (< 300 microL/min).

A structured chitosan-based platform for biomolecule attachment to solid surfaces: application to DNA microarray preparation.

A structured chemical platform based on chitosan, an amine-rich polysaccharide, is presented as an alternative chemistry to functionalize solid support (in this case, glass slides) for grafting biomolecules. This approach has been adopted for generating arrays using amino-modified oligonucleotides with two different lengths (25-mer and 70-mer) for different purposes. Results using these chitosan-activated surfaces indicate high oligonucleotide loading capacity, good availability to hybridization against targets, and effectiveness in enzyme-mediated single nucleotide polymorphism (SNP) detection procedures by DNA polymerase and DNA ligase enzymes with low background.

The role of different phenomena in surface-activated chemical ionization (SACI) performance.

In previous studies, the production of ions in an APCI source without any corona discharge was observed, and the intensity of the ion signals showed significant increases on placing a metallic surface at 45 degrees inside an orthogonal ion source. This method was named surface-activated chemical ionization (SACI). The present study was performed to investigate the mechanisms of ion production with or without the presence of the metallic surface, by varying instrumental parameters and the geometrical configuration.

Surface-activated chemical ionization ion trap mass spectrometry in the analysis of drugs in dilute urine samples. Part II: analysis of morphine and other street drugs.

The new ionization method, called surface-activated chemical ionization (SACI), was employed for the analysis of fives drugs (morphine, codeine, 6-monoacetylmorphine (6-MAM), benzoylecgonine and cocaine) by ion trap mass spectrometry. The results so obtained have been compared with those achieved by using atmospheric pressure chemical ionization (APCI), no-discharge-APCI and electrospray ionization (ESI) clearly showing that SACI is the most sensible one mainly due to the high ionization efficiency and the lower chemical noise. The performance of SACI in terms of sensitivity and linearity was compared with the sensitivity and linearity obtained using APCI, no-discharge-APCI and ESI, showing that the new SACI approach gives rise to the best results.

Bioinformatics in mass spectrometry data analysis for proteomics studies.

Mass spectrometry is a technique widely employed for the identification and characterization of proteins. The role of bioinformatics is fundamental for the elaboration of mass spectrometry data due to the amount of data that this technique can produce. To process data efficiently, new software packages and algorithms are continuously being developed to improve protein identification and characterization in terms of high-throughput and statistical accuracy.

Protein profile changes in the human breast cancer cell line MCF-7 in response to SEL1L gene induction.

The ectopic expression of the gene SEL1L in the human breast carcinoma cell line MCF-7 resulted in a reduction of the aggressive behaviour of these cells in vitro. In addition, in vivo analysis on a series of primary breast carcinomas revealed an association between the SEL1L protein levels and the patient's overall survival. We aimed to find those proteins, associated with SEL1L, which may be involved in modulating the aggressive or invasive behaviour of breast cancer cells.

Surface-activated chemical ionization in the analysis of arginine in plasma samples.

Alterations of arginine plasma levels are involved in several disorders of amino acid metabolism such as hurtnup, argininosuccinic aciduria, histidinemia, citrullinuria, and cystinuria. In this work a new liquid ionization source, surface-activated chemical ionization (SACI), has been used to analyze arginine in human and rat plasma samples. Arginine was extracted and diluted ten times through protein precipitation.

Polymorphism analysis within the HLA-A locus by universal oligonucleotide array.

Human leukocyte antigen (HLA) class I genes present some of the most complex single nucleotide polymorphism (SNP) patterns in the human genome. HLA typing is therefore extremely challenging. In this article, we use the ligation detection reaction (LDR) combined with a universal array (UA) as a robust and efficient method to analyze SNPs within the HLA-A region that includes HLA-A alleles of interest for immunotherapy in tumor diseases.