Prolonged durability of electroporation microarrays as a result of addition of saccharides to nucleic acids

The electroporation microarray is a useful tool for high-throughput analysis of gene functions. However, transfection efficiency is greatly impaired by storage of the microarrays, due to water evaporation from arrayed nucleotides. In this study, we aimed at evaluating the effect of saccharides and sugar alcohols, added to the solution of the plasmid DNA or small interfering RNA (siRNA). Microarrays loaded with plasmids and siRNAs were prepared with various polyols including sugars and sugar alcohols. After storage of these microarrays at different temperatures for various time periods, transfection efficiency was evaluated using human embryonic kidney cells. In the case of plasmid-loaded microarrays, addition of monosaccharides (glucose, fructose), disaccharides (trehalose, sucrose), and trisaccharide (raffinose) served to retain transfection efficiency at a reasonably high level after storage at −20 °C. The observed effects may be because moisture retention serves to maintain the solubility of DNA. In contrast, polysaccharide (dextran) and sugar alcohol (glycerol) had insignificant effects on retention of transfection efficiency. On the other hand, addition of saccharides and sugar alcohols had insignificant effects on the transfection of siRNA after storage of a microarray at 25 °C for 7 days, presumably due to the intrinsically-high solubility of siRNA which consists of short nucleotides. Figure (PPTX 3.80 MB)

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Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Application of XPS and ToF-SIMS for surface chemical analysis of DNA microarrays and their substrates

The chemical composition of the functional surfaces of substrates used for microarrays is one of the important parameters that determine the quality of a microarray experiment. In addition to the commonly used contact angle measurements to determine the wettability of functionalized supports, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are more specific methods to elucidate details about the chemical surface constitution. XPS yields information about the atomic composition of the surface, whereas from ToF-SIMS, information on the molecular species on the surface can be concluded. Applied on printed DNA microarrays, both techniques provide impressive chemical images down to the micrometer scale and can be utilized for label-free spot detection and characterization. Detailed information about the chemical constitution of single spots of microarrays can be obtained by high-resolution XPS imaging. Figure Eye-catching image for the graphical online abstract     

Digital bioanalysis

Digital microfluidics has recently emerged as a new paradigm in the world of lab-on-a-chip technology. A wide variety of bioanalyses have been successfully implemented in this format. This paper reviews the various techniques that have been adapted to digital microfluidic systems, and the current state of the field. Figure A multiplexed digital microfluidic device. Six analytical platforms are wired in series, allowing multiple independent analyses to be performed simultaneously from a single set of controls.     

Multiclass analysis of illicit drugs in plasma and oral fluids by LC-MS/MS

An analytical procedure for the simultaneous determination in human plasma and oral fluids of several illicit drugs belonging to different chemical and toxicological classes is presented. Amphetamine, methamphetamine, morphine, 6-monoacetylmorphine, methylenedioxyamphetamine, methylenedioxyethylamphetamine, methylenedioxymethamphetamine, cocaine, benzoylecgonine, tetrahydrocannabinol, carboxytetrahydrocannabinol, ketamine, and phencyclidine have been quantified in real samples using a very rapid sample treatment, basically a protein precipitation. The quantitative analysis was performed by liquid chromatography–tandem mass spectrometry and has been fully validated. All the analytes were detected in positive ionization mode using a TurboIonSpray source, except carboxytetrahydrocannabinol, which was detected in negative ionization mode. The use of a diverter valve between the column and the mass spectrometer allows the preservation of the ion source performances for high-throughput analysis. Figure Diverter system     

Headspace mass spectrometry methodology: application to oil spill identification in soils

In the present work we report the results obtained with a methodology based on direct coupling of a headspace generator to a mass spectrometer for the identification of different types of petroleum crudes in polluted soils. With no prior treatment, the samples are subjected to the headspace generation process and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of volatiles in the sample analysed. The mass spectrum corresponding to the mass/charge ratios (m/z) contains the information related to the composition of the headspace and is used as the analytical signal for the characterization of the samples. The signals obtained for the different samples were treated by chemometric techniques to obtain the desired information. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation are required. The method is rapid, simple and, in view of the results, highly promising for the implementation of a new approach for oil spill identification in soils. Figure PCA score plots illustrate clear discrimination of types of crude oil in polluted soil samples (e.g. results are shown for vertisol)     

Enzymatic hydrolysis of T-2 toxin for the quantitative determination of total T-2 and HT-2 toxins in cereals

The selective enzymatic deacetylation of T-2 toxin to give HT-2 toxin has been investigated in aqueous crude extracts of different cereals and exploited to develop an analytical method for the determination of the sum of T-2 and HT-2 toxins. The method has been validated for the analysis of total T-2 and HT-2 toxins in maize, wheat, and oats, showing recoveries from 72 to 97% for maize, from 67 to 84% for wheat, and from 61% to 87% for oats, at spiking levels of 20–400 μg/kg, with relative standard deviation lower than 10%. Liquid chromatography-tandem mass spectrometry was used for quantitative toxin determination. The potential biological role of this enzymatic conversion and its perspectives for application in the development of antibody-based analytical techniques are discussed.      

Advances in amino acid analysis

Amino acids are important targets for metabolic profiling. For decades, amino acid analysis has been accomplished by either cation-exchange or reversed-phase liquid chromatography coupled to UV absorbance or fluorescence detection of pre-column or post-column-derivatized amino acids. Recent years have seen great progress in the development of direct-infusion or hyphenated mass spectrometry in the analysis of free amino acids in physiological fluids, because mass spectrometry not only matches optical detection in sensitivity, but also offers superior selectivity. The advent of cryo-probes has also brought NMR spectroscopy within the detection limits required for the analysis of free amino acids. But there is still room for further improvement, including expansion of the analyte spectrum, reduction of sample preparation and analysis time, automation, and synthesis of affordable isotope standards. Figure Fully automated gas chromatography-mass spectrometry analysis of amino acids.     

Recent advances in electric analysis of cells in microfluidic systems

Microfluidics offers an ideal platform to integrate cell-based assays with electric measurements. The technological advances in microfluidics, microelectronics, electrochemistry, and electrophysiology have greatly inspired the development of microfluidic/electric devices that work with a low number of cells or single cells. The applications of these microfluidic systems range from the detecting of cell culture density to the probing of cellular functions at the single-cell level. In this review, we introduce the recent advances in the electric analysis of cells on a microfluidic platform, specifically related to the quantification and monitoring of cells in static solution, on-chip patch-clamp measurement, and examination of flowing cells. We also point out future directions and challenges in this field. Figure Different microfluidic devices applied to electrical analysis of cells     

Playing tag with quantitative proteomics

There is steady need for new proteomic strategies on quantitative measurements that provide essential components for detailing dynamic changes in many cellular functions and processes. Stable isotope labeling is a rapidly evolving field, which can be used either after protein extraction with chemical labeling, or in cell culture with metabolic incorporation. In this review, we explore the most frequently utilized quantitation techniques with particular attention paid to chemical labeling using different isotopic tags, including a recent labeling strategy—soluble polymer-based isotopic labeling (SoPIL)—that achieves efficient labeling in homogeneous conditions. Special care should be devoted to the selection of appropriate quantitation approaches according to the needs of the sample and overall experimental design. We evaluate recent advances in quantitative proteomics using stable isotope labeling and their applications to current insightful biological inquiries. Figure Chemical modules of isotopic tags for quantitative proteomics.     

Analysis of biosensors by chemically specific optical techniques. Chemiluminescence-imaging and infrared spectroscopic mapping ellipsometry

The standard methods currently used to read out microarrays are fluorescent and chemiluminesent imaging techniques. These methods require labeling of a component with a marker and, usually, only the concentration of the marker molecule is detected. A label-free imaging method that also enables quantitative spectroscopic analysis of the composition and component interaction would be of great advantage. In this article it is shown for the first time that IR mapping ellipsometry enables label-free imaging of a biochip before and after incubation with peptide solution. The measurements prove that IR ellipsometry is a sensitive tool for laterally resolved identification of the different materials and determination of the composition of a biochip. The lateral resolution required was achieved by using radiation from an infrared synchrotron beamline.      

Modì: a new mobile instrument for in situ double-pulse LIBS analysis

Laser-induced breakdown spectroscopy (LIBS) is a promising technique for in situ elemental analysis. A new mobile instrument for LIBS analysis, developed in a collaboration between Marwan Technology s.r.l. and the Applied Laser Spectroscopy Laboratory in Pisa, is presented, and some applications of it and results from it are outlined. The innovative experimental set-up, based on the use of two suitably retarded laser pulses and a standardless analysis procedure, which overcomes problems related to matrix effects, greatly improves the potential of this technique for accurate quantitative analysis.      

Intensified biochip system using chemiluminescence for the detection of Bacillus globigii spores

This paper reports the first intensified biochip system for chemiluminescence detection and the feasibility of using this system for the analysis of biological warfare agents is demonstrated. An enzyme-linked immunosorbent assay targeting Bacillus globigii spores, a surrogate species for Bacillus anthracis, using a chemiluminescent alkaline phosphatase substrate is combined with a compact intensified biochip detection system. The enzymatic amplification was found to be an attractive method for detection of low spore concentrations when combined with the intensified biochip device. This system was capable of detecting approximately 1 × 10⁵ Bacillus globigii spores. Moreover, the chemiluminescence method, combined with the self-contained biochip design, allows for a simple, compact system that does not require laser excitation and is readily adaptable to field use. Figure Schematic diagram of the miniature biochip detection system     

Chemiluminescence assay for quinones based on generation of reactive oxygen species through the redox cycle of quinone

A sensitive and selective chemiluminescence assay for the determination of quinones was developed. The method was based on generation of reactive oxygen species through the redox reaction between quinone and dithiothreitol as reductant, and then the generated reactive oxygen was detected by luminol chemiluminescence. The chemiluminescence was intense, long-lived, and proportional to quinone concentration. It is concluded that superoxide anion was involved in the proposed chemiluminescence reaction because the chemiluminescence intensity was decreased only in the presence of superoxide dismutase. Among the tested quinones, the chemiluminescence was observed from 9,10-phenanthrenequinone, 1,2-naphthoquinone, and 1,4-naphthoquinone, whereas it was not observed from 9,10-anthraquinone and 1,4-benzoquinone. The chemiluminescence property was greatly different according to the structure of quinones. The chemiluminescence was also observed for biologically important quinones such as ubiquinone. Therefore, a simple and rapid assay for ubiquinone in pharmaceutical preparation was developed based on the proposed chemiluminescence reaction. The detection limit (blank + 3SD) of ubiquinone was 0.05 μM (9 ng/assay) with an analysis time of 30 s per sample. The developed assay allowed the direct determination of ubiquinone in pharmaceutical preparation without any purification procedure. Figure Chemiluminescence generated through the redox cycle of quinone     

SPME in environmental analysis

Recent advances in the use of solid-phase microextraction (SPME) in environmental analysis, including fiber coatings, derivatization techniques, and in-tube SPME, are reviewed in this article. Several calibration methods for SPME, including traditional calibration methods, the equilibrium extraction method, the exhaustive extraction method, and several diffusion-based calibration methods, are presented. Recent developed SPME devices for on-site sampling and several applications of SPME in environmental analysis are also introduced.      

Analytical prospect of compact disk technology in immunosensing

A sensitive and versatile methodology involving recordable compact disks as molecular screening surfaces and a standard optical CD/DVD drive as detector, is reported. Quantitative immunoanalysis, in microarray format, of a cancer marker (alpha-fetoprotein, AFP) and a selective herbicide (atrazine) on four types of audio-video disc was conducted. Enzyme or gold nanoparticle-labeled antibodies were used as tracers, forming a precipitate on the sensing disk surface. The principle of disk reading is based on capture of analog signals with the disk drive that were proportional to the darkness of the immunoreaction product. Detection limits for AFP (8.0 μg L⁻¹) and for atrazine (0.04 μg L⁻¹) were under the threshold needed to detect nonseminomatous testicular cancer, and below the maximum E.U. residue limit for drinking water, respectively. The described methodology improves the previous developments using CDs and highlights the enormous potential of immunoassay methods using standard audio–video disk surfaces in combination with the CD/DVD drive for clinical analysis, drug discovery, or high-throughput multiresidue screening applications. Figure  Eye-catching image The analytical potential of commercial audio–video discs as molecular screening surfaces in combination with use of a standard CD/DVD drive as detector for quantitative immunoanalysis of a cancer marker and agrochemical residues is demonstrated.     

Characterization of volatile and semivolatile compounds in waste landfill leachates using stir bar sorptive extraction–GC/MS

Stir bar sorptive extraction in combination with thermal desorption coupled online to capillary gas chromatography–mass spectrometry was applied to investigate volatile and semivolatile fractions in two waste leachate samples: old and fresh ones. The present study helps to improve our knowledge of waste leachate organic composition. The aim is to then make use of this knowledge afterwards in order to generate more reliable and specific treatment processes for waste leachates and thus to respect the environmental statute law regarding their rejection. The volatile and semivolatile compounds appeared to be mainly anthropogenic in origin. Moreover, lactic acid and cyclic octaatomic sulfur could potentially be used as microbiological activity indicators, since they occur during organic matter degradation processes within waste leachates. Figure TDU-CGC-MS analytical equipment     

Home-built integrated microarray system (IMAS). A three-laser confocal fluorescence scanner coupled with a microarray printer

Microarray technology covers the urgent need to exploit the accumulated genetic information from large-scale sequencing projects and facilitate investigations on a genome-wide scale. Although most applications focus on DNA microarrays, the technology has expanded to microarrays of proteins, peptides, carbohydrates, and small molecules aiming either at detection/quantification of biomolecules or investigation of biomolecular interactions in a massively parallel manner. Microarray experiments require two specialized instruments: An arrayer (or printer), for construction of microarrays, and a readout instrument (scanner). We have designed, constructed, and characterized the first integrated microarray system (IMAS) that combines the functions of a microarrayer and a three-laser confocal fluorescence scanner into a single instrument and provides excellent flexibility for the researcher. The three-axis robotic system that moves the printing head carrying multiple pins for arraying is also used for moving the microarray slide in front of a stationary optical system during scanning. Since the translation stages are the most expensive and crucial components of microarray printers and scanners, the proposed design reduces considerably the cost of the instrument and enhances remarkably its operative flexibility. Experiments were carried out at resolutions of 2.5, 5, 10, and 20 μm. The scanner detects 0.128 nmol L⁻¹ carboxyfluorescein (spots with diameters of 70 μm) corresponding to 1.8 molecules μm⁻². The linear range extends over 3.5 orders of magnitude (R ² = 0.997) and the dynamic range covers almost five orders of magnitude. DNA microarray model experiments were carried out, including staining with SYBR Green I and hybridization with oligonucleotides labeled with the fluorescent dyes Alexa 488, Alexa 594, and Alexa 633. Figure Lay-out of the home-built integrated microarray system (IMAS). For the first time, the functions of a microarrayer (printer) and a three-laser confocal fluorescence scanner are combined into a single instrument. The three-axis robotic system that moves the printing head for arraying is also used to move the microarray slide in front of a stationary optical system during scanning. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analytical tools for the physicochemical profiling of drug candidates to predict absorption/distribution

The measurement of physicochemical properties at an early phase of drug discovery and development is crucial to reduce attrition rates due to poor biopharmaceutical properties. Among these properties, ionization, lipophilicity, solubility and permeability are mandatory to predict the pharmacokinetic behavior of NCEs (new chemical entities). Due to the high number of NCEs, the analytical tools used to measure these properties are automated and progressively adapted to high-throughput technologies. The present review is dedicated to experimental methods applied in the early drug discovery process for the determination of solubility, ionization constants, lipophilicity and permeability of small molecules. The principles and experimental conditions of the different methods are described, and important enhancements in terms of throughput are highlighted. Figure Scheme of the Drug Research Process.     

Determination of antimicrobial residues and metabolites in the aquatic environment by liquid chromatography tandem mass spectrometry

Antimicrobials are used in large quantities in human and veterinary medicine. Their environmental occurrence is of particular concern due to the potential spread and maintenance of bacterial resistance. After intake by the organisms, the unchanged drug and its metabolized forms are excreted and enter wastewater treatment plants where they are mostly incompletely eliminated, and are therefore eventually released into the aquatic environment. The reliable detection of several antimicrobials in different environmental aqueous compartments is the result of great improvements achieved in analytical chemistry. This article provides an overview of the more outstanding analytical methods based on liquid chromatography tandem mass spectrometry, developed and applied to determine antimicrobial residues and metabolites present in surface, waste, and ground waters.      

Towards single biomolecule handling and characterization by MEMS

Applications of microelectromechanical systems (MEMS) technology are widespread in both industrial and research fields providing miniaturized smart tools. In this review, we focus on MEMS applications aiming at manipulations and characterization of biomaterials at the single molecule level. Four topics are discussed in detail to show the advantages and impact of MEMS tools for biomolecular manipulations. They include the microthermodevice for rapid temperature alternation in real-time microscopic observation, a microchannel with microelectrodes for isolating and immobilizing a DNA molecule, and microtweezers to manipulate a bundle of DNA molecules directly for analyzing its conductivity. The feasibilities of each device have been shown by conducting specific biological experiments. Therefore, the development of MEMS devices for single molecule analysis holds promise to overcome the disadvantages of the conventional technique for biological experiments and acts as a powerful strategy in molecular biology. Figure Towards single bio molecular handling and characterization by MEMS