Assessment of metal ion concentration in water with structured feature selection.

We propose a cost-effective system for the determination of metal ion concentration in water, addressing a central issue in water resources management. The system combines novel luminometric label array technology with a machine learning algorithm that selects a minimal number of array reagents (modulators) and liquid sample dilutions, such that enable accurate quantification. The algorithm is able to identify the optimal modulators and sample dilutions leading to cost reductions since less manual labour and resources are needed. Inferring the ion detector involves a unique type of a structured feature selection problem, which we formalize in this paper. We propose a novel Cartesian greedy forward feature selection algorithm for solving the problem. The novel algorithm was evaluated in the concentration assessment of five metal ions and the performance was compared to two known feature selection approaches. The results demonstrate that the proposed system can assist in lowering the costs with minimal loss in accuracy.

Luminometric Label Array for Counting and Differentiation of Bacteria.

Methods for simple and fast detection and differentiation of bacterial species are required, for instance, in medicine, water quality monitoring, and the food industry. Here, we have developed a novel label array method for the counting and differentiation of bacterial species. This method is based on the nonspecific interactions of multiple unstable lanthanide chelates and selected chemicals within the sample leading to a luminescence signal profile that is unique to the bacterial species. It is simple, cost-effective, and/or user-friendly compared to many existing methods, such as plate counts on selective media, automatic (hemocytometer-based) cell counters, flow cytometry, and polymerase chain reaction (PCR)-based methods for identification. The performance of the method was demonstrated with nine single strains of bacteria in pure culture. The limit of detection for counting was below 1000 bacteria per mL, with an average coefficient of variation of 10% achieved with the developed label array. A predictive model was trained with the measured luminescence signals and its ability to differentiate all tested bacterial species from each other, including members of the same genus Bacillus licheniformis and Bacillus subtilis, was confirmed via leave-one-out cross-validation. The suitability of the method for analysis of mixtures of bacterial species was shown with ternary mixtures of Bacillus licheniformis, Escherichia coli JM109, and Lactobacillus reuteri ATCC PTA 4659. The potential future application of the method could be monitoring for contamination in pure cultures; analysis of mixed bacterial cultures, where examining one species in the presence of another could inform industrial microbial processes; and the analysis of bacterial biofilms, where nonspecific methods based on physical and chemical characteristics are required instead of methods specific to individual bacterial species.

Luminometric Nanoparticle-Based Assay for High Sensitivity Detection of ß-Amyloid Aggregation.

A nanoparticle-based assay utilizing time-resolved luminescence resonance energy transfer (TR-LRET) was developed for the detection of ß-amyloid aggregation. The assay is based on the competitive adsorption of the sample and the acceptor-labeled protein to donor europium(III) polystyrene nanoparticles. The performance of the assay was demonstrated by following the fibrillization of ß-amyloid peptide 1-42 (Aß42) as a function of time and by comparing to the reference methods atomic force microscopy (AFM) and thioflavin T (ThT) assay. The fibrillization leads to reduced adsorption of Aß42 to the nanoparticles increasing the TR-LRET signal. The investigated methods detected fibril formation with equal sensitivities. Eight potential fibrillization inhibitor compounds reported in the literature were tested and the results obtained with each method were compared. It was shown with AFM imaging that the inhibition of fibril formation was not complete with any of the compounds. The developed TR-LRET nanoparticle assay gave corresponding results with the AFM imaging. However, the ThT assay led to contradictory results, as low fluorescence signal was measured in the presence of all tested compounds suggesting inhibition of fibrillization. Our results suggest that the developed TR-LRET nanoparticle assay can be exploited for screening of potential ß-amyloid aggregation inhibitors, whereas some of the tested compounds may be measured as false positive inhibitors with the much-utilized ThT assay.

Luminometric Label Array for Quantification and Identification of Metal Ions.

Quantification and identification of metal ions has gained interest in drinking water and environmental analyses. We have developed a novel label array method for the quantification and identification of metal ions in drinking water. This simple ready-to-go method is based on the nonspecific interactions of multiple unstable lanthanide chelates and nonantenna ligands with sample leading to a luminescence signal profile, unique to the sample components. The limit of detection at ppb concentration level and average coefficient of variation of 10% were achieved with the developed label array. The identification of 15 different metal ions including different oxidation states Cr(3+)/Cr(6+), Cu(+)/Cu(2+), Fe(2+)/Fe(3+), and Pb(2+)/Pb(4+) was demonstrated. Moreover, a binary mixture of Cu(2+) and Fe(3+) and ternary mixture of Cd(2+), Ni(2+), and Pb(2+) were measured and individual ions were distinguished.

Lanthanide Label Array Method for Identification and Adulteration of Honey and Cacao.

A generic, cost-effective, and simple method has been developed to fingerprint liquids to differentiate food brands and ingredients. The method is based on a label array using nonspecific long lifetime unstable luminescent lanthanide labels. The interaction between the liquid sample and the label is typically detrimental to the luminescence of the unstable chelate leading to a sample-dependent luminescence-intensity array. The label-array method is a unique approach as the array of unstable chelates is extremely inexpensive to produce and possesses high sensitivity due to spectral as well as unstable structural properties of the lanthanide label. The global method has been applied to distinguish commercial honey and cacao brands to demonstrate its feasibility as honey and cacao are among the most adulterated food products.

Method for determination of polyethylene glycol molecular weight.

A method utilizing competitive adsorption between polyethylene glycols (PEGs) and labeled protein to nanoparticles was developed for the determination of PEG molecular weight (MW) in a microtiter plate format. Two mix-and-measure systems, time-resolved luminescence resonance energy transfer (TR-LRET) with donor europium(III) polystyrene nanoparticles and acceptor-labeled protein and quenching with quencher gold nanoparticles and fluorescently labeled protein were compared for their performance. MW is estimated from the PEG MW dependent changes in the competitive adsorption properties, which are presented as the luminescence signal vs PEG mass concentration. The curves obtained with the TR-LRET system overlapped for PEGs larger than 400 g/mol providing no information on MW. Distinctly different curves were obtained with the quenching system enabling the assessment of PEG MW within a broad dynamic range. The data was processed with and without prior knowledge of the PEG concentration to measure PEGs over a MW range from 62 to 35,000 g/mol. The demonstration of the measurement independent of the PEG concentration suggests that the estimation of MW is possible with quenching nanoparticle system for neutrally charged and relatively hydrophilic polymeric molecules widening the applicability of the simple and cost-effective nanoparticle-based methods.

Simple nanoparticle-based luminometric method for molecular weight determination of polymeric compounds.

A nanoparticle-based method utilizing time-resolved luminescence resonance energy transfer (TR-LRET) was developed for molecular weight determination. This mix-and-measure nanoparticle method is based on the competitive adsorption between the analyte and the acceptor-labeled protein to donor Eu(III) nanoparticles. The size-dependent adsorption of molecules enables the molecular weight determination of differently sized polymeric compounds down to a concentration level of micrograms per liter. The molecular weight determination from 1 to 10 kDa for polyamino acids and from 0.3 to 70 kDa for polyethylene imines is demonstrated. The simple and cost-effective nanoparticle method as microtiter plate assay format shows great potential for the detection of the changes in molecular weight or for quantification of differently sized molecules in biochemical laboratories and in industrial polymeric processes.

Luminescence stability improvement in liposome-based homogeneous luminescence resonance energy transfer.

A stable liposome-based time-resolved luminescence resonance energy transfer (TR-LRET) assay was developed based on the interaction of biotinylated lipids and streptavidin. Eu(3+) ion chelated to 4,4,4-trifluoro-1-(2-naphthalenyl)-1,3-butanedione and trioctylphosphine oxide was incorporated into liposomes. Acceptor-labeled streptavidin bound to biotinylated lipids of the liposomes enables TR-LRET. A stable assay performance was achieved by optimization. High Eu(3+) signal and stability, low variation, and sensitivity below 100 pM for free biotin was achieved by incorporating the chelate into liposomes containing cholesterol in a carbonate buffer. Potentially, the stable assay compared with the assay without cholesterol offers an improved platform to liposome-based detection systems.

Nonspecific particle-based method with two-photon excitation detection for sensitive protein quantification and cell counting.

A novel easy-to-use homogeneous method utilizing two-photon excitation (TPX) for quantification of proteins or counting of eukaryotic cells in solution has been developed. This highly sensitive technique is based on the adsorption competition between the sample and fluorescently labeled protein to micrometer-sized carboxylate modified polystyrene particles and detection of two-photon excited fluorescence. The adsorption of the labeled protein to the particles was detected as a distinct fluorescence on individual microparticles. Analyte protein or eukaryotic cells interacted with particle surface and reduced the adsorption of labeled protein to the particles resulting in a decrease of the fluorescence. The optimizations of assay conditions were performed separately for protein quantification and cell counting, and the principle of the method was confirmed with the fluorescence microscopy imaging. The protein quantification assay allowed the determination of picogram quantities (1.2 µg/L) of protein, and the cell counting assay allowed three cells in the sample with an average variation of approximately 10% in the signal. The protein assay sensitivity was more than 500-fold improved from the common most sensitive commercial methods. Moreover, the dynamic range of the assay was broad, approximately 4 orders of magnitude. The cell assay has sensitivity comparable to the most sensitive commercial method. The developed method tolerates interfering agents such as neutral detergents found in cell lysate samples even at high concentrations. The method is experimentally fairly simple and allows the expansion for the use of the TPX technology.

Protein quantification using resonance energy transfer between donor nanoparticles and acceptor quantum dots.

A homogeneous time-resolved luminescence resonance energy transfer (TR-LRET) assay has been developed to quantify proteins. The competitive assay is based on resonance energy transfer (RET) between two luminescent nanosized particles. Polystyrene nanoparticles loaded with Eu(3+) chelates (EuNPs) act as donors, while protein-coated quantum dots (QDs), either CdSe/ZnS emitting at 655 nm (QD655-strep) or CdSeTe/ZnS with emission wavelength at 705 nm (QD705-strep), are acceptors. In the absence of analyte protein, in our case bovine serum albumin (BSA), the protein-coated QDs bind nonspecifically to the EuNPs, leading to RET. In the presence of analyte proteins, the binding of the QDs to the EuNPs is prevented and the RET signal decreases. RET from the EuNPs to the QDs was confirmed and characterized with steady-state and time-resolved luminescence spectroscopy. In accordance with the Förster theory, the approximate average donor-acceptor distance is around 15 nm at RET efficiencies, equal to 15% for QD655 and 13% for QD705 acceptor, respectively. The limits of detection are below 10 ng of BSA with less than a 10% average coefficient of variation. The assay sensitivity is improved, when compared to the most sensitive commercial methods. The presented mix-and-measure method has potential to be implemented into routine protein quantification in biological laboratories.

Method for estimation of protein isoelectric point.

Adsorption of sample protein to Eu(3+) chelate-labeled nanoparticles is the basis of the developed noncompetitive and homogeneous method for the estimation of the protein isoelectric point (pI). The lanthanide ion of the nanoparticle surface-conjugated Eu(3+) chelate is dissociated at a low pH, therefore decreasing the luminescence signal. A nanoparticle-adsorbed sample protein prevents the dissociation of the chelate, leading to a high luminescence signal. The adsorption efficiency of the sample protein is reduced above the isoelectric point due to the decreased electrostatic attraction between the negatively charged protein and the negatively charged particle. Four proteins with isoelectric points ranging from ~5 to 9 were tested to show the performance of the method. These pI values measured with the developed method were close to the theoretical and experimental literature values. The method is sensitive and requires a low analyte concentration of submilligrams per liter, which is nearly 10000 times lower than the concentration required for the traditional isoelectric focusing. Moreover, the method is significantly faster and simpler than the existing methods, as a ready-to-go assay was prepared for the microtiter plate format. This mix-and-measure concept is a highly attractive alternative for routine laboratory work.

Sensitive method for determination of protein and cell concentrations based on competitive adsorption to nanoparticles and time-resolved luminescence resonance energy transfer between labeled proteins.

A sensitive mix-and-measure method for the determination of protein and cell concentrations was developed. It is based on the competitive adsorption between the analyte and donor- and acceptor-labeled proteins to carboxylate-modified polystyrene nanoparticles. A high time-resolved luminescence resonance energy transfer (TR-LRET) signal is detected in the absence of the analyte due to the close proximity of the nanoparticle-adsorbed labeled proteins. The increased concentration of the analyte decreases the adsorption of the labeled proteins, leading to the loss of proximity and thus a decrease in the TR-LRET. The detection limit of the assay was 2.6 ng of proteins, which is higher than that of the most sensitive commercial methods. The method was also applied to cell counting, and 200 eukaryotic cells were measured in a microtiter well under the optimized conditions. The average coefficient of variation for both developed assays was approximately 10%, and the protein-to-protein variability for 11 different proteins was no more than 20%. The developed method requires no labeled particles, making the concept optimally applicable to varying targets as the material of the particle may be selected according to the application.

Sensitive luminometric method for protein quantification in bacterial cell lysate based on particle adsorption and dissociation of chelated europium.

A sensitive and rapid assay for the quantification of proteins, based on sample protein adsorption to Eu(3+)-chelate-labeled nanoparticles, was developed. The lanthanide ion of the surface-conjugated Eu(3+) chelate is dissociated at a low pH, decreasing the luminescence signal. The increased concentration of the sample protein prevents dissociation of the chelate, leading to a high luminescence signal due to the nanoparticle-bound protein. The assay sensitivity for the quantification of proteins was 130 pg for bovine serum albumin (BSA), which is an improvement of nearly 100-fold from the most sensitive commercial methods. The average coefficient of variation for the assay of BSA was 8%. The protein-to-protein variability was sufficiently low; the signal values varied within a 28% coefficient of variation for nine different proteins. The developed method is relatively insensitive to the presence of contaminants, such as nonionic detergents commonly found in biological samples. The existing methods tested for the total protein quantification failed to measure protein concentration in the presence of bacterial cell lysate. The developed method quantified protein also in samples containing insoluble cell components reducing the need for additional centrifugal assay steps and making the concept highly attractive for routine laboratory work.

High sensitivity luminescence nanoparticle assay for the detection of protein aggregation.

Nanoparticle assay utilizing time-resolved luminescence resonance energy transfer (TR-LRET) was developed for the detection of protein aggregation. This mix-and-measure nanoparticle assay is based on the competitive adsorption of the sample and the acceptor-labeled protein to donor europium(III) polystyrene particles. The protein aggregation was detected with the developed TR-LRET nanoparticle assay, UV240 absorbance and dynamic light scattering (DLS). All methods well equally detected the aggregation and aggregates, whose size ranged from single protein to more than 1000 nm aggregates. The developed method allowed the aggregation detection of the entire size range at more than 10,000 times lower concentration, 30 µg/L, compared to UV240 and DLS. The simple-to-use and sensitive nanoparticle assay with existing microtiter plate luminometric instrumentation can find use as a routine tool for protein aggregation studies in biochemical laboratories and for quality assessment of protein products in industry.

Sensitive fluorometric nanoparticle assays for cell counting and viability.

We have developed easy-to-use homogeneous methods utilizing time-resolved fluorescence resonance energy transfer (TR-FRET) and fluorescence quenching for quantification of eukaryotic cells. The methods rely on a competitive adsorption of cells and fluorescently labeled protein onto citrate-stabilized colloidal gold nanoparticles or carboxylate-modified polystyrene nanoparticles doped with an Eu(III) chelate. In the gold nanoparticle sensor, the adsorption of the labeled protein to the gold nanoparticles leads to quenching of the fluorochrome. Eukaryotic cells reduce the adsorption of labeled protein to the gold particles increasing the fluorescence signal. In the Eu(III) nanoparticle sensor, the time-resolved fluorescence resonance energy transfer between the nanoparticles and an acceptor-labeled protein is detected; a decrease in the magnitude of the time-resolved energy transfer signal (sensitized time-resolved fluorescence) is proportional to the cell-nanoparticle interaction and subsequent reduced adsorption of the labeled protein. Less than five cells were detected and quantified with the nanoparticle sensors in the homogeneous microtiter assay format with a coefficient of variation of 6% for the gold and 12% for the Eu(III) nanoparticle sensor. The Eu(III) nanoparticle sensor was also combined with a cell impermeable nucleic acid dye assay to measure cell viability in a single tube test with cell counts below 1000 cells/tube. This sensitive and easy-to-use nanoparticle sensor combined with a viability test for a low concentration of cells could potentially replace existing microscopic methods in biochemical laboratories.

Rapid detection of trace amounts of surfactants using nanoparticles in fluorometric assays.

Rapid microtiter assays that utilize the time-resolved fluorescence resonance energy transfer or quenching of dye-labeled proteins adsorbed onto the surfaces of polystyrene or maghemite nanoparticles have been developed for the detection and quantification of trace amounts of surfactants at concentrations down to 10 nM.

Methicillin-resistant Staphylococcus aureus screening by online immunometric monitoring of bacterial growth under selective pressure.

Rapid, high-throughput screening tools are needed to contain the spread of hospital-acquired methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) strains. Most techniques used in current clinical practice still require time-consuming culture for primary isolation of the microbe. We present a new phenotypic assay for MRSA screening. The technique employs a two-photon excited fluorescence (TPX) detection technology with S. aureus-specific antibodies that allows the online monitoring of bacterial growth in a single separation-free process. Different progressions of fluorescence signals are recorded for methicillin-susceptible and -resistant strains when the growth of S. aureus is monitored in the presence of cefoxitin. The performance of the new technique was evaluated with 20 MRSA strains, 6 methicillin-susceptible S. aureus strains, and 7 coagulase-negative staphylococcal strains and two different monoclonal S. aureus-specific antibodies. When either of these antibodies was used, the sensitivity and the specificity of the TPX assay were 100%. All strains were correctly classified within 8 to 12 h, and up to 70 samples were simultaneously analyzed on a single 96-well microtiter plate. As a phenotypic method, the TPX assay is suited for screening purposes. The final definition of methicillin resistance in any S. aureus strain should be based on the presence of the mecA gene. The main benefit afforded by the initial use of the TPX methodology lies in its low cost and applicability to high-throughput analysis.

Ultrasensitive protein concentration measurement based on particle adsorption and fluorescence quenching.

A new easy-to-use method for quantification of proteins in solution has been developed. It is based on adsorption competition of the sample protein and fluorescently labeled bovine serum albumin (BSA) onto gold particles. The protein concentration is determined by observing the magnitude of fluorescence altered by quenching the fluorescence on the gold particles in a homogeneous assay format. Under optimal low pH conditions, the assay allowed the determination of picogram quantities (7.0 microg/L) of proteins with an average variation of 4.5% in a 10 min assay. The assay sensitivity was more than 10-fold improved from those of the commonly used most sensitive commercial methods. In addition, the particle sensor provides a simple and rapid assay format without requirements for hazardous test compounds and elevated temperature. Eleven different proteins were tested with the constructed sensor exhibiting a protein-to-protein variability less than 15% allowing protein concentration measurements without the need for recalibration of different proteins.

Liposome-based homogeneous luminescence resonance energy transfer.

There is an increasing need for developing simple assay formats for biomedical screening purposes. Assays on cell membranes have become important in studies of receptor-ligand interactions and signal pathways. Here luminescence energy transfer was studied on liposomes containing europium ion chelated to 4,4,4-trifluoro-1-(2-naphthalenyl)-1,3-butanedione and trioctylphosphine oxide. Energy transfer efficiency was characterized with biotin-streptavidin interaction, and a model assay concept for a homogeneous time-resolved luminescence resonance energy transfer (LRET) assay was developed. Acceptor-labeled streptavidin was bound to biotinylated lipids on the liposomes, leading to close proximity of the LRET pair. The liposome-based LRET assay was optimized for dye incorporation and concentration, biotinylation degree, liposome size, and kinetics. Sensitivity for a competitive biotin assay was at a picomolar range with a coefficient of variation from 7 to 20%. The developed lipid membrane-based system was feasible in separation free LRET assay concept with high sensitivity, indicating that the assay principle can potentially be used for biologically more relevant target molecules.

Sensitive quantitative protein concentration method using luminescent resonance energy transfer on a layer-by-layer europium(III) chelate particle sensor.

A particle-based protein quantification method was developed. The method relies on adsorption of proteins on particles and time-resolved fluorescence resonance energy transfer (TR-FRET). Layer-by-layer (LbL) particles containing europium(III) chelate donor were prepared. A protein labeled with an acceptor was adsorbed onto the particles and near-infrared energy transfer signal was detected in time-gated detection mode. Sample proteins efficiently occupied the particle surface preventing binding of the acceptor-labeled protein leading to a particle sensor with a significant signal change. We detected subnanomolar protein concentration using the rapid and simple mix-and-measure method with a coefficient of variation below 10%. Compared to known protein concentration methods, the developed method required no hazardous substances or elevated temperature to reach the high-sensitivity level.