Magnetic-molecularly imprinted polymers in electrochemical sensors and biosensors.

Magnetic particles, as well as molecularly imprinted polymers, have revolutionized separation and bioanalytical methodologies in the 1980s due to their wide range of applications. Today, biologically modified magnetic particles are used in many scientific and technological applications and are integrated in more than 50,000 diagnostic instruments for the detection of a huge range of analytes. However, the main drawback of this material is their stability and high cost. In this work, we review recent advances in the synthesis and characterization of hybrid molecularly imprinted polymers with magnetic properties, as a cheaper and robust alternative for the well-known biologically modified magnetic particles. The main advantages of these materials are, besides the magnetic properties, the possibility to be stored at room temperature without any loss in the activity. Among all the applications, this work reviews the direct detection of electroactive analytes based on the preconcentration by using magnetic-MIP integrated on magneto-actuated electrodes, including food safety, environmental monitoring, and clinical and pharmaceutical analysis. The main features of these electrochemical sensors, including their analytical performance, are summarized. This simple and rapid method will open the way to incorporate this material in different magneto-actuated devices with no need for extensive sample pretreatment and sophisticated instruments.

Osteoblastic exosomes. A non-destructive quantitative approach of alkaline phosphatase to assess osteoconductive nanomaterials.

Alkaline phosphatase (ALP) is an essential biomarker of osteoblastic activity. Currently, ALP activity has been used to study bone mineralization mechanisms and osteoactive biomaterials among others. The ALP quantification is usually performed by destructive methods either on growing cells or cells lysate in which the osteoconductive biomaterial is being assessed. This work addresses the evaluation of a non-destructive colorimetric approach for the determination of ALP activity on osteoblast-derived exosomes from culture supernatants. The efficiency of the method was evaluated on osteoconductive electrospun scaffolds of PCL compounded with ZnO as a reference biomaterial. The results demonstrated that the osteoblast cell line mineralization induced by osteoconductive scaffolds can be monitorized over time by the non-destructive measurement of ALP activity on osteoblast derived exosomes. Consequently, this non-destructive approach suggested to be a reliable alternative technique for the quantification of biomaterials osteoconductivity or even evaluation of osteoblastic response at stem cells.

DL4papers: a deep learning approach for the automatic interpretation of scientific articles.

MOTIVATION: In precision medicine, next-generation sequencing and novel preclinical reports have led to an increasingly large amount of results, published in the scientific literature. However, identifying novel treatments or predicting a drug response in, for example, cancer patients, from the huge amount of papers available remains a laborious and challenging work. This task can be considered a text mining problem that requires reading a lot of academic documents for identifying a small set of papers describing specific relations between key terms. Due to the infeasibility of the manual curation of these relations, computational methods that can automatically identify them from the available literature are urgently needed. RESULTS: We present DL4papers, a new method based on deep learning that is capable of analyzing and interpreting papers in order to automatically extract relevant relations between specific keywords. DL4papers receives as input a query with the desired keywords, and it returns a ranked list of papers that contain meaningful associations between the keywords. The comparison against related methods showed that our proposal outperformed them in a cancer corpus. The reliability of the DL4papers output list was also measured, revealing that 100% of the first two documents retrieved for a particular search have relevant relations, in average. This shows that our model can guarantee that in the top-2 papers of the ranked list, the relation can be effectively found. Furthermore, the model is capable of highlighting, within each document, the specific fragments that have the associations of the input keywords. This can be very useful in order to pay attention only to the highlighted text, instead of reading the full paper. We believe that our proposal could be used as an accurate tool for rapidly identifying relationships between genes and their mutations, drug responses and treatments in the context of a certain disease. This new approach can certainly be a very useful and valuable resource for the advancement of the precision medicine field. AVAILABILITY AND IMPLEMENTATION: A web-demo is available at: http://sinc.unl.edu.ar/web-demo/dl4papers/. Full source code and data are available at: https://sourceforge.net/projects/sourcesinc/files/dl4papers/. CONTACT: lbugnon@sinc.unl.edu.ar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comparing nucleic acid lateral flow and electrochemical genosensing for the simultaneous detection of foodborne pathogens.

Due to the increasing need of rapid tests for application in low resource settings, WHO summarized their ideal features under the acronym ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, Delivered to those who need it). In this work, two different platforms for the rapid and simultaneous testing of the foodborne pathogens E. coli O157:H7 and Salmonella enterica, in detail a nucleic acid lateral flow and an electrochemical magneto-genosensor are presented and compared in terms of their analytical performance. The DNA of the bacteria was amplified by polymerase chain reaction using a quadruple-tagging set of primers specific for E. coli eaeA (151bp) and Salmonella enterica yfiR (375bp) genes. During the amplification, the amplicons were labelled at the same time with biotin/digoxigenin or biotin/fluorescein tags, respectively. The nucleic acid lateral flow assay was based on the use of streptavidin gold nanoparticles for the labelling of the tagged amplicon from E. coli and Salmonella. The visual readout was achieved when the gold-modified amplicons were captured by the specific antibodies. The features of this approach are discussed and compared with an electrochemical magneto-genosensor. Although nucleic acid lateral flow showed higher limit of detection, this strategy was able to clearly distinguish positive and negative samples of both bacteria being considered as a rapid and promising detection tool for bacteria screening.

Magnetic molecularly imprinted polymer for the isolation and detection of biotin and biotinylated biomolecules.

Magnetic separation based on biologically-modified magnetic particles is a preconcentration procedure commonly integrated in magneto actuated platforms for the detection of a huge range of targets. However, the main drawback of this material is the low stability and high cost. In this work, a novel hybrid molecularly-imprinted polymer with magnetic properties is presented with affinity towards biotin and biotinylated biomolecules. During the synthesis of the magneto core-shell particles, biotin was used as a template. The characterization of this material by microscopy techniques including SEM, TEM and confocal microscopy is presented. The application of the magnetic-MIPs for the detection of biotin and biotinylated DNA in magneto-actuated platforms is also described for the first time. The magnetic-MIP showed a significant immobilization capacity of biotinylated molecules, giving rise to a cheaper and a robust method (it is not required to be stored at 4°C) with high binding capacity for the separation and purification under magnetic actuation of a wide range of biotinylated molecules, and their downstream application including determination of their specific targets.

Yoctomole electrochemical genosensing of Ebola virus cDNA by rolling circle and circle to circle amplification.

This work addresses the design of an Ebola diagnostic test involving a simple, rapid, specific and highly sensitive procedure based on isothermal amplification on magnetic particles with electrochemical readout. Ebola padlock probes were designed to detect a specific L-gene sequence present in the five most common Ebola species. Ebola cDNA was amplified by rolling circle amplification (RCA) on magnetic particles. Further re-amplification was performed by circle-to-circle amplification (C2CA) and the products were detected in a double-tagging approach using a biotinylated capture probe for immobilization on magnetic particles and a readout probe for electrochemical detection by square-wave voltammetry on commercial screen-printed electrodes. The electrochemical genosensor was able to detect as low as 200 ymol, corresponding to 120 cDNA molecules of L-gene Ebola virus with a limit of detection of 33 cDNA molecules. The isothermal double-amplification procedure by C2CA combined with the electrochemical readout and the magnetic actuation enables the high sensitivity, resulting in a rapid, inexpensive, robust and user-friendly sensing strategy that offers a promising approach for the primary care in low resource settings, especially in less developed countries.

Spontaneous symmetry breaking on ordered, racemic monolayers of achiral theophylline: formation of unichiral stripes on Au(111).

We report the observation of spontaneous chiral symmetry breaking within ordered, racemic monolayers of theophylline, manifesting itself as extended, nanoscale unichiral stripes at the interface between molecular domains. Theophylline is a xanthine derivative playing an important role in several biochemical processes. Molecular chirality is induced by adsorption on the Au(111) surface, resulting in extended domains with two different racemic, ordered structures, coexisting with a disordered phase. By combining low-temperature scanning tunneling microscopy (LT-STM) and ab initio density functional theory calculations, we first provide a detailed picture of the interactions within the ordered assemblies, and we uncover the origin of the distinct contrast features in STM images. Secondly, experiments reveal the existence of nanoscale stripes of unichiral molecules separating racemic domains of one of the two ordered phases, giving rise to a local enantiomeric imbalance. Systematic theoretical investigation of their structure and chiral composition confirm their unichirality, with the specific handedness related to the registry between the two ordered domains facing the stripes. These findings can open the way to new insights into the elusive mechanisms leading to local chiral imbalances in racemic systems, possibly at the origin of biomolecular homochirality, as well as suggest novel approaches for stereoselective heterogeneous catalysis.

CD4 quantification based on magneto ELISA for AIDS diagnosis in low resource settings.

The Acquired Immune Deficiency Syndrome (AIDS) affects the life of millions of people around the world. Although rapid and low cost screening tests are widely available for the diagnosis of HIV infection, the count of CD4+ T lymphocytes remains a drawback in the areas mostly affected by the HIV, being this control imperative for assessing the deterioration of the immunological system and the progression towards AIDS, when the counting of cells falls down 200cellsµL(-1). This paper describes a high-throughput, simple and rapid method for CD4+ T lymphocytes quantification, directly in whole blood, based on a magneto ELISA. The CD4 cells are separated and preconcentrated from whole blood in magnetic particles, and labeled with an enzyme for the optical readout performed with a standard microplate reader. The magneto ELISA is able to reach the whole CD4 counting range of medical interest, being the limit of detection as low as 50 CD4+ cells per µL of whole blood, without any pretreatment. This method is a highly suitable alternative diagnostic tool for the expensive flow cytometry at the community and primary care level, providing a sensitive method but by using instrumentation widely available in low-resource settings laboratories and requiring low-maintenance, as is the case of a microplate reader operated by filters.

Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy.

Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate.

Electrochemical magneto-actuated biosensor for CD4 count in AIDS diagnosis and monitoring.

The counting of CD4(+) T lymphocytes is a clinical parameter used for AIDS diagnosis and follow-up. As this disease is particularly prevalent in developing countries, simple and affordable CD4 cell counting methods are urgently needed in resource-limited settings. This paper describes an electrochemical magneto-actuated biosensor for CD4 count in whole blood. The CD4(+) T lymphocytes were isolated, preconcentrated and labeled from 100 µL of whole blood by immunomagnetic separation with magnetic particles modified with antiCD3 antibodies. The captured cells were labeled with a biotinylated antiCD4 antibody, followed by the reaction with the electrochemical reporter streptavidin-peroxidase conjugate. The limit of detection for the CD4 counting magneto-actuated biosensor in whole blood was as low as 44 cells µL(-1) while the logistic range was found to be from 89 to 912 cells µL(-1), which spans the whole medical interest range for CD4 counts in AIDS patients. The electrochemical detection together with the immunomagnetic separation confers high sensitivity, resulting in a rapid, inexpensive, robust, user-friendly method for CD4 counting. This approach is a promising alternative for the costly standard flow cytometry and suitable as diagnostic tool at decentralized practitioner sites in low resource settings, especially in less developed countries.

A portable electrochemical magnetoimmunosensor for detection of sulfonamide antimicrobials in honey.

A new electrochemical magnetoimmunosensor (EMIS) has been developed for the screening of residues of sulfonamide antimicrobials in honey samples. The immunosensor is able to detect up to ten different sulfonamide congeners at levels below the action points established in some European countries (25 µg kg(-1)) after a hydrolysis step in which the sulfonamides are released from the corresponding conjugates formed in samples of this type. In spite of the complexity of the sample after the hydrolysis procedure, the EMIS could perform quantitative measurements, directly in these samples, without any additional sample cleanup or extraction step. For example, sulfapyridine, used as a reference, can be detected in hydrolyzed honey with a limit of detection (IC90) of 0.1 ± 0.03 µg kg(-1). Considering that the use of antibiotics for bee treatment is prohibited in the European Union, the immunosensor presented here could be an excellent screening tool. Moreover, several samples can be processed in parallel, which facilitates the analysis, reducing the necessity to use more costly confirmatory methods for just screening. As a proof of concept, a set of blind honey samples (spiked and incurred) were analyzed and the results were compared with those obtained by high-performance liquid chromatography-tandem mass spectrometry, demonstrating the potential of the EMIS as a screening tool.

An electrochemical magneto immunosensor (EMIS) for the determination of paraquat residues in potato samples.

An electrochemical magneto immunosensor for the detection of low concentrations of paraquat (PQ) in food samples has been developed and its performance evaluated in a complex sample such as potato extracts. The immunosensor presented uses immunoreagents specifically developed for the recognition of paraquat, a magnetic graphite-epoxy composite (m-GEC) electrode and biofunctionalized magnetic micro-particles (PQ1-BSAMP) that allow reduction of the potential interferences caused by the matrix components. The amperometric signal is provided by an enzymatic probe prepared by covalently linking an enzyme to the specific antibodies (Ab198-cc-HRP). The use of hydroquinone, as mediator, allows recording of the signal at a low potential, which also contributes to reducing the background noise potentially caused by the sample matrix. The immunocomplexes formed on top of the modified MP are easily captured by the m-GEC, which acts simultaneously as transducer. PQ can be detected at concentrations as low as 0.18 ± 0.09 µg L(-1). Combined with an efficient extraction procedure, PQ residues can be directly detected and accurately quantified in potato extracts without additional clean-up or purification steps, with a limit of detection (90% of the maximum signal) of 2.18 ± 2.08 µg kg(-1), far below the maximum residue level (20 µg kg(-1)) established by the EC. The immunosensor presented here is suitable for on-site analysis. Combined with the use of magnetic racks, multiple samples can be run simultaneously in a reasonable time.

Magneto immunosensor for gliadin detection in gluten-free foodstuff: towards food safety for celiac patients.

Gliadin is a constituent of the cereal protein gluten, responsible for the intolerance generated in celiac disease. Its detection is of high interest for food safety of celiac patients, since the only treatment known until now is a lifelong avoidance of this protein in the diet. Therefore, it is essential to have an easy and reliable method of analysis to control the contents in gluten-free foods. An electrochemical magneto immunosensor for the quantification of gliadin or small gliadin fragments in natural or pretreated food samples is described for the first time and compared to a novel magneto-ELISA system based on optical detection. The immunological reaction was performed on magnetic beads as solid support by the oriented covalent immobilization, of the protein gliadin on tosyl-activated beads. Direct, as well as indirect competitive immunoassays were optimized, achieving the best analytical performance with the direct competitive format. Excellent detection limits (in the order of µg L(-1)) were achieved, according to the legislation for gluten-free products. The matrix effect, as well as the performance of the assays was successfully evaluated using spiked gluten-free foodstuffs (skimmed milk and beer), obtaining excellent recovery values in the results.

Magneto immunoassays for Plasmodium falciparum histidine-rich protein 2 related to malaria based on magnetic nanoparticles.

Magneto immunoassay-based strategies for the detection of Plasmodium falciparum histidine-rich protein 2 (HRP2) related to malaria are described for the first time by using magnetic micro- and nanoparticles. The covalent immobilization of a commercial monoclonal antibody toward the HRP2 protein in magnetic beads and nanoparticles was evaluated and compared. The immunological reaction for the protein HRP2 was successfully performed in a sandwich assay on magnetic micro- and nanoparticles by using a second monoclonal antibody labeled with the enzyme, horseradish peroxidase (HRP). Then, the modified magnetic particles were easily captured by a magneto sensor made of graphite-epoxy composite (m-GEC) which was also used as the transducer for the electrochemical detection. The performance of the immunoassay-based strategy with the electrochemical magneto immunosensors was successfully evaluated and compared with a novel magneto-ELISA based on optical detection using spiked serum samples. Improved sensitivity was obtained when using 300 nm magnetic nanoparticles in both cases. The electrochemical magneto immunosensor coupled with magnetic nanoparticles have shown better analytical performance in terms of limit of detection (0.36 ng mL(-1)), which is much lower than the LOD reported by other methods. Moreover, at a low level of HRP2 concentration of 31.0 ng mL(-1), a signal of 15.30 µA was reached with a cutoff value of 0.34 µA, giving a clear positive result with a non-specific adsorption ratio of 51. Due to the high sensitivity, this novel strategy offers great promise for rapid, simple, cost-effective, and on-site detection of falciparum malaria disease in patients, but also to screen out at-risk blood samples for prevention of transfusion-transmitted malaria.

A novel strategy for screening-out raw milk contaminated with Mycobacterium bovis on dairy farms by double-tagging PCR and electrochemical genosensing.

SUMMARY: A highly sensitive assay for rapidly screening-out Mycobacterium bovis in contaminated samples was developed based on electrochemical genosensing. The assay consists of specific amplification and double-tagging of the IS6110 fragment, highly related to M. bovis, followed by electrochemical detection of the amplified product. PCR amplification was carried out using a labeled set of primers and resulted in a amplicon tagged at each terminus with both biotin and digoxigenin. Two different electrochemical platforms for the detection of the double-tagged amplicon were evaluated: (i) an avidin biocomposite (Av-GEB) and (ii) a magneto sensor (m-GEC) combined with streptavidin magnetic beads. In both cases, the double- tagged amplicon was immobilized through its biotinylated end and electrochemically detected, using an antiDig-HRP conjugate, through its digoxigenin end. The assay was determined to be highly sensitive, based on the detection of 620 and 10 fmol of PCR amplicon using the Av-GEB and m-GEC strategies, respectively. Moreover, the m-GEC assay showed promising features for the detection of M. bovis on dairy farms by screening for the presence of the bacterium's DNA in milk samples. The obtained results are discussed and compared with respect to those of inter-laboratory PCR assays and tuberculin skin testing.

A novel strategy for screening-out raw milk contaminated with Mycobacterium bovis on dairy farms by double-tagging PCR and electrochemical genosensing

A highly sensitive assay for rapidly screening-out Mycobacterium bovis in contaminated samples was developed based on electrochemical genosensing. The assay consists of specific amplification and double-tagging of the IS6110 fragment, highly related to M. bovis, followed by electrochemical detection of the amplified product. PCR amplification was carried out using a labeled set of primers and resulted in a amplicon tagged at each terminus with both biotin and digoxigenin. Two different electrochemical platforms for the detection of the double-tagged amplicon were evaluated: (i) an avidin biocomposite (Av-GEB) and (ii) a magneto sensor (m-GEC) combined with streptavidin magnetic beads. In both cases, the double- tagged amplicon was immobilized through its biotinylated end and electrochemically detected, using an antiDig-HRP conjugate, through its digoxigenin end. The assay was determined to be highly sensitive, based on the detection of 620 and 10 fmol of PCR amplicon using the Av-GEB and m-GEC strategies, respectively. Moreover, the m-GEC assay showed promising features for the detection of M. bovis on dairy farms by screening for the presence of the bacterium's DNA in milk samples. The obtained results are discussed and compared with respect to those of inter-laboratory PCR assays and tuberculin skin testing (AU)

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Impedimetric detection of influenza A (H1N1) DNA sequence using carbon nanotubes platform and gold nanoparticles amplification.

In this work we report the use of an impedimetric genosensor for the model detection of H1N1 swine flu correlated DNA sequence. An oligonucleotide DNA probe, complementary to the target H1N1 virus sequence, was immobilized onto the electrode surface by covalent binding. Two different protocols, i.e. direct hybridization with the DNA target and a sandwich scheme, were employed and compared. In both cases the resulting hybrid was biotin-labelled to allow the additional conjugation with streptavidin gold nanoparticles (strept-AuNPs). The latter were used with the aim of enhancing the impedimetric signal, thus improving the sensitivity of the technique. The best limit of detection, obtained with the sandwich scheme after signal amplification step was 7.5 fmol (corresponding to 577 pmol L(-1)). Furthermore, a gold enhancement treatment was performed in order to compare the presence and distribution of gold nanoparticles onto the electrode surface. As an alternative way of visualization, streptavidin conjugate quantum dots (strept-QD) were employed to obtain fluorescence images of the DNA-biotin-strept-QD electrode surface. Finally, a comparison between impedance and microscopy was performed in terms of viability and feasibility of the techniques.

Electrochemical immunosensor for the diagnosis of celiac disease.

A novel electrochemical immunosensing strategy for the detection of antibodies to tissue transglutaminase (tTG) in human serum is presented. The proposed immunosensor consists of the immobilization by physical adsorption of tTG from guinea pig liver on graphite-epoxy composite (GEC) electrodes. After the reaction with the human serum (containing the specific antibodies in the case of celiac disease), the electrode was incubated with different kinds of secondary labeled antibodies, namely, horseradish peroxidase (HRP)-conjugated goat antibodies to human whole immunoglobulins (Igs), to human IgG, and finally to human IgA. Among the different classes of antibodies in human serum toward tTG, the best results were achieved when anti-tTG IgA antibodies were investigated. In total, 10 positive and 10 negative serum samples were processed, obtaining a sensitivity of 70% and a specificity of 100% compared with the commercial enzyme-linked immunosorbent assay (ELISA) method performed in a hospital laboratory. This strategy offers great promise for a simple, cost-effective, and user-friendly analytical method that allows point-of-care diagnosis of celiac disease.

Double-tagging polymerase chain reaction with a thiolated primer and electrochemical genosensing based on gold nanocomposite sensor for food safety.

A novel material for electrochemical biosensing based on rigid conducting gold nanocomposite (nano-AuGEC) is presented. Islands of chemisorbing material (gold nanoparticles) surrounded by nonreactive, rigid, and conducting graphite epoxy composite are thus achieved to avoid the stringent control of surface coverage parameters required during immobilization of thiolated oligos in continuous gold surfaces. The spatial resolution of the immobilized thiolated DNA was easily controlled by merely varying the percentage of gold nanoparticles in the composition of the composite. As low as 9 fmol (60 pM) of synthetic DNA were detected in hybridization experiments when using a thiolated probe. Moreover, for the first time a double tagging PCR strategy was performed with a thiolated primer for the detection of Salmonella sp., one of the most important foodborne pathogens affecting food safety. This assay was performed by double-labeling the amplicon during the PCR with a -DIG and -SH set of labeled primers. The thiolated end allows the immobilization of the amplicon on the nano-AuGEC electrode, while digoxigenin allows the electrochemical detection with the antiDIG-HRP reporter in the femtomole range. Rigid conducting gold nanocomposite represents a good material for the improved and oriented immobilization of biomolecules with excellent transducing properties for the construction of a wide range of electrochemical biosensors such as immunosensors, genosensors, and enzymosensors.

Immunoassay for folic acid detection in vitamin-fortified milk based on electrochemical magneto sensors.

An immunoassay-based strategy for folic acid in vitamin-fortified milk with electrochemical detection using magneto sensors is described for the first time. Among direct and indirect competitive formats, best performance was achieved with an indirect competitive immunoassay. The immunological reaction for folic acid (FA) detection was performed, for the first time on the magnetic bead as solid support by the covalent immobilization of a protein conjugate BSA-FA on tosyl-activated magnetic bead. Further competition for the specific antibody between FA in the food sample and FA immobilized on the magnetic bead was achieved, followed by the reaction with a secondary antibody conjugated with HRP (AntiIgG-HRP). Then, the modified magnetic beads were easily captured by a magneto sensor made of graphite-epoxy composite (m-GEC) which was also used as the transducer for the electrochemical detection. The performance of the immunoassay-based strategy with electrochemical detection using magneto sensors was successfully evaluated using spiked-milk samples and compared with a novel magneto-ELISA based on optical detection. The detection limit was found to be of the order of microgl(-1) (13.1 nmoll(-1), 5.8 microgl(-1)) for skimmed milk. Commercial vitamin-fortified milk samples were also evaluated obtaining good accuracy in the results. This novel strategy offers great promise for rapid, simple, cost-effective and on-site analysis of biological and food samples.