Selection of fluorescent aptamer beacons that light up in the presence of zinc

In order to generate nucleic acid biosensors that could undergo a reversible conformation change in the presence of the metal zinc, a random sequence pool of single-stranded DNA was immobilized on an oligonucleotide affinity column. In the presence of zinc, those species that underwent a conformational change were released from the column, collected, and amplified. A series of negative and positive selections refined the metal specificity of the selected aptamer beacons. Since the aptamer beacons contained a fluorophore, while the bound oligonucleotide contained a quencher, zinc binding also resulted in an increase in fluorescence. One of the selected beacons, Zn-6m2, bound zinc in the low micromolar range, gave a dose-dependent fluorescence signal, and showed an approximately sixfold increase in fluorescence on zinc binding. While some cross-reactivity with cadmium was observed, it should nonetheless prove possible to use the novel selection method to generate and tune the specificity of a variety of reversible metal biosensors. Such biosensors could potentially be used for continuous monitoring of metals in environmental samples.     

Recent developments in analytical applications of quantum dots

This review discusses the application of quantum dots (QDs) to chemical and biological detection, for which they have excellent features, particularly size-dependent optical properties.We can summarize the main areas discussed in this review as follows:(1) QDs associated with enzyme-linked immunosorbent assay (ELISA), chip detection and capillary electrophoresis (CE) enhance the sensitivity and the speed of detection of residues;(2) QDs are applied with other techniques, including polymerase chain reaction (PCR), fluorescence resonance-energy transfer (FRET) analysis, fluorescence in-situ hybridization (FISH) and western blot analysis; and,(3) QDs combined with the above techniques can successfully detect DNA and protein.We also cover perspectives and challenges in analytical applications of QDs.     

Imprinted polymer particles for selenium uptake: synthesis, characterization and analytical applications

This work reports the preparation of molecularly imprinted polymer (MIP) particles for selective extraction and determination of selenium ions from aqueous media. Polymerization was achieved in a glass tube containing SeO₂, o-phenylenediamine, 2-vinylpyridine (VP), ethyleneglycoldimethacrylate (EDMA), 2,2′-azobisisobutyronitrile (AIBN). The polymer block obtained was ground and sieved (55-75 μm) and the Se-o-phenylenediamine complex was removed from polymer particles by leaching with 2 M of HCl, which leaves a cavity in the polymer particles. The polymer particles both prior to and after leaching have been characterized by IR and thermogravimetric (TG) studies. The effect of different parameters, such as pH, extraction time, type and least amount of eluent for elution of complex from polymer were evaluated. Extraction efficiencies >99% were obtained by elution of the polymers with 15 mL of methanol-acetonitrile mixture (1:2, v/v). The limit of detection of the proposed method followed by hydride generation atomic absorption spectroscopy (HG-AAS) was found to be 3.3 μg L⁻¹ and a dynamic linear range (DLR) of 10-200 μg L⁻¹ was obtained. The relative standard deviations (R.S.D.s) at 30.0 μg L⁻¹ of Se were below than 8.1%. The influence of various cationic interferences on percent recovery of complex was studied. The method was applied to the recovery and determination of selenium in different real samples.     

In-vivo and in-vitro testing to assess the bioaccessibility and the bioavailability of arsenic, selenium and mercury species in food samples

In-vivo and in-vitro gastrointestinal (GI) extractions, also known as oral bioaccessibility and bioavailability, are important approaches to assess chemical risk to humans. We give an overview of in-vivo and in-vitro bioaccessibility and bioavailability assays for testing arsenic, selenium and mercury (As, Se and Hg) species from food samples. We critically evaluate the parameters affecting in-vivo and in-vitro processes. In addition, we consider the effect of cooking food on bioaccessibility and bioavailability, and stability and transformation, of species during in-vivo or in-vitro processes. The bioaccessibility and bioavailability of As, Se and Hg species are affected by the sample matrix, cooking food and the experimental conditions applied (gastric and intestinal pH, incubation temperature and residence time). Regarding species degradation and transformation during in-vitro procedures, good stability has been observed for most As species, except for certain arsenosugars. Important transformations during in-vitro processes have been reported for Se species [e.g., conversion of γ-glu-Se-MeSeCys to Se-MeSeCys, and organic Se species (MeSeCys, SeCys2 and SeMet) degradation to inorganic Se]. Finally, we summarize speciation and detection conditions for As, Se and Hg speciation, and quality control to assure reliable measurements.     

Recent progress in the chemistry and chemical biology of microbial signaling molecules: quorum-sensing pheromones and microbial hormones

Communication among microorganisms is mediated by secretion and detection of microbial signaling molecules such as quorum-sensing pheromones and microbial hormones. The molecules elicit the regulation of important genes necessary for microbial survival and often play important roles in interspecies or even inter-kingdom communication. Recent progress in the study of the signaling molecules has enabled us to eavesdrop on microbial conversations to gain insight on their intercellular communication system. This review summarizes the recent advances in the chemistry and chemical biology of these important microbial signaling molecules: acyl-homoserine lactones (AHLs), AI-2, CAI-1 related α-hydroxy ketones (AHKs), ComX pheromones, diffusible signal factors (DSFs), diffusible extracellular factor (DF), and Phytophthora mating hormones.     

Dual-color upconversion fluorescence and aptamer-functionalized magnetic nanoparticles-based bioassay for the simultaneous detection of Salmonella Typhimurium and Staphylococcus aureus

A sensitive luminescent bioassay for the simultaneous detection of Salmonella Typhimurium and Staphylococcus aureus was developed using aptamer-conjugated magnetic nanoparticles (MNPs) for both recognition and concentration elements and using upconversion nanoparticles (UCNPs) as highly sensitive dual-color labels. The bioassay system was fabricated by immobilizing aptamer 1 and aptamer 2 onto the surface of MNPs, which were employed to capture and concentrate S. Typhimurium and S. aureus. NaY_0.78F₄:Yb_0.2,Tm_0.02 UCNPs modified aptamer 1 and NaY_0.28F₄:Yb_0.70,Er_0.02 UCNPs modified aptamer 2 further were bond onto the captured bacteria surface to form sandwich-type complexes. Under optimal conditions, the correlation between the concentration of S. Typhimurium and the luminescent signal was found to be linear within the range of 10¹–10⁵ cfu mL⁻¹ (R² = 0.9964), and the signal was in the range of 10¹–10⁵ cfu mL⁻¹ (R² = 0.9936) for S. aureus. The limits of detection of the developed method were found to be 5 and 8 cfu mL⁻¹ for S. Typhimurium and S. aureus, respectively. The ability of the bioassay to detect S. Typhimurium and S. aureus in real water samples was also investigated, and the results were compared to the experimental results from the plate-counting methods. Improved by the magnetic separation and concentration effect of MNPs, the high sensitivity of UCNPs, and the different emission lines of Yb/Er- and Yb/Tm-doped NaYF₄ UCNPs excited by a 980 nm laser, the present method performs with both high sensitivity and selectivity for the two different types of bacteria.     

Electrochemical detection of nicotinamide adenine dinucleotide based on molecular beacon-like DNA and E. coli DNA ligase

An electrochemical method for nicotinamide adenine dinucleotide (NAD⁺) detection with high sensitivity and selectivity has been developed by using molecular beacon (MB)-like DNA and Escherichia coli DNA ligase. In this method, MB-like DNA labeled with 5′-SH and 3′-biotin was self-assembled onto a gold electrode in its duplex form by means of facile gold-thiol chemistry, which resulted in blockage of electronic transmission. It was eT OFF state. In the presence of NAD⁺, E. coli DNA ligase was activated, and the two nucleotide fragments which were complementary to the loop of the MB-like DNA could be ligated by the NAD⁺-dependent E. coli DNA ligase. Hybridization of the ligated DNA with the MB-like DNA induced a large conformational change in this surface-confined DNA structure, which in turn pushed the biotin away from the electrode surface and made the electrons exchange freely with the electrode. Then the generated electrochemical signals can be measured by differential pulse voltammetry (DPV). Under optimized conditions, a linear response to logarithmic concentration of NAD⁺ range from 3 nM to 5 μM and a detection limit of 1.8 nM were obtained. Furthermore, the proposed strategy had sufficient selectivity to discriminate NAD⁺ from its analogues.     

A dual-color flow cytometry protocol for the simultaneous detection of Vibrio parahaemolyticus and Salmonella typhimurium using aptamer conjugated quantum dots as labels

A sensitive, specific method for the collection and detection of pathogenic bacteria was demonstrated using quantum dots (QDs) as a fluorescence marker coupled with aptamers as the molecular recognition element by flow cytometry. The aptamer sequences were selected using a bacterium-based SELEX strategy in our laboratory for Vibrio parahaemolyticus and Salmonella typhimurium that, when applied in this method, allows for the specific recognition of the bacteria from complex mixtures including shrimp samples. Aptamer-modified QDs (QD-apt) were employed to selectively capture and simultaneously detect the target bacteria with high sensitivity using the fluorescence of the labeled QDs. The signal intensity is amplified due to the high photostability of QDs nanoparticles, resulting in improved sensitivity over methods using individual dye-labeled probes. This proposed method is promising for the sensitive detection of other pathogenic bacteria in food stuff if suitable aptamers are chosen. The method may also provide another potential platform for the application of aptamer-conjugated QDs in flow cytometry.     

Immunomagnetic separation and rapid detection of bacteria using bioluminescence and microfluidics

This paper describes an immunomagnetic separation of target bacterial cells from others by using magnetic bead. The surface of bead was coated with antibodies which can capture specific organism. The binding efficiency of immunomagnetic bead (IMB) capturing target bacterial cells was higher than 98% when the concentrations of target and interferent bacterial cells were at the same level. The concentration of bacteria was determined indirectly by detecting adenosine 5′-triphosphate (ATP) employing bioluminescence (BL) reaction of firefly luciferin-ATP. Benzalkonium chloride (BAC) was used as an ATP extractant from living bacterial cells. We found that BAC could enhance the light emission when the concentration of BAC was less than 5.3 × 10⁻²% (w/v) and the BL intensity reached its maximum at the concentration of BAC was 2.7 × 10⁻²%, which was 10-fold stronger than that without BAC. Based on the principle of the IMB, a microfluidic chip combined with immunofluorescence assay for separating and detecting bacteria simultaneously was also developed. The IMBs were magnetically fixed in the bead-beds of chip channels with a 3-mm diameter of NdFeB permanent magnet. The target bacterial cells can be captured magnetically and observed by a fluorescent microscope.     

Sensitive and simple detection of Escherichia coli strain based on time-resolved fluorescence DNA hybridization assay

A two-probe tandem DNA hybridization assay based on time-resolved fluorescence was employed to detect Escherichia coli strain. The amino modified capture probe was covalently immobilized on the common glass slide surface. The Eu(TTA)₃(5-NH₂-phen) with the characteristics of long lifetime and intense luminescence was labeled with reporter probe. The original extracted DNA samples without the purification and amplification process were directly used in the hybridization assay. The concentration of capture probe, hybridization temperature, hybridization and washing time were optimized. The detection limit is about 1.49 × 10³ CFU mL⁻¹E. coli cells, which is comparable to the value of most microbiology methods. The proposed method has the advantages of easy operation, satisfactory sensitivity and specificity, which can provide a promising technique for monitoring the microorganisms.     

Synthesis and binding properties of carboxylphenyl-modified calix[4]arenes and cytochrome c

Two novel carboxylphenyl-modified calix[4]arenes, tetrakis-carboxylphenylcalix[4]arene (TCPC) and 1,3-bis-carboxylphenylcalix[4]arene (BCPC), as well as a corresponding analogue for comparison, tetrakis-phenylcalix[4]arene (TPC), have been synthesized by palladium-catalyzed Suzuki cross-coupling of arylboronic acid and tetrabromocalix[4]arene as a key step. The binding properties of these calix[4]arene derivatives with bovine heart cytochrome c (cyt c) in dimethylformamide (DMF) was investigated by fluorescence spectroscopy. The binding affinity in the order of TCPC > BCPC ? TPC reflects a clear dependence on the number of carboxyl ligating groups attached onto a receptor and suggests the electrostatic force may be the predominant factor driving the complexing process. The stable 1:1 complexes of TCPC and BCPC with cyt c were evidenced with the binding constants of 3.15 × 10⁶ and 5.85 × 10⁵ L mol⁻¹, respectively. Due to a large overlap between the emission spectrum of TCPC and the absorption spectrum of cyt c, and a short interaction distance (estimated to be 5.6 nm) between them, the fluorescence quenching of TCPC upon complexation with cyt c is attributed to an efficient energy transfer.     

Natural product inhibitors of fatty acid biosynthesis: synthesis of the marine microbial metabolites pseudopyronines A and B and evaluation of their anti-infective activities

Total syntheses of the title natural products, pseudopyronines A (1) and B (2), have been achieved using methyl β-oxo carboxylic ester starting materials. The natural products and a small set of structurally related compounds were evaluated for growth inhibitory activity against a range of pathogenic microorganisms and were found to exhibit good potency (IC₅₀≥0.46 μg/mL) and selectivity towards Leishmania donovani. Several of the compounds inhibited recombinant fatty acid biosynthesis enzymes from both Plasmodium falciparum and Mycobacterium tuberculosis, validating these targets in the search for new anti-infective agents.     

A phage-displayed chicken single-chain antibody fused to alkaline phosphatase detects Fusarium pathogens and their presence in cereal grains

Fusarium and its poisonous mycotoxins are distributed worldwide and are of particular interest in agriculture and food safety. A simple analytical method to detect pathogens is essential for forecasting diseases and controlling mycotoxins. This article describes a proposed method for convenient and sensitive detection of Fusarium pathogens that uses the fusion of single-chain variable fragment (scFv) and alkaline phosphatase (AP). A highly reactive scFv antibody specific to soluble cell wall-bound proteins (SCWPs) of F. verticillioides was selected from an immunized chicken phagemid library by phage display. The antibody was verified to bind on the surface of ungerminated conidiospores and mycelia of F. verticillioides. The scFv–AP fusion was constructed, and soluble expression in bacteria was confirmed. Both the antibody properties and enzymatic activity were retained, and the antigen-binding capacity of the fusion was enhanced by the addition of a linker. Surface plasmon resonance measurements confirmed that the fusion displayed 4-fold higher affinity compared with the fusion's parental scFv antibody. Immunoblot analyses showed that the fusion had good binding capacity to the components from SCWPs of F. verticillioides, and enzyme-linked immunosorbent assays revealed that the detection limit of the fungus was below 10⁻² μg mL⁻¹, superior to the scFv antibody. The fusion protein was able to detect fungal concentrations as low as 10⁻³ mg g⁻¹ of maize grains in both naturally and artificially contaminated samples. Thus, the fusion can be applied in rapid and simple diagnosis of Fusarium contamination in field and stored grain or in food.     

Development and evaluation of a loop-mediated isothermal amplification method in conjunction with an enzyme-linked immunosorbent assay for specific detection of Salmonella serogroup D

Loop-mediated isothermal amplification in conjunction with enzyme-linked immunosorbent assay (LAMP-ELISA) provides a sensitive, specific and cost-effective method for detection of etiological causes of infections. The present study developed a reliable LAMP-ELISA diagnostic kit for identification of Salmonella serogroup D strains and evaluated its potential use in the detection of Salmonella serovars Enteritidis and Typhi. The LAMP-ELISA assay used a serogroup D/A-specific primer set to amplify a region of the prt gene, followed by hybridization of the digoxigenin-labeled products to a highly specific oligonucleotide probe for exact identification of serogroup D serovars. Among the bacteria tested, a positive reaction was only observed for strains belong to Salmonella serogroup D. The detection limit of the LAMP-ELISA assay was 4 CFU per tube, which was lower than PCR-ELISA assay with the same target gene (50 CFU per tube). Finally, the technique was successfully applied to an artificially contaminated meat sample with a detection limit 10³ CFU mL⁻¹, which was 10 times more sensitive than PCR-ELISA. Overall, the LAMP-ELISA assay could be used as a sensitive alternative method to PCR-ELISA for the specific detection of Salmonella serogroup D serovars in routine food microbiology or clinical laboratories worldwide.     

New approaches to the structural modification of olean-type pentacylic triterpenes via microbial oxidation and glycosylation

Microbial transformation of 4 olean-type pentacyclic triterpenes (OPTs), 3-oxo oleanolic acid (1), 3-acetyl oleanolic acid (2), oleanolic acid (3), and esculentoside A (4) was studied. After the screening of 12 strains of microbes, preparative biotransformation by two strains of Streptomyces griseus ATCC 13273 and Aspergillus ochraceus CICC 40330 resulted in the isolation of 10 metabolites. The microbial catalyzed high efficient regio-selective methyl oxidation and glycosylation were discovered, which could be provided as an alternative method to expand the structural diversity of OPTs. All the structures of the metabolites were elucidated unambiguously by ESI-MS, ¹H NMR, ¹³C NMR, and 2D-NMR spectroscopy.     

New CE-ESI-MS analytical method for the separation, identification and quantification of seven phenolic acids including three isomer compounds in virgin olive oil

A sensitive and expeditious CE-ESI-MS analytical method for the separation, identification and determination of seven selected antioxidants (cinnamic and benzoic acids), including three isomers of coumaric acid (ortho-, meta- and para-) has been developed. In order to obtain the analytical separation, capillary electrophoresis and CE-MS interface parameters (e.g., buffer pH and composition, sheath liquid and gas flow rates, sheath liquid composition, electrospray voltage, etc.) were carefully optimized.The polar fraction containing the selected phenolic acids was obtained using a previously optimized SPE pretreatment. An MS detector in order to extract structural information about the target compounds and facilitate their qualitative analysis was used in the negative ion mode. The proposed off-line SPE CE-ESI-MS method was validated by assessing its precision, LODs and LOQs, linearity range and accuracy.The optimized and validated method was used in order to quantify the selected antioxidants in various samples of virgin olive oil and extra-virgin olive oil obtained from the main olive varieties cropped in Castilla-La Mancha, Spain. Salicylic acid was used as internal standard throughout in order to ensure reproducibility in the quantitative analysis of the oil samples.The results confirmed the presence of hydroxyphenyl acetic, p-coumaric, ferulic and vanillic acids in substantial amounts (μg g⁻¹ level) in all samples.     

Glucose biosensors prepared by electropolymerization of p-chlorophenylamine with and without Nafion

Two different glucose biosensors for the amperometric determination of glucose, based on poly(p-chlorophenylamide) (PCPA) and bilayer film of PCPA and Nafion (PCPA/Nafion), are successfully developed. These two biosensors show linear amperometric responses to glucose ranging from 2.0×10⁻⁴ to 3.5×10⁻² mol l⁻¹ and 5.0×10⁻⁴ to 7.5×10⁻² mol l⁻¹, respectively, with the same correlation coefficient of 0.9988. Effects of polymerization potential and polymerization time on the performance of enzyme sensors are studied. It is found that PCPA, as a non-conducting polymer, can largely reduce the influence of electroactive interferents. Introduction of inner Nafion membrane not only further eliminates the influence of ascorbic acid on the sensor response but also increases electrode stability.     

Synthesis and characterization of glycoconjugate tin(IV) complexes: In vitro DNA binding studies, cytotoxicity, and cell death

New glycosyl derived ligand and its complexes, with SnCl₄·5H₂O (1) and (CH₃)₂SnCl₂(2) were synthesized and characterized by spectroscopic (IR, ¹H, ¹³C, and ¹¹⁹Sn NMR, UV-vis, ESI-MS) and analytical methods. Interaction studies of 1 and 2 with CT DNA were studied by using various biophysical techniques, which showed high binding affinity of 2 with CT DNA. In vitro cytotoxicity of complexes 1 and 2 were evaluated against different human cancer cell lines of different histological origins by employing SRB Assay. The organotin(IV) complex 2 exhibited remarkable activity against DWD (oral cancer) cell lines with GI₅₀ values <10 μg/ml. Complex 2 induced apoptosis of DWD cell line at a very low concentration of 1-4 μg/mL.