A label-free, quadruplex-based functional molecular beacon (LFG4-MB) for fluorescence turn-on detection of DNA and nuclease

We demonstrate a novel concept for the construction of a label-free, quadruplex-based functional molecular beacon (LFG4-MB) by using G-quadruplex motif as a substitute for Watson-Crick base pairing in the MB stem and a specific G-quadruplex binder, N-methyl mesoporphyrin IX (NMM) as a reporter. It shows high sensitivity in assays for UDG activity/inhibition and detection of DNA sequence based on the unique fluorescence increase that occurs as a result of the strong interaction between NMM and the folded quadruplex upon removal of uracil by UDG or displacement of block sequence by target DNA. The LFG4-MB is simple in design, fast in operation and could be easily transposed to other biological relevant target analysis by simply changing the recognition portion. The LFG4-MB does not require any chemical modification for DNA, which offers the advantages of simplicity and cost efficiency and obviates the possible interference with the affinity and specificity of the MB as well as the kinetic behavior of the catalysts caused by the bulky fluorescent groups. More importantly, the LFG4-MB offers great extent of freedom to tune the experimental conditions for the general applicability in bioanalysis.     

Physical and chemical properties of a durably efficacious ammonium bicarbonate as a fertilizer and its yield-increasing mechanism

A new fertilizer of cocrystal type,known as durably efficacious ammonium bicarbonate (DEAB),has been developed by adding a certain amount of dicyandiamide (DCD) as an ammonia-stabilizing agent to ammonium bearbenate(AB)during the process of its production.As compared with AB,DEAB was found to have a reduction of direct volatilization loss by 53%,a fertilizer availability period prolonged from 35-45 to 90-110 d,and an increase in the rate of nitrogen in fertilizer being utilized by 5.9%-10.2%,and a saving of the amount of fertilizer to be ap-phed by 20%-30% for the same level of yield,or an increase of the crop yield by over 10% for the same level of ni-tregen fertilization;in addition,it was found to show usually a function of promoting the crop to early mature.It can be apptied as basal dressing all in one time to soil and thus also used as a labour-saving and crop yield-increasing fertil-izer for is non-mtertillage,plastics film covering and water-saving agriculture     

Organic synthesis--art or science?

The LHASA rules for finding strategic bonds in polycyclic target structures are analyzed with respect to the following question: Do the strategic bonds tend to give the greatest simplification upon disconnection, as measured by recently introduced indices of molecular complexity? The answer is yes, at least for the more general rules. This result implies that the bonds most useful for retrosynthetic disconnection can now be identified by a simple calculation rather than by application of a body of rules. It is concluded that organic synthesis, as far as described by these rules, has a mathematical basis and consequently can be considered a science as well as an art.     

A polyaniline-containing filter paper that acts as a sensor, acid, base, and endpoint indicator and also filters acids and bases

In this paper we report a new idea for synthesizing polyaniline in an ordinary filter paper. The synthesis was carried out by a process in which aqueous acidic aniline solution and the oxidizing agent H(2)O(2) was added to the paper drop by drop and in sequence. Uniform polymerization could be obtained with the addition of reagents in either sequence. The polymer formation led to a green coloration of the paper. Formation of the emeraldine salt of polyaniline was confirmed by UV-vis and FTIR spectroscopy. Scanning electron microscopic measurements were made for surface characterization of the polymer formed in the paper. The same paper was used as a sensor for ammonia in vapor and in solution, for acid and base as well as endpoint indication, and also to filter acids and bases. We found that, using the polymer-containing paper, ammonia concentrations in a solution as low as 14 ppm could be measured.     

Simple functionalization of cellulose beads with pre-propargylated chitosan for clickable scaffold substrates

Concerning the increased market for bio-based materials and environmentally safe practices, cellulose-based beads are one of the more attractive alternatives. Thus, this work focuses on the generation of functional cellulose-based beads with a relatively simple and direct method of blending a pre-modified chitosan bearing the targeted functional groups and cellulose, prior to the formation of the beads, as a mean to have functional groups in the formed structure. To this end, chitosan was chemically modified with propargyl bromide in homogenous reaction conditions and then combined with cellulose in sodium hydroxide/urea solution and coagulated in nitric acid to produce spherical shaped beads. The successful chemical modification of chitosan was assessed by elemental analysis, as well as by Fourier-transform infrared spectroscopy, Raman spectroscopy and X-ray photoelectron spectroscopy. The alkynyl moieties from the chitosan derivative, served as reactive functional groups for click-chemistry as demonstrated by the tagging of the commercial fluorophore Azide-Fluor 488 via CuI-catalysed alkyne-azide cycloaddition reaction, in aqueous media. This work demonstrates the one-step processing of multiple polysaccharides for functional spherical beads as a template for bio-based scaffolds such as enzyme immobilization for stimuli-response applications and bioconjugations.

     

Ionic-liquid-mediated active-site control of MoS2 for the electrocatalytic hydrogen evolution reaction

The layered crystal MoS(2) has been proposed as an alternative to noble metals as the electrocatalyst for the hydrogen evolution reaction (HER). However, the activity of this catalyst is limited by the number of available edge sites. It was previously shown that, by using an imidazolium ionic liquid as synthesis medium, nanometre-size crystal layers of MoS(2) can be prepared which exhibit a very high number of active edge sites as well as a de-layered morphology, both of which contribute to HER electrocatalytic activity. Herein, it is examined how to control these features synthetically by using a range of ionic liquids as synthesis media. Non-coordinating ILs with a planar heterocyclic cation produced MoS(2) with the de-layered morphology, which was subsequently shown to be highly advantageous for HER electrocatalytic activity. The results furthermore suggest that the crystallinity, and in turn the catalytic activity, of the MoS(2) layers can be improved by employing an IL with specific solvation properties. These results provide the basis for a synthetic strategy for increasing the HER electrocatalytic activity of MoS(2) by tuning its crystal properties, and thus improving its potential for use in hydrogen production technologies.     

Boron‐Containing Probes for Non‐optical High‐Resolution Imaging of Biological Samples

Boron has been employed in materials science as a marker for imaging specific structures by electron energy loss spectroscopy (EELS) or secondary ion mass spectrometry (SIMS). It has a strong potential in biological analyses as well; however, the specific coupling of a sufficient number of boron atoms to a biological structure has proven challenging. Herein, we synthesize tags containing closo‐1,2‐dicarbadodecaborane, coupled to soluble peptides, which were integrated in specific proteins by click chemistry in mammalian cells and were also coupled to nanobodies for use in immunocytochemistry experiments. The tags were fully functional in biological samples, as demonstrated by nanoSIMS imaging of cell cultures. The boron signal revealed the protein of interest, while other SIMS channels were used for imaging different positive ions, such as the cellular metal ions. This allows, for the first time, the simultaneous imaging of such ions with a protein of interest and will enable new biological applications in the SIMS field.     

Experimental design in the optimization of a microwave acid digestion procedure for the determination of metals in biomorphic ceramic samples by inductively coupled plasma mass spectrometry and atomic absorption spectrometry

In the present paper, we have synthesized a biomorphic ceramic material from oak wood as biological template structure and infiltration with zirconia-sol. After the material characterization, we have optimized the sample dissolution by acid attack in an oven under microwave irradiation. Experimental designs were used as a multivariate strategy for the effect's evaluation of varying several variables. This article describes the development by response surface methodology (RSM) of a procedure for zirconium determination, and other ions, such as copper and nickel by inductively coupled plasma mass spectrometry (ICP-MS) and others, such as iron, calcium and magnesium determination by flame atomic absorption spectrometry (FAAS) in the synthesized sample after digestion. A full factorial design (3³) was used to find optimal conditions for the procedure through response surface study. Three variables (time, HNO₃ volume and HF volume) were regarded as factors and as response to the concentration of different metal ions in the optimization study.     

Fe3O4 nanoparticles-enhanced SPR sensing for ultrasensitive sandwich bio-assay

Magnetic nanoparticles (MNPs) have been receiving increasing attention because of its great potentials in bioseparation. However, the separation products are difficult to be detected by general method due to their extremely small size. Here, we demonstrate that MNPs can greatly enhance the signal of surface plasmon resonance spectroscopy (SPR). Features of MNPs-aptamer conjugates as a powerful amplification reagent for ultrasensitive immunoassay are reported in this work for the first time. In order to evaluate the sensing ability of MNPs-aptamer conjugates as an amplification reagent, a sandwich SPR sensor is constructed by using thrombin as model analyte. Thrombin, captured by immobilized anti-thrombin aptamer on SPR gold film, is sensitively detected by SPR spectroscopy with a lowest detection limit of 0.017 nM after MNPs-aptamer conjugates is used as amplification reagent. At the same time, the excellent selectivity of the present biosensor is also confirmed by using three kinds of proteins (BSA, human IgM and human IgE) as controls. These results confirm that MNPs is a powerful sandwich element and an excellent amplification reagent for SPR based sandwich immunoassay and SPR has a great potential for the detection of MNPs-based bioseparation products.     

Formation of polymeric nano-emulsions by a low-energy method and their use for nanoparticle preparation

Formation of polymeric O/W nano-emulsions has been studied in the water/polyoxyethylene 4 sorbitan monolaurate/ethylcellulose solution system by the phase inversion composition (PIC) method. These nano-emulsions were used for the preparation of nanoparticles by solvent evaporation. Composition variables such as O/S ratio or final water content as well as emulsification path have been found to play a key role in the formation of stable, nanometer sized emulsions. Nano-emulsions with a constant water content of 90 wt.% and O/S ratios from 50/50 to 70/30 showed an average droplet size of about 200 nm as assessed by dynamic light scattering. Mean nanoparticle diameters, as determined by transmission electron microscopy image analysis, were of the order of 50 nm and showed a slight increase as well as a broader size distribution at increasing O/S ratios. The findings verify that the low-energy emulsification methods are not only valid for aliphatic and semipolar oils, but also for a highly polar solvent such as ethylacetate containing a preformed polymer.     

A Comprehensive Study on Tetraaryltetrabenzoporphyrins

Tetraaryltetrabenzoporphyrins (TATBPs) show, due to their optoelectronic properties, rising potential as dyes in various fields of physical and biomedical sciences. However, unlike in the case of porphyrins, the potential structural diversity of TATBPs has been explored only to little extent, owed mainly to synthetic hurdles. Herein, we prepared a comprehensive library of 30 TATBPs and investigated their fundamental properties. We elucidated structural properties by X-ray crystallography and found explanations for physical properties such as solubility. Fundamental electronic aspects were studied by optical spectroscopy as well as by electrochemistry and brought in context to the stability of the molecules. Finally, we were able to develop a universal synthetic protocol, utilizing a readily established isoindole synthon, which gives TATBPs in high yields, regardless of the nature of the used arylaldehyde and without meticulous chromatographic purifications steps. This work serves as point of orientation for scientists, that aim to utilize these molecules in materials, nanotechnological, and biomedical applications.     

Metabolic profiling of intracellular metabolites in fermentation broths from β-lactam antibiotics production by liquid chromatography–tandem mass spectrometry methods

An analytical platform comprising three LC–ESI-MS/MS methods is presented for qualitative and quantitative profiling of more than 200 intracellular metabolites. Employing a silica based zwitterionic stationary phase in the HILIC mode, in total 223 hydrophilic metabolites can be determined. In particular, amino acids, organic acids as well as nucleotide sugars were found to be well separable and detectable under acidic mobile phase conditions, while in comparison especially phosphates such as nucleotides, coenzymes or sugar phosphates as well as sugars and sugar acids performed better at higher pH. Additionally, 21 less polar analytes turned out to be amenable for separation and analysis on a pentafluorophenyl modified silica stationary phase in RP mode. Solutes were detected by tandem mass spectrometry on a triple quadrupole instrument in the selected reaction monitoring (SRM) mode and specific SRM transitions for 258 metabolites are provided. All three methods were validated with respect to the limit of quantification, linear dynamic range, precision and accuracy. Applicability of the analytical platform was evaluated by analysis of the targeted metabolites in extracts of β-lactam antibiotics fermentation broths. Thereby, 87 metabolites were determined qualitatively in penicillin fermentation broths, and 94 compounds were found in cephalosporin extracts. In addition, a number of selected metabolites that can be determined by at least two of the presented LC–MS/MS methods was analyzed quantitatively by both, external calibration using pure standards as well as by matrix-matched calibration performing standard addition. Quantitative results obtained with the different methods agreed well, however, for some analytes external calibration was found to be ill-suited due to matrix effects.     

Comparison of immunoassay and gas chromatography-mass spectrometry for measurement of polycyclic aromatic hydrocarbons in contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are frequently encountered in the environment and may pose health concerns due to their carcinogenicity. A commercial enzyme-linked immunosorbent assay (ELISA), was evaluated as a screening method for monitoring PAHs at contaminated sites. The ELISA was a carcinogenic PAH (C-PAH) RaPID assay testing kit that cross-reacts with several PAHs and utilizes benzo[a]pyrene (BaP) as a calibrator. Soil samples were extracted with 50% acetone in dichloromethane (DCM) for analysis by ELISA and gas chromatography-mass spectrometry (GC-MS). The overall method precision was within ±30% for ELISA and within ±20% for GC-MS. Recovery data for spiked soils ranged from 46 to 140% for BaP as determined by ELISA. Recoveries data of the GC-MS surrogate standards, 2-fluorobiphenyl and chrysene, were greater than 70%. The GC-MS procedure detected a total of 19 priority PAHs (2-6-ring PAHs) including seven probable human carcinogens (4-6-ring B2-PAHs). The ELISA results were compared to GC-MS summation results for the total 19 target PAHs as well as for the subset of the seven B2-PAH compounds. For all soil samples, the PAH concentrations derived from ELISA were greater than the sum of B2-PAH concentrations obtained by GC-MS. ELISA determinations were also frequently greater than the results obtained by GC-MS for the total 19 PAH compounds. This discrepancy can be expected, since the ELISA is a screening assay for the detection of several related PAHs while the GC-MS procedure detects priority PAH compounds. Thus, only a subset of PAHs (e.g. 19 PAHs) in the soil samples were measured by GC-MS while additional PAHs, including alkylated PAHs, and PAH derivatives have been demonstrated to be cross-reactive in the C-PAH ELISA. Results of paired tests show that the PAH data from ELISA and GC-MS methods are significantly different (P<0.001), but highly correlated. The ELISA data had a strong positive relationship with the GC-MS summation data for the B2-PAHs as well as for the 19 PAHs targeted by the GC-MS method. Results indicate that the ELISA may be useful as a broad screen for monitoring PAHs in environmental samples.     

Fractal geometry analysis of chemical structure of natural starch modification as a green biopolymeric product

Public concerns and official pressures around environmental protection as well as exhausting petroleum resources have brought about preferences in studying and applying environmental-friendly polymers instead of synthetic petroleum-based polymers. For this aim, biopolymers can have outstanding advantages in biodegradability by saving time, energy and effort spent on increasingly costs of polymeric wastes. Natural starch (being studied in this work), as one of the most abundant natural resources for polymer materials, is inexpensive and biodegradable. As starch necessarily needs for modifications and processing before being used as ideal green polymer material, it is vital to perform feature extraction and defect detection measures in structure by some method like image analysis. Fractal as a new geometry has circumstantially progressed recently in the fields of image processing, physical space–time, medical image analysis, electrochemical patterns, digital images, sounds etc. Box Count Fractal Dimension as a very important and popular part of fractal geometry can be a useful factor in feature extraction and pattern recognition. This paper presents a new method for defect detection in the structure of natural starch modification images using the fractal dimension (FD) along with mean and standard deviation of image color. This is performed via feature extraction based on artificial intelligence by MatLab R2013a for box counting algorithms. Otsu’s graythresh method by MatLab R2013a is applied to binarize the images. The results of proposed methodology are illustrated as log–log curves where the fractal dimensions are recognized by curve fitting (CF) tool with more than 95% accuracy. The outputs express that starch samples’ FD vary in the range from 1.636 to 1.926 among which the last is identified as non-defective polymer. Non-defective feature is of great importance for quality control measures and chemical reactivity being here highlighted as biodegradability.     

Single-label kinase and phosphatase assays for tyrosine phosphorylation using nanosecond time-resolved fluorescence detection

The collision-induced fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by hydrogen atom abstraction from the tyrosine residue in peptide substrates was introduced as a single-labeling strategy to assay the activity of tyrosine kinases and phosphatases. The assays were tested for 12 different combinations of Dbo-labeled substrates and with the enzymes p60c-Src Src kinase, EGFR kinase, YOP protein tyrosine phosphatase, as well as acid and alkaline phosphatases, thereby demonstrating a broad application potential. The steady-state fluorescence changed by a factor of up to 7 in the course of the enzymatic reaction, which allowed for a sufficient sensitivity of continuous monitoring in steady-state experiments. The fluorescence lifetimes (and intensities) were found to be rather constant for the phosphotyrosine peptides (ca. 300 ns in aerated water), while those of the unphosphorylated peptides were as short as 40 ns (at pH 7) and 7 ns (at pH 13) as a result of intramolecular quenching. Owing to the exceptionally long fluorescence lifetime of Dbo, the assays were alternatively performed by using nanosecond time-resolved fluorescence (Nano-TRF) detection, which leads to an improved discrimination of background fluorescence and an increased sensitivity. The potential for inhibitor screening was demonstrated through the inhibition of acid and alkaline phosphatases by molybdate.     

Self-assembled arene-ruthenium-based rectangles for the selective sensing of multi-carboxylate anions

Novel arene-ruthenium [2+2] metalla-rectangles 4 and 5 have been synthesized by self-assembly using dipyridyl amide ligand 3 and arene-ruthenium acceptors (arene: benzoquinone (1), naphthacenedione (2)) and characterized by NMR spectroscopy and ESI-MS. The solid-state structure of 5 was determined by X-ray diffraction and shows encapsulated diethyl ether molecule in the rectangular cavity of 5. The luminescent 5 was further used for anion sensing with the amidic linkage serving as a hydrogen-bond donor site for anions and the ruthenium moiety serving as a signaling unit. A UV/Vis titration study demonstrated that although 5 interacts very weakly with common monoanions as well as with flexible dicarboxylate anions such as malonate and succinate, it displays significant binding affinity (K>10(3) in MeOH) for rigid multi-carboxylate anions such as oxalate, citrate, and tartrate, exhibiting a 1:1 stoichiometry. It has been suggested that 1:1 bidentate hydrogen bonding assisted by appropriate geometrical complementarity is mainly responsible for the increased affinity of 5 towards such anions. A fluorescence titration study revealed a large fluorescence enhancement of 5 upon binding to multi-carboxylate anions, which can be attributed to the blocking of the photoinduced electron-transfer process from the arene-Ru moiety to the amidic donor in 5 as a result of hydrogen bonding between the donor and the anion.     

Antibody adsorption and orientation on hydrophobic surfaces

The orientation of a monoclonal, anti-streptavidin human IgG1 antibody on a model hydrophobic, CH(3)-terminated surface (1-dodecanethiol self-assembled monolayer on gold) was studied by monitoring the mechanical coupling between the adsorbed layer and the surface as well as the binding of molecular probes to the antibodies. In this study, the streptavidin antigen was used as a probe for the Fab portions of the antibody, while bacteria-derived Protein G' was used as a probe for the Fc region. Bovine serum albumin (BSA) acted as a blocking protein. Monolayer coverage occurred around 468 ng/cm(2). Below 100 ng/cm(2), antibodies were found to adsorb flat-on, tightly coupled to the surface and unable to capture their antigen, whereas the Fc region was able to bind Protein G'. At half-monolayer coverage, there was a transition in the mechanism of adsorption to allow for vertically oriented antibodies, as evidenced by the binding of both Protein G' and streptavidin as well as looser mechanical coupling with the surface. Monolayer coverage was characterized by a reduced level in probe binding per antibody and an even less rigid coupling to the surface.     

The doping effect of fluorinated aromatic solvents on the rate of ruthenium-catalysed olefin metathesis

A study concerning the effect of using a fluorinated aromatic solvent as the medium for olefin metathesis reactions catalysed by ruthenium complexes bearing N-heterocyclic carbene ligands is presented. The use of fluorinated aromatic hydrocarbons (FAH) as solvents for olefin metathesis reactions catalysed by standard commercially available ruthenium pre-catalysts allows substantially higher yields of the desired products to be obtained, especially in the case of demanding polyfunctional molecules, including natural and biologically active compounds. Interactions between the FAH and the second-generation ruthenium catalysts, which apparently improve the efficiency of the olefin metathesis transformation, have been studied by X-ray structure analysis and computations, as well as by carrying out a number of metathesis experiments. The optimisation of reaction conditions by using an FAH can be regarded as a complementary approach for the design of new improved ruthenium catalysts. Fluorinated aromatic solvents are an attractive alternative medium for promoting challenging olefin metathesis reactions.     

Equilibrium partitioning of Ficoll in composite hydrogels

Equilibrium partition coefficients (phi, the concentration in the gel divided by that in free solution) of fluorescein-labeled Ficolls in pure agarose and agarose-dextran composite gels were measured as a function of gel composition and Ficoll size. The four narrow fractions of Ficoll, a spherical polysaccharide, had Stokes-Einstein radii ranging from 2.7 to 5.9 nm. Gels with agarose volume fractions of 0.040 and 0.080 were studied, with dextran volume fractions (calculated as if the chain were a long fiber) up to 0.011. As expected, phi generally decreased as the Ficoll size increased (for a given gel composition) or as the amount of dextran incorporated into the gel increased (for a given agarose concentration and Ficoll size). The decrease in phi that accompanied dextran addition was predicted well by an excluded volume theory in which agarose and dextran were both treated as rigid, straight, randomly positioned and oriented fibers. Modeling dextran as a spherical coil within a fibrous agarose gel produced much less accurate predictions. The diffusional permeabilities of these gels were assessed by combining the current partitioning data with relative diffusivities (Kd, the diffusivity in the gel divided by that in free solution) reported previously. The values of phi Kd for a synthetic gel with 8.0% agarose and 1.1% dextran (by volume) were found to be very similar to those for the glomerular basement membrane, a physiologically important material which also has a total solids content of approximately 10%.