Proteomic analysis of a spring wheat cultivar in response to prolonged cold stress

Cold represents one of the major abiotic factors influencing plant growth and development worldwide. We analysed the long-term responsiveness of an Iranian spring wheat (cv. Kohdasht) to cold from a proteomic point of view, in order to unravel the molecular mechanisms helping a cold-sensitive cultivar to survive exposure to suboptimal temperatures. Plants were grown at 20 or 4°C until entering the reproductive stage and a cross-comparison on the leaf proteomes was performed. Quantitative analyses on protein alterations occurring upon low-temperature exposure showed a reinforcement in ascorbate recycling (dehydroascorbate reductase, ascorbate peroxidase) and protein processing (proteasome subunit, cysteine proteinase), as well as the accumulation of the enzyme devoted to tetrapyrrole resynthesis (glutamate semialdehyde aminomutase). In contrast, among proteins down-regulated after cold stress, we could identify some key Krebs cycle enzymes (isocitrate dehydrogenase, malate dehydrogenase), together with many photosynthesis-related proteins (oxygen-evolving complex proteins, ATP synthase subunits, ferredoxin NADPH oxidoreductase and some Calvin cycle enzymes). Physiological and biochemical parameters (such as shoot apex dissection, chlorophyll, proline and sugar content determination) sustained proteomics findings allowing the present research to contribute to the current knowledge on these long-term responses, which may be crucial to stress adaptation under field conditions.     

Multifunctional microgel magnetic/optical traps for SERS ultradetection

We report on the fabrication of a SERS substrate comprising magnetic and silver particles encapsulated within a poly(N-isopropylacrylamide) (pNIPAM) thermoresponsive microgel. This colloidal substrate has the ability to adsorb analytes from solution while it is expanded (low temperature) and reversibly generate hot spots upon collapse (high temperature or drying). Additionally, the magnetic functionality permits concentration of the composite particles into small spatial regions, which can be exploited to decrease the amount of material per analysis while improving its SERS detection limit. Proof of concept for the sequestration of uncommon molecular systems is demonstrated through the first SERS analysis of pentachlorophenol (PCP), a chlorinated ubiquitous environmental pollutant.     

Effect of synthesis conditions on the microstructure of TEOS derived silica hydrogels synthesized by the alcohol-free sol–gel route

Silica matrices synthesized from a pre-hydrolysis step in ethanol followed by alcohol removal at low pressure distillation, and condensation in water, are suitable for encapsulation of biomolecules and microorganisms and building bioactive materials with optimized optical properties. Here we analyze the microstructure of these hydrogels from the dependence of I(q) data acquired from SAXS experiments over a wide range of silica concentration and pH employed in the condensation step. From the resulting data it is shown that there is a clear correlation between the microscopic parameters—cluster fractal dimension (D), elementary particle radius (a) and cluster gyration radius (R)—with the attenuation of visible light when the condensation step proceeds at pH < 6. At higher pHs, there is a steep dependence of the cluster density (~R ^D−3) with the condensation pH, and non-monotonous changes of attenuance are less than 20%, revealing the complexity of the system. These results, which were obtained for a wide pH and silica concentration range, reinforce the idea that the behavior of gels determined in a restricted interval of synthesis variables cannot be extrapolated, and comparison of gelation times is not enough for predicting their properties.     

DNA-binding small-ligand-immobilized surface plasmon resonance biosensor for detecting thymine-related single-nucleotide polymorphisms

A surface plasmon resonance (SPR) biosensor that carries DNA-binding small ligands has been developed for the detection of single-nucleotide polymorphisms (SNPs). 3,5-Diaminopyrazine derivatives, with a hydrogen-bonding profile fully complementary to the thymine base, were utilized as recognition elements on the sensor surface, and a target single-stranded DNA sequence was hybridized with a DNA probe containing an abasic site to place this site opposite a nucleobase to be detected. In a continuous flow of sample solutions buffered to pH 6.4 (0.25 M NaCl), the 3,5-diaminopyrazine-based SPR sensor can detect an orphan nucleobase in the duplex with a clear selectivity for thymine over cytosine, guanine, and adenine (5'-GTT GGA GCT GXG GGC GTA GGC-3'/3'-CAA CCT CGA CNC CCG CAT CCG-5'; X=abasic site, N=target nucleobase G, C, A, or T). The SPR response was linear in the concentration range 10-100 nM. Allele discrimination is possible based on the combination of different binding surfaces in a flow cell of the SPR system, which is demonstrated for the analysis of the thymine/cytosine mutation present in 63-meric polymerase chain reaction (PCR) amplification products (Ha-ras gene, codon 12, antisense strand). Comparison with a bulk assay based on 3,5-diaminopyrazine/DNA binding shows that the immobilization of 3,5-diaminopyrazine derivatives on the SPR sensor allows more sensitive detection of the target DNA sequence, and binding selectivity can be tuned by controlling the salt concentration of sample solutions. These features of the DNA-binding small-molecule-immobilized SPR sensor are discussed as a basis for the design of SPR biosensors for SNP genotyping.     

Surface swabbing technique for the rapid screening for pesticides using ambient pressure desorption ionization with high-resolution mass spectrometry

A rapid screening method for pesticides has been developed to promote more efficient processing of produce entering the United States. Foam swabs were used to recover a multiclass mixture of 132 pesticides from the surfaces of grapes, apples, and oranges. The swabs were analyzed using direct analysis in real time (DART) ionization coupled with a high‐resolution Exactive Orbitrap? mass spectrometer. By using a DART helium temperature gradient from 100–350°C over 3 min, a minimal separation of analytes based on volatility differences was achieved. This, combined with the Exactive's mass resolution of 100 000, allowed the chromatographic step, along with the typical compositing and extraction steps associated with gas chromatography/mass spectrometry (GC/MS) or liquid chromatography/mass spectrometry (LC/MS) approaches, to be eliminated. Detection of 86% of the analytes present was consistently achieved at levels of 2 ng/g (per each apple or orange) and 10 ng/g (per grape). A resolution study was conducted with four pairs of isobaric compounds analyzed at a mass resolution of 100 000. Baseline separation was achieved with analyte ions differing in mass by 25 ppm and analyte ions with a mass difference of 10 ppm were partially resolved. In addition, field samples that had undergone traditional sample preparation using QuEChERS (quick, easy, cheap, rugged, and safe) were analyzed using both LC/MS and DART‐MS and the results from the two techniques were found to be comparable in terms of identification of the pesticides present. The use of swabs greatly increased sample throughput by reducing sample preparation and analysis time. Published in 2010 by John Wiley & Sons, Ltd.     

Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks--on the benefit of restoring the cyclic sugar backbone

Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.     

Thiocyanate and nitrite analysis using miniaturised isotachophoresis on a planar polymer chip

A new method has been developed to improve the determination of thiocyanate using isotachophoresis. This method uses complexation with copper(II) as a mechanism for improving the separation of thiocyanate from chlorate and perchlorate. By using a pH of 3.25 the method can also be used to analyse nitrite. Separations were carried out using a miniaturised poly(methyl methacrylate) (PMMA) separation device. Linearity was observed from 1.25 to 75 mg dm(-3) with a correlation coefficient of 0.998 for both thiocyanate and nitrite. Limits of detection for these two species were calculated to be 0.8 mg dm(-3) and 0.9 mg dm(-3) respectively. The method was successfully applied to the analysis of these anions in a range of samples including explosive residues.     

A simplified Quick, Easy, Cheap, Effective, Rugged and Safe approach for the determination of trihalomethanes and benzene, toluene, ethylbenzene and xylenes in soil matrices by fast gas chromatography with mass spectrometry detection

A method based on simplified QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) extraction followed by large-injection volume-fast gas chromatography and mass spectrometry detection has been developed for the determination of trihalomethanes (chloroform, bromodichloromethane, dibromochloromethane and bromoform) and BTEX (benzene, toluene, ethylbenzene and xylenes) in soil samples.The simplified version of QuEChERS used meets the requirements of the “green chemistry” and provides reliable results with high sample throughput, low solvent consumption, little labour and the use of materials commonly employed in laboratories. The GC device used is equipped with a programmable temperature vaporizer (PTV), with a liner packed with Tenax-TA^®. Using the solvent-vent mode, the PTV allows the injection of large volumes of sample, affording an improvement in the sensitivity of the method. The chromatographic conditions used here allowed the separation of the compounds in less than 5.50 min. Good linearity was obtained for all the target compounds, with highly satisfactory repeatability and reproducibility values. The limits of detection were in the 0.2 to 15 μg kg⁻¹ range. The method was validated by the analysis of two certified reference materials.     

An organocatalytic approach to enantiomerically enriched α-arylcyclohexenones and cyclohexanones

The presence of a p-nitrophenyl group converts acetone into an excellent and versatile nucleophile in organocatalytic processes, able to react with α,β-unsaturated aldehydes affording β-substituted α-arylcyclohexenones via a Michael reaction/aldol reaction/dehydration sequence, which occurs in good yields, ee up to 96% and complete diastereoselectivity. The resulting compounds are excellent synthons for the diastereoselective preparation of a variety of synthetically useful polysubstituted cyclohexanones and derivatives.     

Immobilization of peroxidase on SiO2 surfaces with the help of a dendronized polymer and the avidin-biotin system

Horseradish peroxidase (HRP) is immobilized in three easy steps on SiO(2) surfaces with the help of a polycationic second generation dendronized polymer (denpol) and the biotin-avidin system. This stepwise immobilization process is monitored and quantitatively analyzed with the transmission interferometric adsorption sensor. Partially biotinylated denpol is first adsorbed onto SiO(2) , followed by addition of avidin and then of biotinylated HRP. Denpols in their molecular structure combine properties of polymers as well as dendrimers which are found to be of clear advantage for this type of non-covalent enzyme immobilization. With respect to the reproducibility of the adsorption process and with respect to the stability of the adsorbed polymer layer, the denpol is superior to α-poly-D-lysine which is used as a reference polymer. Furthermore, HRP immobilized with the denpol on commercial glass slides remains considerably more active upon storage as compared to HRP immobilized with the help of α-poly-D-lysine with a similar number of repeating units. The ease of the denpol-mediated HRP immobilization and the high stability of the immobilized enzyme are promising for bioanalytical applications.