Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Radioisotopes of thirteen elements in intertidal coastal and estuarine sediments in the Irish Sea

A survey has been carried out of⁴⁰K,⁶⁰Co,⁹⁹Tc,¹⁰⁶Ru,¹²⁵Sb,¹²⁹I,¹³⁴Cs,¹³⁷Cs,¹⁵⁴Eu,²²⁶Ra,²²⁸Ra,²³⁷Np,²³⁸Pu,^239,240Pu,²⁴¹Pu,²⁴¹Am,²⁴²Cm, and^243,244Cm activities in sediments from the Irish Sea. Several of these radionuclides were measured independently at two separate laboratories to enable the intercomparison of the results produced. The comprehensive data set generated allows the present spatial distributions of these radionuclides in coastal sediments to be examined in relation to sediment textural characteristics and by comparison with earlier survey, enables the temporal trends in their activities to be determined. In general all artificial radionuclides showed lower activities in sediments in response to falling discharges from Sellafield and relationships with either grain size, distance from Sellafield or both. Isotope ratios were similar to cumulative weighted activity ratios rather than present day values due to sediment mixing. Pu levels supplied evidence for the lag in response of sediment deposits with increasing distance from Sellafield due to sediment transport.     

Participation of lipid peroxidation in rat pertussis vaccine pleurisy. III. Thiobarbituric acid (TBA) reactant and lysosomal enzyme

Activity of lysosomal enzymes, such as N-acetyl-beta-D-glucosaminidase (NAG), was assayed in exudate on a rat model of Bordetella pertussis vaccine pleurisy. Thiobarbituric acid (TBA)-reactive substances (TBA.R) and superoxide dismutase (SOD) activity were then monitored in the exudate on the acute phase response in this inflammatory model. Retention of the exudate in the pleural space increased rapidly after the challenge, and the exudate volume at 24 h reached about three times the volume at 6 h. The activity of SOD at 6 h was shown to be higher than that at 24 h after the challenge, thus showing negative correlations with TBA-R levels and exudate volume. The levels of TBA.R rapidly increased and reached maximum values at 24 h. It was concluded that the above three parameters correlated to the acute phase response in this inflammatory model.     

Synthetic studies on quassinoids: a stereoselective construction of the picrasane skeleton

12β-Hydroxypicrasan-3-one, a compound having the correct relative stereochemistry of all the six ring-juncture chiral centers of the picrasane skeleton, was synthesized from a known tricyclic compound, using the orthoester Claisen rearrangement and lead tetraacetate oxidation as key reactions.     

Precise control and consecutive modulation of spin transition temperature using chemical migration in porous coordination polymers

Precise control of spin transition temperature (T(c)) is one of the most important challenges in molecular magnetism. A Hofmann-type porous coordination polymer {Fe(pz)[Pt(II)(CN)(4)]} (1; pz = pyrazine) exhibited cooperative spin transition near room temperature (T(c)(up) = 304 K and T(c)(down) = 284 K) and its iodine adduct {Fe(pz)[Pt(II/IV)(CN)(4)(I)]} (1-I), prepared by oxidative addition of iodine to the open metal sites of Pt(II), raised the T(c) by 100 K. DSC and microscopic Raman spectra of a solid mixture of 1-I and 1 revealed that iodine migrated from 1-I to 1 through the grain boundary after heating above 398 K. We have succeeded in precisely controlling the iodine content of {Fe(pz)[Pt(CN)(4)(I)(n)]} (1-In; n = 0.0-1.0), which resulted in consecutive modulation of T(c) in the range 300-400 K while maintaining the hysteresis width. Furthermore, it was demonstrated that iodine migration in the solid mixture was triggered by the spin transition of 1-I. The magnetically bistable porous framework decorating guest interactive open-metal-site in the pore surface makes it possible to modulate T(c) ad arbitrium through unique postsynthetic method using iodine migration.     

Rhodium-catalyzed asymmetric 1,4-addition of sodium tetraarylborates to β,β-disubstituted α,β-unsaturated esters

A rhodium-catalyzed 1,4-addition of sodium tetraarylborates to β,β-disubstituted α,β-unsaturated esters has been developed. Highly efficient asymmetric catalysis has also been described to create quaternary carbon stereocenters at the β-position of esters by tuning the ester group of substrates and employing a readily available chiral diene ligand.     

Direct catalytic enantio- and diastereoselective aldol reaction of thioamides

A direct catalytic asymmetric aldol reaction of thioamides using a soft Lewis acid/hard Br?nsted base cooperative catalyst comprising (R,R)-Ph-BPE/[Cu(CH(3)CN)(4)]PF(6)/LiOAr is described. Exclusive enolate generation from thioacetamides through a soft-soft interaction with the soft Lewis acid allowed for a direct aldol reaction to α-nonbranched aliphatic aldehydes, which are usually susceptible to self-condensation under conventional basic conditions. A hard Lewis basic phosphine oxide has emerged as an effective additive to constitute a highly active ternary soft Lewis acid/hard Br?nsted base/hard Lewis base cooperative catalyst, enabling a direct enantio- and diastereoselective aldol reaction of thiopropionamides. Strict control of the amount of the hard Lewis base was essential to drive the catalytic cycle efficiently with a minimized retro-aldol pathway, affording syn-aldol products with high stereoselectivity. Divergent transformation of the thioamide functionality is an obvious merit of the present aldol methodology, allowing for a facile transformation of the aldol product into the corresponding aldehyde, ketone, amide, amine, and ketoester. An aldehyde derived from the direct aldol reaction was subjected to a second direct aldol reaction, which proceeded in a catalyst-controlled manner to provide 1,3-diols with high stereoselectivity.     

Preparation of α-trialkylsilyl ketones from α-phenylseleno derivatives via their silyl enol ethers

On treatment with metallic lithium in the presence of dimethylaminonaphthalene, trialkylsilyl enol ethers of α-phenylseleno ketones were converted into the corresponding α-trialkylsilyl ketones in good yields.     

Structured Catalysts Prepared by Electroless Plating Technique onto a Metal Substrate, for a Wall-Type Hydrogen Production System

This article reviews our works on the structured catalysts for a wall-type hydrogen production system including methanol steam reforming (MSR), CO shift reaction (CO SR) and methanol decomposition (MD). The structured catalysts were copper-based, palladium-based and nickel-based catalysts. Such a series of structured catalysts were prepared by the electroless plating technique that is a novel method for preparing a structured type catalyst onto a metal-substrate. The copper-based catalyst exhibited high performance for MSR and CO SR, the palladium-based catalyst high for MSR, and the nickel-based catalyst high for MD. The catalytic properties of these catalysts were affected by the difference of the plating condition and the pretreatment condition prior to the reaction. In the copper-based catalyst, the reforming and shift activities were enhanced by the oxidation treatment. One of the factors of such activity enhancement by the oxidation was thought to be in close proximity existence of copper and zinc atoms. A lot of monodentate-type formate species having high reactivity was formed on the oxidized catalyst, which would be correlated to the activity enhancement. In the palladium-based catalyst, the reforming activity was improved by the continuous reduction treatment followed by the oxidation. Such continuous pretreatment formed the PdZn alloy species thought to be a reforming site in the surface layer. The decomposition performance of the nickel-based catalyst depended on the ratio of the crystallite size of nickel particles to that of aluminum particles. The electronic influence of zinc and phosphorous components incorporated in the plated layer contributed to the improvement of the selectivity of product.