i-RUBY: a novel software for quantitative analysis of highly accurate shotgun-proteomics liquid chromatography/tandem mass spectrometry data obtained without stable-isotope labeling of proteins

We developed a novel software named i-RUBY (identification-Related qUantification-Based strategY algorithm for liquid chromatography/tandem mass spectrometry (LC/MS/MS) data) that enables us to perform fully automatic ion current-based spectral feature analysis of highly accurate data obtained by LC/MS/MS. At the 1st step, this software utilizes accurate peptide/protein identification information for peak detection and peak matching among measurements. Then, at the 2nd step, it picks yet unidentified peaks and matches them to the peaks identified at the 1st step by a linear interpolation algorithm. The analysis of human plasma externally spiked with a known amount of yeast alcohol dehydrogenase 1 showed a good linear relationship between the amount of protein spiked and the quantitative values obtained by i-RUBY analysis. Experiment using human plasma digests spiked with a mixture of known amounts of synthetic peptides derived from two yeast proteins, alcohol dehydrogenase 1 and glucose-6-phospate isomerase, showed the expansion by the 2nd step of i-RUBY of the lower quantification limits to 1/10 to 1/1000 of those reached only by identified peaks at the 1st step. Good correlations between the i-RUBY results and the amount of proteins were confirmed by the analysis of real samples, i.e., sera of normal subjects and cancer patients, by comparing quantitative values of acute-phase proteins obtained by i-RUBY analysis of LC/MS/MS data with those obtained by an immunological method using Bio-Plex. These results taken together show that i-RUBY is a useful tool for obtaining dependable quantitative information from highly accurate shotgun-proteomics LC/MS/MS data.     

Bound H dibaryon in flavor SU(3) limit of lattice QCD

The flavor-singlet H dibaryon, which has strangeness -2 and baryon number 2, is studied by the approach recently developed for the baryon-baryon interactions in lattice QCD. The flavor-singlet central potential is derived from the spatial and imaginary-time dependence of the Nambu-Bethe-Salpeter wave function measured in N(f)=3 full QCD simulations with the lattice size of L?2,3,4 fm. The potential is found to be insensitive to the volume, and it leads to a bound H dibaryon with the binding energy of 30-40 MeV for the pseudoscalar meson mass of 673-1015 MeV.     

Efficient homodyne measurement of picosecond squeezed pulses with pulse shaping technique

We report on the detection of picosecond pulsed squeezed light generated by an optical parametric amplification in a periodically poled MgO:LiNbO(3) waveguide. By using a temporally shaped local oscillator in a balanced homodyne detection, we obverved the squeezing of -5.0 dB below the shot noise level. The squeezing level at the exit of the waveguide was estimated to be -9.7±0.8 dB.     

Regioselective synthesis of 1,4-di(organo)[60]fullerenes through DMF-assisted monoaddition of silylmethyl Grignard reagents and subsequent alkylation reaction

Monoaddition of Grignard reagents, in particular tri(organo)silylmethylmagnesium chlorides, to [60]fullerene took place smoothly in the presence of dimethylformamide to produce (organo)(hydro)[60]fullerenes, C60R(1)H, in good yield (up to 93% isolated yield). The hydrofullerene was then deprotonated to generate the corresponding anion, C60R(-), which was then alkylated to obtain 58pi-electron di(organo)[60]fullerenes, C60R(1)R(2), in good to high yield (up to 93% overall yield). The two-step methodology provides a wide variety of 1,4-di(organo)[60] fullerenes bearing the same or different organic addends on the [60] fullerene core. By changing the addends, one can control the chemical and physical properties of the compounds at the molecular and bulk levels.     

The Photocatalytic Degradation of Imazapyr

The degradation of imazapyr, an imidazolinone herbicide, in aqueous solution has been investigated with TiO₂ slurry as photocatalyst at 30°C under UV radiation. The depletion of imazapyr concentration in an aqueous suspension followed 1^st order kinetic behavior. The influence of pH and the charge densities of imazapyr geometries were calculated at the semi-empirical AM1 level, and the effect of temperature was investigated. The addition of electron acceptors such as potassium persulfate and hydrogen peroxide showed that the rate constant doubled at least. At higher persulfate concentrations the herbicide degradation was more efficient in direct photolysis than TiO₂-photocatalysis. The degradation rate constant increased by 38% upon variation of the temperature between 20.0 and 50.0°C and displayed non-Arrhenius behavior.     

A Ruthenium Bridge in Fullerene–Ferrocene Arrays: Synthesis of [Ru(C60Me5)R(CO)2] (R=C6H4Fc,C≡CFc) and Their Charge‐Transfer Properties

New fullerene–ferrocene arrays, [Ru(C₆₀Me₅)(C₄H₆Fc)(CO)₂] (Fc=ferrocenyl) and [Ru(C₆₀Me₅)(CCFc)(CO)₂], in which the ruthenium complex functions as a conjugative bridge, were synthesized by the reaction of [Ru(C₆₀Me₅)Cl(CO)₂] with FcC₆H₄MgBr and FcCCLi, respectively. These compounds were investigated by electrochemical measurement, single‐crystal X‐ray structural analysis, and photophysical measurement. Upon photoirradiation, the former compound was converted rapidly into the corresponding triplet state in toluene (τ_singlet=21 ps), whereas the charge‐separated state was predominant in THF (τ_singlet=10.5 ps; τ_CS=355 ps). The latter compound, on the other hand, formed the charge‐separated state in both toluene and THF (τ_singlet=3.0 ps; τ_CS=152 ps). Thus, the structural difference between the phenylene and acetylene bridges in 1 and 2 , respectively, was found to change the outcome of the photophysical processes.     

Unusual temperature dependence of enantioselectivity in asymmetric reductions by chiral NADH models

[reaction: see text] Unusual stereoselectivity changes, i.e., enhancement and inversion of enantioselectivity with increasing temperature, were observed in the asymmetric reduction of methyl benzoylformate with chiral 1,4-dihydropyridines possessing amino acid residues as ligating chiral auxiliaries. The differential activation parameters, DeltaDeltaH(S-R) and DeltaDeltaS(S-R), obtained from the Eyring plots demonstrate that the entropy term controls the enantiodifferentiating step, accounting for the observed unique temperature dependencies.     

Synthesis of Orthorhombic Mo‐V‐Sb Oxide Species by Assembly of Pentagonal Mo6O21 Polyoxometalate Building Blocks

Mix and match : The pentagonal [Mo₆O₂₁]^n? polyoxomolybdate building block assembles with other sources of Mo, V, and Sb ions to form an orthorhombic Mo‐V‐Sb oxide. The first single‐crystal X‐ray analysis of an orthorhombic Mo–V‐based oxide, a promising catalyst for light alkane selective oxidation known as the “M1 phase”, revealed the structure of the compound.

     

Hybridization Assay by Time-Resolved Capillary Gel Electrophoresis with a Lanthanide Chelate

Capillary electrophoresis of crude biological samples with time-resolved fluorescence (TRF) detection enables elimination of interference from organic fluorophores and from light scattering. Because the fluorescence lifetime of biological substances and impurities overlaps the fluorescence lifetime of conventional labeling dyes, TRF detection with conventional organic labeling dyes suffers from background fluorescence. In this work, we synthesized a luminescent lanthanide chelating reagent to covalently bind the 5′-end of DNA through its dichroic functional group while retaining the unique luminescent properties of the lanthanide chelate, i.e. large Stokes shift, sharp emission, and a long luminescence lifetime in the microsecond to millisecond range. The luminescence of lanthanide chelates is inherently quenched by dissociation of the central metals in typical biological buffers containing a strong chelator, for example EDTA or phosphate; the synthesized Eu³⁺ chelate reagent, however, was stable even in EDTA solutions. In addition to stability in biological buffer solution, the synthesized Eu³⁺ chelate reagent enabled direct labeling of single-stranded oligonucleotides, and was used for DNA hybridization assay by time-resolved capillary gel electrophoresis. DNA hybridization assay in fetal bovine serum was also demonstrated.