Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) is the best MS technology for obtaining exact mass measurements owing to its great resolution and accuracy, and several outstanding FT-ICR/MS-based metabolomics approaches have been reported. A reliable annotation scheme is needed to deal with direct-infusion FT-ICR/MS metabolic profiling. Correlation analyses can help us not only uncover relations between the ions but also annotate the ions originated from identical metabolites (metabolite derivative ions). In the present study, we propose a procedure for metabolite annotation on direct-infusion FT-ICR/MS by taking into consideration the classification of metabolite-derived ions using correlation analyses. Integrated analysis based on information of isotope relations, fragmentation patterns by MS/MS analysis, co-occurring metabolites, and database searches (KNApSAcK and KEGG) can make it possible to annotate ions as metabolites and estimate cellular conditions based on metabolite composition. A total of 220 detected ions were classified into 174 metabolite derivative groups and 72 ions were assigned to candidate metabolites in the present work. Finally, metabolic profiling has been able to distinguish between the growth stages with the aid of PCA. The constructed model using PLS regression for OD₆₀₀ values as a function of metabolic profiles is very useful for identifying to what degree the ions contribute to the growth stages. Ten phospholipids which largely influence the constructed model are highly abundant in the cells. Our analyses reveal that global modification of those phospholipids occurs as E. coli enters the stationary phase. Thus, the integrated approach involving correlation analyses, metabolic profiling, and database searching is efficient for high-throughput metabolomics. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A Novel Double‐Network Hydrogel Induces Spontaneous Articular Cartilage Regeneration in vivo in a Large Osteochondral Defect

We have developed a novel method to induce spontaneous hyaline cartilage regeneration in vivo for a large osteochondral defect by implanting a plug made from a double‐network hydrogel composed of poly(2‐acrylamido‐2‐methylpropanesulfonic acid) and poly(N,N′‐dimethylacrylamide) at the bottom of the defect, leaving the cavity vacant. In cells regenerated in the treated defect, type‐2 collagen, Aggrican, and SOX9 mRNAs were highly expressed and the regenerated matrix was rich in proteoglycan and type‐2 collagen at 4 weeks. This fact gave a significant modification to the commonly established concept that hyaline cartilage tissue cannot regenerate in vivo. This study prompted an innovative strategy in the field of joint surgery to repair an osteochondral defect using an advanced, high‐function hydrogel.

     

Synthesis,physical properties,and structure of TIPS-difuranoacenes

The synthesis, physical properties, and structure of triisopropylsilylethynyltetracenodifuran (2) and pentacenodifuran (3) derivatives were reported. There showed high stability in solution in the dark, yet decomposed under light. Single crystal of pentacenodifuran was analyzed by X-ray diffraction analysis, and showed one dimensional packing array along the c-axis. The molecules were stacked with a 3.30 Å interlayer distance. The crystals exhibited a high thermal stability under an ambient condition.     

Anthracene based organic dipolar compounds for sensitized solar cells

Organic dyes that consist of an anthracene moiety between a triphenylamine donor group and a cyanoacrylic acid acceptor group displayed remarkable solar-to-energy conversion efficiency in dye-sensitized solar cells. The planar geometry of anthracene and its bulky substituents helped the dyes to form a high quality monolayer on the surface of TiO₂. A typical device made with the dye AN-Bu displayed a maximal photon-to-current conversion efficiency (IPCE) 65% in the region of 350–510 nm, a short-circuit photocurrent density (J_sc) 12.78 mA cm⁻², an open-circuit photovoltage (V_oc) 0.73 V, and a fill factor (FF) 0.67, corresponding to an overall conversion efficiency 6.23%. In an experiment of using deoxycholic acid (DCA) as a co-absorbent, the values of V_oc stayed in a similar range, yet the values of J_sc were reduced in ca. 11% due to a decrease of loading amounts. This result indicated that the quality of the dye films cannot be further improved by the adding of DCA. The photophysical properties were analyzed with the aid of a time-dependent density functional theory (TDDFT) model with the B3LYP functional.     

Hydrolysis of Diazonium Salts Using a Two‐Phase System (CPME and Water)

A new method for the hydrolysis of diazonium salts, without the formation of tar, was developed. A two‐phase system consisting of cyclopentyl methyl ether (CPME) and water is very effective for the hydrolysis of diazonium salts. Using this solvent system, the diazonium salt prepared from 3‐(4‐nitrophenoxy)aniline gave 3‐(4‐nitrophenoxy)phenol in high yield (96%) within 20 min. The synthesized phenol is an industrially important raw material in polymer syntheses. Furthermore, the use of the present two‐phase system of CPME and water successfully brought about the efficient conversions of several m‐substituted anilines into the corresponding m‐substituted phenols. This is the first example of hydrolysis of diazonium salts using the two‐phase system (CPME and water).     

Delocalization of positive charge in π-stacked multi-benzene rings in multilayered cyclophanes

In the present study, delocalization of a positive charge in π-stacked multi-benzene rings in multilayered para- and meta-cyclophanes, in which benzene rings are connected by propyl chains to form a chromophore array with the face-to-face structure, was investigated by means of transient absorption spectroscopy during the pulse radiolysis using dichloroethane as a solvent. The local excitation and charge resonance (CR) bands were successfully observed. It was revealed that the CR band shifted to the longer wavelength side with the number of the benzene rings. The stabilization energy estimated from the peak position of the CR band showed the efficient charge delocalization over the cyclophanes. Furthermore, the CR bands showed the slight spectral change attributable to the change in distribution of the conformers. The substantially long lifetime of the CR band can be explained on the basis of the smaller charge distribution on the outer layers of the multilayered cyclophanes.     

Double-threaded dimer and supramolecular oligomer formed by stilbene modified cyclodextrin: effect of acyl migration and photostimuli

We observed changing supramolecular structures of stilbene-α-cyclodextrin (StiO-α-CD) by photoirradiation and migration. Stilbene derivatives show photoinduced isomerization under irradiation with λ = 340 nm to give 2-cis-StiO-α-CD and with λ = 254 nm to give 2-trans-StiO-α-CD. Photoisomerization of StiO-α-CD shows the photostationary state during 30 min. 2D NMR and diffusion coefficient studies revealed that 2-trans-StiO-α-CD forms a double-threaded dimer but 2-cis-StiO-α-CD changes to a supramolecular oligomer by photoirradiation. We found that the mutual migration of a stilbene group (StiO) on α-CD occurs under neutral conditions. The StiO group of α-CD (StiO-α-CD) moves between the C2 and C3 positions on the secondary hydroxyl group of StiO-α-CD (the wider rim of α-CD) to give 3-trans-StiO-α-CD. 3-trans-StiO-α-CD forms a supramolecular oligomer, whereas 3-cis-StiO-α-CD changes to a double-threaded dimer, indicating that 3-StiO-α-CDs gives the opposite results in the supramolecular structures of 2-StiO-α-CDs. The thermal isomerization (migration) is very slow. It takes about 300 h to reach the equilibrium state. Moreover, the migration rate constant (k(trans3→2)) of the trans-StiO group from the C3 position to the C2 position of α-CD is faster than k(trans2→3) from the C2 position to the C3 position of α-CD. On the other hand, k(cis2→3) of the cis-StiO group from the C2 position to the C3 position of α-CD is faster than k(cis3→2) from the C3 position to the C2 position, meaning k(cis2→3) > k(cis3→2), which is the opposite result for k(trans3→2) > k(trans2→3). The formation of a stable double-threaded dimer would suppress the migration of the StiO group of StiO-α-CDs in aqueous solutions.     

A compact TOF-SANS using focusing lens and very cold neutrons

We are developing a high-resolution small angle neutron scattering instrument for very cold neutrons (VCN). Our concept includes a magnetic lens for focusing of the beam at the detector plane. The lens consists of one permanent-magnet sextupole array rotating outside another stationary sextupole array, to focus a pulsed white beam of neutrons. Thus the instrument operates in time of flight mode. The prototype magnetic lens has a bore of 15 mm diameter and length of 66 mm, producing a magnetic field gradient oscillating from 1.5×10⁴ to 5.9×10⁴ T/m², with frequency ≤25 Hz. A torque-canceling magnet around the lens suppresses the torque of rotation from the outer array to 1/3.We have demonstrated the performance of the lens, over wavelength range from 30 to 48 Å, on the PF2-VCN beam line at the Institut Laue-Langevin, France. The focused beam image was the same size as the source, without chromatic aberration, with focal length of 1.14 m. We also studied the performance of this configuration for high-resolution SANS, in a compact geometry (just 5 m long). The measurable q range of this system was 0.009 Å⁻¹≤q≤0.3 Å⁻¹ or 0.004 Å⁻¹≤q≤0.08 Å⁻¹ for sample to detector distances of 100 and 465 mm, respectively. Here, we present the results of our lens characterization study along with the SANS results on a tri-block copolymer (F127 Pluronic) and on a stretched polymer blend (with the Shish-Kebab structure).