Effect of glycosaminoglycan structure on all-trans-retinoic acid-induced neural differentiation of P19 embryonal carcinoma cells.

Glycosaminoglycan polysaccharides are components of animal extracellular matrices and regulate cell functions based on their various sulfation and epimerization pattern structures. The present study aimed to find glycosaminoglycan structures to promote neural differentiation. We investigated the effect of exogenous glycosaminoglycans with well-defined structures on the all-trans-retinoic acid-induced neural differentiation of P19 embryonal carcinoma cells, which is an ideal model culture system for studying neural differentiation. We found that chondroitin sulfate E and heparin, but not any other glycosaminoglycans, upregulated the expressions of neural specific markers but not a grail specific marker. Chondroitin sulfate E was suggested to function during spheroid formation, however, equimolar concentration of its oligosaccharide did not show promotive effect on the neural differentiation. Another finding was that hyaluronan oligosaccharide mixture markedly downregulated the expressions of a myelin specific marker. These findings suggested that the specific sulfation pattern and/or chain length of exogenous added glycosaminoglycan is important to regulate neural differentiation and myelination.

Characterization of 20-fs VUV pulses by plasma-mirror frequency-resolved optical gating.

We demonstrate that vacuum ultraviolet (VUV) pulses (λ∼160 nm) with 20-fs duration can be fully characterized by plasma-mirror frequency-resolved optical gating. Plasma is formed as an ultrafast optical switch on a fused silica surface by irradiation of an intense near-infrared (NIR) femtosecond laser pulse. We measure the spectra of the VUV pulses reflected off plasma as a function of the delay with respect to the NIR pulse and reconstruct it to simultaneously extract a nearly Fourier-transform limited VUV pulse shape and a time-dependent reflectivity of plasma using the least-squares generalized projections algorithm. We show that there is almost no spatial dependence of the VUV pulse shape, whereas the plasma mirror reflectivity strongly depends on the spatial region.

Frequency-resolved optical gating for characterization of VUV pulses using ultrafast plasma mirror switching.

We propose and experimentally demonstrate a method for characterizing vacuum ultraviolet (VUV) pulses based on time-resolved reflection spectroscopy of fused silica pumped by an intense laser pulse. Plasma mirror reflection is used as an ultrafast optical switch, which enables us to measure frequency-resolved optical gating (FROG) traces. The VUV temporal waveform can be retrieved from the measured FROG trace using principal component generalized projections algorithm with modification. The temporal profile of the plasma mirror reflectivity is also extracted simultaneously.

Specificity of DNA damage formation induced by femtosecond near-infrared laser filamentation in water.

We investigated the deoxyribonucleic acid (DNA) damage induced by laser filamentation, which was generated by focusing femtosecond near-infrared Ti:Sapphire laser light in water at several repetition rates ranging from 1000 Hz to 10 Hz. Using plasmid DNA (pUC19), the single-strand break, double-strand break, nucleobase lesions, and the fragmented DNA were analyzed and quantified by agarose gel electrophoresis. Additionally, the H2O2 concentration after irradiation was determined. We observed that (1) the DNA damage per laser shot and (2) the enzyme-sensitive base lesions per total DNA damage decreased as the laser repetition rate increased. Furthermore, (3) extraordinarily short DNA fragments were likely to be produced, compared with those produced using X-rays, and (4) most OH radicals could be eliminated by recombination to generate H2O2, preventing them from damaging the DNA. The Monte-Carlo simulation of the strand break formation implies that the observed dependency of strand break efficiency on the laser repetition rate is mainly due to diffusion of DNA molecules. These findings quantitatively and qualitatively revealed that an intense laser pulse induces a specific DNA damage profile that is not induced by X-rays, a sparsely ionizing radiation source.

Deformation of an inner valence molecular orbital in ethanol by an intense laser field.

Valence molecular orbitals play a crucial role in chemical reactions. Here, we reveal that an intense laser field deforms an inner valence orbital (10a') in the ethanol molecule. We measure the recoil-frame photoelectron angular distribution (RFPAD), which corresponds to the orientation dependence of the ionization probability of the orbital, using photoelectron-photoion coincidence momentum imaging with a circularly polarized laser pulse. Ab initio simulations show that the orbital deformation depends strongly on the laser field direction and that the measured RFPAD cannot be reproduced without taking the orbital deformation into account. Our findings suggest that the laser-induced orbital deformation occurs before electron emission on a suboptical cycle time scale.

Isotopically selective infrared multiphoton dissociation of 2,3-dihydropyran.

Oxygen isotopic selectivity on infrared multiphoton dissociation of 2,3-dihydropyran has been studied by the examination of the effects of excitation frequency, laser fluence, and gas pressure on the dissociation probability of 2,3-dihydropyran and isotopic composition of products. Oxygen-18 was enriched in a dissociation product: 2-propenal. The enrichment factor of 18O and the dissociation probability were measured at a laser frequency between 1033.5 and 1057.3 cm-1, the laser fluence of 2.2-2.3 J/cm2, and the 2,3-dihydropyran pressure of 0.27 kPa. The dissociation probability decreases as the laser frequency being detuned from the absorption peak of 2,3-dihydropyran around 1081 cm-1. On the other hand, the enrichment factor increases with detuning the frequency. The enrichment factor of 18O increases with increasing the 2,3-dihydropyran pressure at the laser fluence of 2.7 J/cm2 or less and the laser frequency of 1033.5 cm-1, whereas the yield of 2-propenal decreases with increasing the pressure. A very high enrichment factor of 751 was obtained by the irradiation of 0.53 kPa of 2,3-dihydropyran at 2.1 J/cm2. Collisional effect of vibrationally excited molecules with ambient molecules on isotopic selectivity is discussed on the basis of a rate equation model including a collisional vibrational de-excitation process.

Similarity in the Structure of tetD-Carrying Mobile Genetic Elements in Bacterial Strains of Different Genera Isolated from Cultured Yellowtail.

Structure analysis was performed on the antibiotic-resistance-gene region of conjugative plasmids of four fish farm bacteria.The kanamycin resistance gene, IS26, and tetracycline resistance gene (tetA(D)) were flanked by two IS26s in opposite orientation in Citrobacter sp. TA3 and TA6, and Alteromonas sp. TA55 from fish farm A. IS26-Inner was disrupted with ISRSB101. The chloramphenicol resistance gene, IS26 and tetA (D) were flanked by two IS26s in direct orientation in Salmonella sp. TC67 from farm C. Structures of tetA (D) and IS26 were identical among the four bacteria, but there was no insertion within the IS26-Inner of Salmonella sp. TC67. Horizontal gene transfer between the strains of two different genera in fish farm A was suggested by the structure homologies of mobile genetic elements and antibiotic resistance genes.

Structure determination of molecules in an alignment laser field by femtosecond photoelectron diffraction using an X-ray free-electron laser.

We have successfully determined the internuclear distance of I2 molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I2 molecules in an alignment Nd:YAG laser field of 6 × 1011 W/cm2 is elongated by from 0.18 to 0.30 Å "in average" relatively to the equilibrium internuclear distance of 2.666 Å. Thus, the present experiment constitutes a critical step towards the goal of femtosecond imaging of chemical reactions and opens a new direction for the study of ultrafast chemical reaction in the gas phase.

Photoelectron diffraction from laser-aligned molecules with X-ray free-electron laser pulses.

We report on the measurement of deep inner-shell 2p X-ray photoelectron diffraction (XPD) patterns from laser-aligned I2 molecules using X-ray free-electron laser (XFEL) pulses. The XPD patterns of the I2 molecules, aligned parallel to the polarization vector of the XFEL, were well matched with our theoretical calculations. Further, we propose a criterion for applying our molecular-structure-determination methodology to the experimental XPD data. In turn, we have demonstrated that this approach is a significant step toward the time-resolved imaging of molecular structures.

Structural variation of Tn10 that carries tetB found in fish farm bacteria.

Three variants of the composite transposon Tn10 were extracted from transferable plasmids of fish farm bacteria. These variants were identical in insertions with IS10, but differed in another class I transposon insertion and a region of homologous recombination downstream of tetB.

Theoretical Study on the Structure and the Frequency of Isomers of the Naphthalene Dimer.

The structures of the naphthalene monomer and dimer were investigated with performing vibrational analysis. The MP2 optimization showed that the naphthalene monomer has a nonplanar geometry in the 6-31G, 6-31G*, 6-31+G*, and 6-311G basis sets, while it has a planar geometry in the 6-31G*(0.25) and Dunning's correlation consistent basis sets. The MP2/cc-pVDZ calculation showed the presence of the four stable isomers, which were part of the isomers in the previous MP2/6-31G* calculation (Walsh, T. R. Chem. Phys. Lett. 2002, 363, 45). The presence of extra structures in the MP2/6-31G* calculation is attributed to a poor description of the potential energy surface, which is evident from the nonplanar structure of the monomer in the MP2/6-31G* calculation. The relative stability among the isomers in the MP2/cc-pVDZ calculation without counterpoise correction was maintained in both the single-point calculation at the MP2/aug-cc-pVDZ//MP2/cc-pVDZ level and the counterpoise-corrected optimization at the MP2/cc-pVDZ level. The relative stability among the isomers suggested an enhancement of the π-π interaction in the structure with lower symmetry, which could be explained using a molecular-orbital model. The vibrational analysis in MP2/cc-pVDZ without the counterpoise correction suggested that the isomers of the naphthalene dimer were distinguishable by the observation of the infrared spectrum in the low-frequency region (150-600 cm(-)(1)).

Selective OD bond dissociation of HOD: photodissociation of vibrationally excited HOD in the 5nu(OD) state.

Exclusively selective OD bond dissociation of HOD has been demonstrated by the ultraviolet photodissociation at 243.1 nm through the fourth overtone state of the OD stretching mode (5nu(OD)). Branching ratio between the OH and OD bond dissociation channels has been determined by detecting H and D atoms, utilizing a (2+1) resonance-enhanced multiphoton ionization (REMPI) process. The OD bond dissociation has been solely observed with the branching ratio phi(D+OH)/phi(H+OD)>12, which has been determined by the detection limit for the H atom. Time-dependent wave-packet calculations reveal two important features for the highly selective OD bond dissociation: (1) strong local-mode character of the 5nu(OD) state and (2) limitation of the total excitation energy lower than the saddle point between the OH and OD dissociation channels in the A state. Additionally, the recoil velocity and angular distribution of the nascent D atom are roughly evaluated by analyzing the Doppler-resolved REMPI spectrum. Based on these results, the dynamics of the selective OD dissociation has been discussed in detail.

Bond-selective photodissociation of partially deuterated ammonia molecules: photodissociations of vibrationally excited NHD(2) in the 5nu(NH) state and NH(2)D in the 5nu(ND) state.

Ultraviolet photodissociation of NHD(2) excited to the fourth overtone state of the NH stretching mode (5nu(NH)) and NH(2)D excited to that of the ND stretching mode (5nu(ND)) has been investigated by using a crossed laser and molecular beams method. Branching ratio between the NH and ND bond dissociations has been determined by utilizing a (2+1) resonance enhanced multiphoton ionization scheme of H and D atoms. For the photolysis of NHD(2) in the 5nu(NH) state, the NH dissociation cross section is 5.1+/-1.4 times as large as the ND dissociation cross section per bond. On the other hand, for the photolysis of NH(2)D in the 5nu(ND) state, the ratio of the NH dissociation cross section per bond to the ND dissociation cross section decreases to 0.68+/-0.16. In comparison with the branching ratios for the photolysis of vibrationally unexcited NH(2)D and NHD(2), the present results indicate that the excitation of the NH stretching mode enhances the NH dissociation with ca. two times larger NH/ND branching ratio, whereas the excitation of the ND stretching mode results in the preferential ND dissociation with ca. 3-4 times larger ND/NH branching ratio than that for the vibrational ground states. The mechanism of the bond-selective enhancement has been discussed in terms of the energetics and dynamics of wave packet.