Application of mid-infrared free-electron laser for structural analysis of biological materials.

A mid-infrared free-electron laser (MIR-FEL) is a synchrotron-radiation-based femto- to pico-second pulse laser. It has unique characteristics such as variable wavelengths in the infrared region and an intense pulse energy. So far, MIR-FELs have been utilized to perform multi-photon absorption reactions against various gas molecules and protein aggregates in physical chemistry and biomedical fields. However, the applicability of MIR-FELs for the structural analysis of solid materials is not well recognized in the analytical field. In the current study, an MIR-FEL is applied for the first time to analyse the internal structure of biological materials by using fossilized inks from cephalopods as the model sample. Two kinds of fossilized inks that were collected from different strata were irradiated at the dry state by tuning the oscillation wavelengths of the MIR-FEL to the phosphoryl stretching mode of hydroxyapatite (9.6 µm) and to the carbonyl stretching mode of melanin (5.8 µm), and the subsequent structural changes in those materials were observed by using infrared microscopy and far-infrared spectroscopy. The structural variation of these biological fossils is discussed based on the infrared-absorption spectral changes that were enhanced by the MIR-FEL irradiation, and the potential use of MIR-FELs for the structural evaluation of biomaterials is suggested.

Measurement of angular distribution of soft X-ray radiation from thin targets in the tabletop storage ring MIRRORCLE-20SX.

The only available tabletop electron storage rings are the machines from the MIRRORCLE series. The electrons are accelerated in a microtron and injected into the storage ring. During its circulation, each electron passes through a tiny target many times, emitting a photon beam. Both the spectrum and the angular distribution of the radiation depend on the material, the thickness and the shape of the target. In this paper measured angular distributions of the radiation from several different targets in the magnetic field of the 20 MeV storage ring MIRRORCLE-20SX are presented. The detector comprises a 3 mm × 3 mm × 8.5 µm plastic scintillator (PS) coupled to a photomultiplier by a bundle of optical fibers. The output of the photomultiplier is digitized by an IF converter. This detector is sensitive mostly to soft X-ray radiation, and its PS is moved by a mechanical system in a plane perpendicular to the radiation axis. The measured angular distributions for Mo and Sn targets contain an annulus which is attributed to transition radiation. The angular distributions for Al, carbon nanotube and diamond-like carbon (DLC) targets show some suppression of the radiation along the magnetic field. This is the first evidence of observation of the angular distribution of synchrotron Cherenkov radiation, which represents Cherenkov radiation in a magnetic field. The power radiated from the DLC target is estimated.

Molecular epidemiology of Salmonella enterica serovar typhimurium isolates from cattle in hokkaido, Japan: evidence of clonal replacement and characterization of the disseminated clone.

The molecular epidemiology of 545 Salmonella enterica serovar Typhimurium isolates collected between 1977 and 2009 from cattle in Hokkaido, Japan, was investigated using pulsed-field gel electrophoresis (PFGE). Nine main clusters were identified from 116 PFGE patterns. Cluster I comprised 248 isolates, 243 of which possessed a sequence specific to definitive phage type 104 (DT104) or U302. The cluster I isolates were dominant in 1993 to 2003, but their numbers declined beginning in 2004. Beginning in 2002, an increase was observed in the number of cluster VII isolates, consisting of 21 PFGE patterns comprising 165 isolates. A total of 116 isolates representative of the 116 PFGE profiles were analyzed by multilocus variable-number tandem-repeat analysis (MLVA). Other than two drug-sensitive isolates, 19 isolates within cluster VII were classified in the same cluster by MLVA. Among the cluster VII isolates, an antibiotic resistance type showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, tetracycline, kanamycin, cefazolin, and sulfamethoxazole-trimethoprim and a resistance type showing resistance to ampicillin, streptomycin, sulfonamides, tetracycline, and kanamycin were found in 23 and 125 isolates, respectively. In the 19 isolates representative of cluster VII, the bla(TEM-1) gene was found on a Salmonella serotype Typhimurium virulence plasmid, which was transferred to Escherichia coli by electroporation along with resistance to two to four other antimicrobials. Genomic analysis by subtractive hybridization and plasmid analysis suggested that the bla(TEM-1)-carrying virulence plasmid has a mosaic structure composed of elements of different origin. These results indicate an emerging multidrug-resistant S. Typhimurium clone carrying a virulence-resistance plasmid among cattle in Hokkaido, Japan.

Characterization of an x-ray phase contrast imaging system based on the miniature synchrotron MIRRORCLE-6X.

PURPOSE: The implementation of in-line x-ray phase contrast imaging (PCI) for soft-tissue patient imaging is hampered by the lack of a bright and spatially coherent x-ray source that fits into the hospital environment. This article provides a quantitative characterization of the phase-contrast enhancement of a PCI system based on the miniature synchrotron technology MIRRORCLE-6X. METHODS: The phase-contrast effect was measured using an edge response of a plexiglass plate as a function of the incident angle of radiation. We have developed a comprehensive x-ray propagation model based on the system's components, properties, and geometry in order to interpret the measurement data. Monte-Carlo simulations are used to estimate the system's spectral properties and resolution. RESULTS: The measured ratio of the detected phase-contrast to the absorption contrast is currently in the range 100% to 200%. Experiments show that with the current implementation of the MIRRORCLE-6X, a target smaller than 30-40 µm does not lead to a larger phase-contrast. The reason for this is that the fraction of x-rays produced by the material (carbon filament and glue) that is used for mounting the target in the electron beam is more than 25% of the total amount of x-rays produced. This increases the apparent source size. The measured phase-contrast is at maximum two times larger than the absorption contrast with the current set-up. CONCLUSIONS: Calculations based on our model of the present imaging system predict that the phase-contrast can be up to an order of magnitude larger than the absorption contrast in case the materials used for mounting the target in the electron beam do not (or hardly) produce x-rays. The methods described in this paper provide vital feedback for guiding future modifications to the design of the x-ray target of MIRRORCLE-type system and configuration of the in-line PCI systems in general.

Simultaneous measurement of X-ray specular reflection and off-specular diffuse scattering from liquid surfaces using a two-dimensional pixel array detector: the liquid-interface reflectometer of BL37XU at SPring-8.

An X-ray reflectometer for simultaneous measurement of specular and off-specular reflection of liquid surfaces is described. The reflectometer, equipped with a two-dimensional single X-ray photon-counting pixel array detector obtained the full range of X-ray specular and off-specular reflections in an extremely short time (1 s). Both the specular and off-specular reflection of water exhibited good agreement with the predicted capillary-wave theory within the appropriate instrumental resolution. The approach is also demonstrated on an aqueous solution of 1-dodecyl-3-methylimidazolium chloride. The monolayer in which the dodecyl chain faces upwards and the Cl(-) anion locates next to the imidazolium ring formed on the water surface was found to be laterally homogeneous. The use of a pixel array detector will be particularly powerful for in situ measurements to investigate both out-of-plane and in-plane structures simultaneously, not only for liquid surfaces but also for other thin films.

New polar constituents in the pupae of the silkworm Bombyx mori L. (II): developmental changes of the constituents.

A correlation between the quantitative changes in L-methionine analogs, the ratio of D-serine/L-serine during the pupal stage, and metamorphosis was observed. The glycoside appearing at low blood sugar values during the pupal stage was isolated and characterized as D-glucosyl-L-tyrosine. (1)H-NMR indicated the appearance and increase of this glycoside, and Mirrorcle Ray CV4 equipment was used to take X-ray pictures of the pupal bodies. The results indicate that γ-cyclic di-L-glutamate and L-methionine sulfone might be concerned with ammonia assimilation in the pupae, and that D-glucosyl-L-tyrosine served as a switch for the fatty acid (pupal oil) dissimilation hybrid system.

Intermolecular vibrational study in liquid water and ice by using far infrared spectroscopy with synchrotron radiation of MIRRORCLE 20.

Far infrared absorption measurements for distilled water and ice Ih were performed in the frequency range from 20 cm(-1) to 1000 cm(-1) with Fourier Transform Infrared Spectrometer (FTIR) utilizing SR of a portable synchrotron. Four vibrational bands were separated from measured spectra in liquid water. We found that a peak frequency of 40±1 cm(-1) did not depend on the temperature in a range between 10.0°C and 70.0°C; however, any low energy excitation modes were not observed in the ice spectrum. It is concluded that this band is caused by collective vibrations specific to the dynamical structure in liquid water.

Performance of the far-IR beamline of the 6 MeV tabletop synchrotron light source.

The performance of the far-infrared (FIR) beamline of the 6 MeV tabletop synchrotron light source MIRRORCLE-6FIR dedicated to far-infrared spectroscopy is presented. MIRRORCLE-6FIR is equipped with a perfectly circular optical system (PhSR) placed around the 1 m-long circumference electron orbit. To illustrate the facility of this light source, the FIR output as well as its spectra were measured. The optimum optical system was designed by using the ray-tracing simulation code ZEMAX. The measured FIR intensity with the PhSR in place is about five times higher than that without the PhSR, which is in good agreement with the simulation results. The MIRRORCLE-6FIR spectral flux is compared with a standard thermal source and is found to be 1000 times greater than that from a typical thermal source at approximately 15 cm(-1). It is also observed that the MIRRORCLE-6FIR radiation has a highly coherent nature. The broadband infrared allows the facility to reach the spectral range from 10 cm(-1) to 100 cm(-1). MIRRORCLE-6FIR, owing to a large beam current, the PhSR mirror system, a large dynamic aperture and small ring energy, can deliver a bright flux of photons in the FIR/THz region useful for broadband spectroscopy.

Driving force behind adsorption-induced protein unfolding: a time-resolved X-ray reflectivity study on lysozyme adsorbed at an air/water interface.

Time-resolved X-ray reflectivity measurements for lysozyme (LSZ) adsorbed at an air/water interface were performed to study the mechanism of adsorption-induced protein unfolding. The time dependence of the density profile at the air/water interface revealed that the molecular conformation changed significantly during adsorption. Taking into account previous work using Fourier transform infrared (FTIR) spectroscopy, we propose that the LSZ molecules initially adsorbed on the air/water interface have a flat unfolded structure, forming antiparallel beta-sheets as a result of hydrophobic interactions with the gas phase. In contrast, as adsorption continues, a second layer forms in which the molecules have a very loose structure having random coils as a result of hydrophilic interactions with the hydrophilic groups that protrude from the first layer.

Surface structure of a neat ionic liquid investigated by grazing-incidence x-ray diffraction.

Grazing-incidence x-ray diffraction measurements were carried out to observe the surface structure of [bmim][PF(6)]. At an incident angle of less than the critical angle, a diffraction pattern from 10 nm beneath the surface was obtained. A broad Debye-Scherrer ring was observed in the diffraction patterns, indicating that the [bmim][PF(6)] molecules near the surface are randomly orientated, similar to those in the bulk liquid. The distance of the nearest anions was estimated to be 4.2 A, which is very close to that for bulk [bmim][I], suggesting that the liquid structure of [bmim][PF(6)] is determined by the packing of the cation.

Refraction contrast 11x-magnified X-ray imaging of large objects by MIRRORCLE-type table-top synchrotron.

The high-quality aspects of magnified X-ray images recorded using MIRRORCLE-6X are reported. MIRRORCLE-6X is inherently suitable for hard X-ray imaging owing to its magnified projection X-ray imaging, micrometre-size X-ray source point, wide radiation emission angle, X-ray spectrum ranging from 10 keV to 6 MeV, natural refraction contrast imaging and high flux output. Images produced with 11x geometrical magnification display a sharply enhanced edge effect when generated using a 25 microm rod electron target. Image contrast is enhanced 2x owing to refraction when compared with absorption contrast images. An imitation tumour implanted in a human chest phantom was made clearly visible by using edge enhancement on images. Soft tissue becomes highly visible as a natural consequence of refraction contrast when using hard X-rays for imaging. The authors believe that novel imaging provided by MIRRORCLE makes it a superior instrument for medical diagnosis.