Nd:YAG laser Thomson scattering diagnostics for a laboratory magnetosphere.

A new Nd:YAG laser Thomson scattering (TS) system has been developed to explore the mechanism of high-beta plasma formation in the RT-1 device. The TS system is designed to measure electron temperatures (Te) from 10 eV to 50 keV and electron densities (ne) of more than 1.0 × 1017 m-3. To measure at the low-density limit, the receiving optics views the long scattering length (60 mm) using a bright optical system with both a large collection window (260-mm diameter) and large collection lenses (300-mm diameter, a solid angle of ∼68 × 10-3 str). The scattered light of the 1.2-J Nd:YAG laser (repetition frequency: 10 Hz) is detected with a scattering angle of 90° and is transferred via a set of lenses and an optical fiber bundle to a polychromator. After Raman scattering measurement for the optical alignment and an absolute calibration, we successfully measured Te = 72.2 eV and ne = 0.43 × 1016 m-3 for the coil-supported case and Te = 79.2 eV and ne = 1.28 × 1016 m-3 for the coil-levitated case near the inner edge in the magnetospheric plasmas.

Coherence-imaging spectroscopy for 2D distribution of ion temperature and flow velocity in a laboratory magnetosphere.

A coherence-imaging spectroscopy (CIS) technique was developed to investigate plasma confinement in a dipole system that imitates a planetary magnetosphere. Optical interference generated using birefringent crystals enables two-dimensional Doppler spectroscopy to measure ion temperatures and flow velocities in plasmas. CIS covers the entire dynamics of the pole areas as well as of the core and edge areas on a dipole confinement device. The two-dimensional visualization of these quantities in the magnetospheric-plasma device RT-1 was demonstrated using CIS.

Esophageal atresia with double tracheoesophageal fistula--a case report and review of the literature.

Esophageal atresia with double tracheoesophageal fistula (TEF) is a very rare anomaly, and the accurate preoperative diagnosis of proximal TEF is very difficult. This paper describes a baby girl who presented with esophageal atresia with double, proximal, and distal TEF. The distal TEF was diagnosed before operation, whereas the proximal TEF was found intraoperatively. Overlooking the presence of proximal TEF can lead to increased morbidity and mortality due to severe respiratory infection and the necessity of a second operation. Great care must therefore be taken to not overlook the presence of proximal TEF in patients with this anomaly.

Ice-water interface migration by temperature controlling for stretching of DNA molecules.

This report shows a new DNA stretching method using migration of an ice-water interface. DNA molecules were stretched accompanying the migration of the solid-liquid interface and immobilized in frozen area. This simple method needs no chemical modification to keep DNA in the stretched form. For full stretching of DNA molecules, one terminus of the DNA molecules were anchored on silanized substrate. The anchored DNA molecules were stretched by freezing the DNA solution. The stretched DNA molecules were observed after sublimation of the frozen solution keeping its stretched form on silanized surface which had no attractive interaction with DNA molecules except for the SH-modified terminus in solution. An infrared (IR) laser beam was introduced to a frozen DNA solution through an objective lens for local area melting of the solution. Scanning of the laser irradiation caused stretching and enclosing of DNA molecules in the frozen area followed by migration of the solid-liquid interface.

Manipulation of a Large DNA Molecule using the Phase Transition.

A conventional method of DNA sequencing can determine up to 1000 base pairs at one time. Therefore, long DNA should be cut into many short fragments that are suitable for DNA sequencing. Those fragments, however, lose their order information. If the fragments are prepared from the terminus of the long DNA, the reorganization process can be omitted. This process consists of following unit operations; manipulation of genomic DNA, fixation with a stretched form, cutting from the terminus, recovery and amplification. In these unit operations, manipulation and cutting of DNA are focused in this report. Globular transformation suppresses break down of long genome DNA and permits manipulation of large DNA. Because globular transition is reversible, the coiled DNA can be sequentially spun from the globular DNA like a spindle. Thespun DNA was successfully fixed on a glass surface in an arbitrary pattern. To prepare fragments from the stretched DNA molecule, a method to cut DNA moleculen was developed. Since most restriction enzyme requires magnesium ion for their activation, the restriction enzyme was successfully activated only when magnesium ion was electrochemically supplied.

Dietary fiber showed no preventive effect against colon and rectal cancers in Japanese with low fat intake: an analysis from the results of nutrition surveys from 23 Japanese prefectures.

BACKGROUND: Since Fuchs' report in 1999, the reported protective effect of dietary fiber from colorectal carcinogenesis has led many researchers to question its real benefit. The aim of this study is to evaluate the association between diet, especially dietary fiber and fat and colorectal cancer in Japan. METHODS: A multiple regression analysis (using the stepwise variable selection method) was performed using the standardized mortality ratios (SMRs) of colon and rectal cancer in 23 Japanese prefectures as objective variables and dietary fiber, nutrients and food groups as explanatory variables. RESULTS: As for colon cancer, the standardized partial correlation coefficients were positively significant for fat (1,13, P = 0.000), seaweeds (0.41, P = 0.026) and beans (0.45, P = 0.017) and were negatively significant for vitamin A (-0.63, P = 0.003), vitamin C (-0.42, P = 0.019) and yellow-green vegetables (-0.37, P = 0.046). For rectal cancer, the standardized partial correlation coefficient in fat (0.60, P = 0.002) was positively significant. Dietary fiber was not found to have a significant relationship with either colon or rectal cancers. CONCLUSIONS: This study failed to show any protective effect of dietary fiber in subjects with a low fat intake (Japanese) in this analysis, which supports Fuchs' findings in subjects with a high fat intake (US Americans).

Real-time observation of a single DNA digestion by lambda exonuclease under a fluorescence microscope field.

A fluorescence microscopy technique has been developed to visualize the behavior of individual DNA and protein molecules. Real-time direct observation of a single DNA molecule can be used to investigate the dynamics of DNA-protein interactions, such as the DNA digestion reaction by lambda exonuclease. In conventional methods it is impossible to analyze the dynamics of an individual lambda exonuclease molecule on a DNA because they can only observe the average behavior of a number of exonuclease molecules. Observation of a single molecule, on the other hand, can reveal processivity and binding rate of an individual exonuclease molecule. To evaluate the dynamics of lambda exonuclease, a stained lambda DNA molecule with one biotinylated terminal was fixed on an avidin-coated coverslip and straightened using a d.c. electric field. Microscopic observation of digestion of a straightened DNA molecule by lambda exonuclease revealed that the DNA digestion rate was approximately 1000 bases/s and also demonstrated high processivity.

Indirect micromanipulation of single molecules in water-in-oil emulsion.

Based on real-time observation and micromanipulation, analytical methods for single DNA molecules have been under development for some time. Precise manipulation, however, is still difficult because single molecules are too small for conventional techniques. We have developed a chemical reaction system that uses water droplets in oil as containers of materials. The water droplets can be manipulated by optical force. The manipulation of the water droplets permits the fusion of two selected droplets. This process corresponds to mixing of different samples. We designate this system as "w/o (water-in-oil emulsion) microreactor system", and each droplet can be thought of as a "microreactor". In this system, single molecules can be manipulated readily, as a molecule can be contained in a microm-sized microreactor. The microreactor utilizes extremely small quantities of samples, therefore, reactions are rapid, as diffusion times in the microreactor are very short. The manipulation technique of the microreactors based on optical force has been applied to induce fusion between microreactors loaded with DNA and YOYO, a fluorescent dye that binds to DNA. This fusion induced a rapid binding of YOYO.

Atomic force microscopy of RecA--DNA complexes using a carbon nanotube tip.

We report high resolution images of RecA-double stranded (ds) DNA complexes obtained by atomic force microscopy (AFM). When a carbon nanotube (CNT) tip was used, AFM images visualized the 10-nm pitch of RecA-dsDNA complexes and RecA filaments as three-dimensional surface topography without reconstruction analysis. The depth of the notch between two pitches was less than 1 nm. When adsorbed on a soft surface covered with proteins, naked DNA, RecA monomers, RecA hexamers, and short RecA filaments were all clearly resolved in one image. The high resolution images with a CNT tip provided valuable information on the initiation process of RecA-dsDNA complex formation.

Alterations in Ca2+-binding on plasma membrane after adaptation to salt stress of tobacco cells in suspension.

Electrophoresis was used to study effects of salinity on the characteristics of Ca2+ binding to the outer surface of plasma membrane (PM) of protoplasts isolated from two types of tobacco (Nicotiana tabacum L., cv. Bright Yellow) cultured cells that were adapted (tolerant) and unadapted (sensitive) to 50 mM NaCl stress. Electrophoretic analysis of salt-sensitive NaCl-unadapted cells shows that Na+ induced an appreciably higher degree of reduction in the amount of Ca2+ bound to PM compared with K+ with increasing concentration from 0.1 to 30 mM. In salt-tolerant NaCl-adapted cells, however, both Na+ and K+ ions induced almost the same degree of reduction in the amount of Ca2+ bound to PM in the physiological concentration range of Ca2+ in the medium between 2 and 4 mM. These results suggest that, under the physiological conditions, PM of salt-sensitive NaCl-unadapted cells has an appreciable amount of PM-bound Ca2+ that is desorbed much easier by Na+ than K+, whereas PM of salt-tolerant NaCl-adapted cells has the PM-bound Ca2+ that can be equally desorbed by Na+ and K+.

Nasal mupirocin treatment of pharynx-colonized methicillin resistant Staphylococcus aureus: preliminary study with 10 carrier infants.

BACKGROUND: Nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infection in infants has become a serious concern and a new means of preventing the transmission of MRSA in the community needs to be considered. METHODS: We performed nasal mupirocin treatment on 10 infants who were MRSA-positive either in the nose or the pharynx and evaluated the effect of mupirocin on the eradication of MRSA. RESULTS: Eradication of MRSA from the nose was successful in two cases and eradication from the pharynx in six (66.6%) of nine cases. The number of treatments required to achieve eradication varied; within three courses for nose carriers and from one to seven courses for pharynx carriers. Eradication was unsuccessful even after five to seven treatments in three pharynx-limited carriers. CONCLUSIONS: These data suggest that the effect of nasal mupirocin treatment on pharynx-colonized MRSA is limited and that repetitive treatment is necessary in some cases. However, in view of the possibility of preferential pharyngeal colonization of Staphylococcus aureus in infancy, nasal mupirocin treatment deserves further evaluation for eradication not only of nose- but also of pharynx-colonized MRSA.

Manipulation of globular DNA molecules for sizing and separation.

Handling large DNA molecules, such as chromosomal DNA, has become necessary due to recent developments in genome science. However, large DNA molecules are fragile and easily broken by shear stress accompanying flow in solution. This fragility causes difficulties in the preparation and handling of large DNA molecules. This study demonstrates the transition of DNA from a coiled to a globular form, which is highly condensed. This state suppresses DNA fragmentation due to shear stress in solution. The transition enables large DNA molecules to undergo mechanical manipulation. We confirmed that the fluorescence intensity of stained globular DNA increases with increasing length, suggesting that the resistance of globular DNA to shear stress is the factor that allows analysis of large DNA by flow cytometry.

RecA-double stranded DNA complexes studied by atomic force microscopy.

RecA-double stranded (ds) DNA complexes have been studied by atomic force microscopy (AFM). When the complexes were prepared in the presence of ATP gamma S, fully covered RecA-dsDNA filaments were observed by AFM. When the concentration of RecA proteins was lower, various lengths of filaments were found. The variation of the observed structures may directly reflect the real distribution of the intermediate complexes in the reaction mixture, as the mixture was simply deposited on a mica surface for AFM observation without special fixation or staining. The use of a carbon nanotube (CNT) AFM tip enabled high resolution to reveal the periodicity of RecA-dsDNA filaments. Our observations demonstrated the potential of the AFM method for the structural studies of the RecA-dsDNA complexes, especially their intermediate states.

Direct laser trapping of single globular DNA molecules.

We show herein that a single T4 phage DNA molecule which was transformed from coiled to globular state, was trapped directly by Nd:YAG laser (1064 nm). We also estimated trapping force of globular DNA molecules.

Direct laser trapping of single DNA molecules in the globular state.

A sharply focused laser is able to trap small particles at the laser focal point due to the difference in refractive index of the particles and that of the surrounding medium. This technique, called laser trapping, can be used to manipulate animal or bacterial cells without any contact and has been widely applied in biological research. However, it has been difficult to trap biological macromolecules such as DNA molecules, because these molecules give a low difference in refractive index and cannot overcome Brownian motion. DNA molecules can be transformed to a condensed globular state. This transformation results in a higher refractive index of DNA due to its increased density. We demonstrate in this paper that a single DNA molecule can be optically trapped using a Nd:YAG laser (1064 nm wavelength) upon transformation from the coiled state to the globular state.

Characterization of factors that suppress linear DNA replication in SV40 in vitro replication system.

The in vitro simian virus 40 (SV40) replication system has been developed as a model system of cellular DNA replication, because the replication initiated from the replication origin of SV40 and replication fork proceeds bidirectionally. In this system, SV40 T-antigen (TAg) is the only factor provided by viral genes, while all other factors are supplied by the host cells. A suppression of replication has been observed in the linear template containing SV40 replication origin, compared with the closed circular template in the SV40 in vitro replication system using a crude extract of HeLa cells. However in the in vitro replication system reconstituted from partially purified factors, less preference was observed for the replication of the closed circular DNA over the linear DNA. In a mono-polymerase system supplemented by crude extracts, a suppression of replication in a linear template was also observed, when compared with a closed circular template. This suppression effect of crude extract was abolished by heat treatment, suggesting that the suppression was induced by some protein factors. A crude extract of HeLa cells was fractionated by stepwise elution with buffers containing 0.2 M, 0.4 M, 0.6 M and 1 M NaCl on a phosphocellulose column, and characterization of factors that suppress linear DNA replication has been done. Both fractions that were eluted at 0.4 M and 0.6 M from phosphocellulose were necessary to suppress linear DNA replication efficiently. The factors in the 0.6 M fraction that suppressed linear DNA replication synergistically with the 0.4 M fraction were partially purified by successive chromatography with heparin-sepharose and dsDNA-cellulose followed by glycerol gradient centrifugation. These results suggested that multiple factors are required to suppress DNA replication of the linear template.

Statistical mechanical approach for predicting the transition to non-B DNA structures in supercoiled DNA.

Supercoiling causes global twist of DNA structure and the supercoiled state has wide influence on conformational transition. A statistical mechanical approach was made for prediction of the transition probability to non-B DNA structures under torsional stress. A conditional partition function was defined as the sum over all possible states of the DNA sequence with basepair 1 and basepair n being in B-form helix and a recurrence formula was developed which expressed the partition function for basepair n with those for less number of pairs. This new definition permits a quick enumeration of every configuration of secondary structures. Energetic parameters of all conformations concerned, involving B-form, interior loop, cruciform and Z-form, were included in the equation. The probability of transition to each non-B conformation could be derived from these conditional partition functions. For treatment of effects of superhelicity, supercoiling energy was considered, and a twist of each conformation was determined to minimize the supercoiling energy. As the twist itself affects the transition probability, the whole scheme of equations was solved by renormalization technique. The present method permits a simultaneous treatment of several types of conformations under a common torsional stress. A set of energetic parameters of DNA secondary structures has been chosen for calculation. Some DNA sequences were submitted to the calculation, and all the sequences that we submitted gave stable convergence. Some of them have been investigated the critical supercoil density for the transition to non-B DNA structures. Even though the reliability of the set of parameters was not enough, the prediction of secondary structure transition showed good agreement with reported observation. Hence, the present algorithm can estimate the probability of local conformational change of DNA under a given supercoil density, and also be employed to predict some specific sequences in which conformational change is sensitive to superhelicity.

[In vivo observation of crystalline lens changes in the early post-vitrectomy stage].

Crystalline lens changes of 17 cases of eye undergoing simple vitrectomy were observed from the post-operative 1st to 21st month. Changes in the crystalline lenses were detected through a slitlamp microscope or by methods of image analysis, the Opacity Lensmeter and the laser scattering spectroscopy. Increases of the scattering light intensity of the anterior and posterior deep cortical layers were observed from the early post-operative stage in 9 cases. Seven cases progressed to nuclear opacification during the observation period, however, one case showed no nuclear changes even at the 12 post-operative month. No relationships were observed between the early cortical changes and surgical invasion, patient age, or cause of vitreous opacification. Quantitative evaluation by image analysis revealed early post-operative crystalline lens changes in cases undergoing vitreous surgery.

Five new alleles of plasma Zn-alpha 2-glycoprotein variants phenotyped by isoelectric focusing and immunoblotting in twelve populations.

Human Zn-alpha 2-glycoprotein (ZAG) in plasma samples from twelve populations was tested by immunoblotting after polyacrylamide gel isoelectric focusing. Eleven ZAG phenotypes produced by one common and nine rare alleles, including five new ones (ZAG*6-ZAG*10), were detected. Additionally, an application of separator IEF with N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) was found to be useful for discriminating the rare ZAG 7 band.