bluuebunny/crossref_metadata_2025 huggingface dataset:
High gain amplifiers: Power oscillations and harmonic generation
Authors: Dattoli G. , Ottaviani P. L. , Pagnutti S.
Published: August 2007

We discuss the power oscillations in saturated high gain free electron laser amplifiers and show that the relevant period can be written in terms of the gain length. We use simple arguments following from the solution of the pendulum equation in terms of Jacobi elliptic functions. Nontrivial effects due to nonlinear harmonic generation and inhomogeneous broadening are discussed too, as well as the saturated dynamics of short pulses.
Magnetocaloric effect of electron-doped manganite La0.9Te0.1MnO3
Authors: Yang J. , Lee Y. P. , Li Y.
Published: August 2007

The magnetocaloric effect of an electron-doped manganite La0.9Te0.1MnO3 has been investigated. The sample of La0.9Te0.1MnO3 undergoes the paramagnetic-ferromagnetic transition at 239K. It is obtained that the effective magnetic moment (μeff=4.923μB) and the saturation moment (μS=4.08μB∕Mn) are close to the respective expected values. The isothermal magnetization versus applied magnetic field at various temperatures between 180 and 300K was measured, and the temperature dependence of magnetic entropy change ∣ΔSM∣ for La0.9Te0.1MnO3 was understood. It is found that the sample shows a large magnetic entropy change near TC and the magnitude of magnetic entropy change is comparable to some hole-doped manganites. However, the relative cooling power of the electron-doped manganite La0.9Te0.1MnO3 is higher than that of some hole-doped manganites, which is an advantage for the engineer to design the magnetic refrigeration materials. Moreover, the temperature dependence of magnetic entropy change ∣ΔSM∣ cannot be explained well based on the Landau theory of phase transition, and the contribution of the Jahn-Teller effect needs to be taken into account for La0.9Te0.1MnO3.
Giant elasticity of photopolymer nanowires
Authors: Nakanishi Sana , Shoji Satoru , Kawata Satoshi , Sun Hong-Bo
Published: August 2007

Giant elasticity, reflected by a shear modulus three order smaller than seen in the bulk of the same materials, is found in polymer nanowires, which are prepared by two-photon polymerization into a shape of spring: geometry capable to magnify mechanical deformations. An approach intervening the competitive processes of dissolving and polymerization in the course of rinsing of written structures was proposed for continuously tuning the shear modulus and fixing them at desired level. These results not only reveal a characteristic of polymers when the material size enters into the regime of hundreds of nanometers but also indicate prospect polymer microelectromechanical system for biocompatible applications.
Spin-torque ferromagnetic resonance measurements of damping in nanomagnets
Authors: Fuchs G. D. , Sankey J. C. , Pribiag V. S. , Qian L. , Braganca P. M. , Garcia A. G. F. , Ryan E. M. , Li Zhi-Pan , Ozatay O. , Ralph D. C. , Buhrman R. A.
Published: August 2007

The authors directly measure the magnetic damping parameter α in thin-film CoFeB and Permalloy (Py) nanomagnets at room temperature using a recently developed ferromagnetic resonance technique where the precessional mode of an individual nanomagnet can be excited by microwave-frequency spin-transfer torque and detected by the giant magnetoresistance effect. The authors obtain αCoFeB=0.014±0.003 and αPy=0.010±0.002, values comparable to measurements for extended thin films, establishing that patterned nanomagnets can exhibit magnetic damping that is consistent with that of unpatterned bulk material.
Implantation-induced nonequilibrium reaction between Zn ions of 60keV and SiO2 target
Authors: Amekura H. , Yoshitake M. , Plaksin O. A. , Kishimoto N. , Buchal Ch. , Mantl S.
Published: August 2007

Silica glass (SiO2) was implanted with 60keV Zn+ ions to a fluence of 1.0×1017ions∕cm2, and the chemical states were investigated along the depth in as-implanted state by x-ray excited Auger electron spectroscopy and x-ray photoelectron spectroscopy. The metallic Zn and Zn2SiO4 phases were found to have, respectively, formed in the shallow and deep regions of the SiO2, whereas thermodynamics predicts the Zn phase only. Oxygen atoms in SiO2 are preferentially displaced to the deeper region because of the lighter mass. The excess oxygen in the deep region and athermal energy from the implantation drive the formation of Zn2SiO4.
Controllable nanocrystallization in amorphous Nd9Fe85B6 via combined application of severe plastic deformation and thermal annealing
Authors: Li Wei , Li Lanlan , Nan Yun , Li Xiaohong , Zhang Xiangyi , Gunderov D. V. , Stolyarov V. V. , Popov A. G.
Published: August 2007

The control of nanocrystal formation in amorphous alloys is of particular importance for the development of advanced nanocrystalline materials. In the present study, the authors succeeded in controlling α-Fe and Nd2Fe14B nanocrystallization processes in amorphous Nd9Fe85B6 by a combination of severe plastic deformation at room temperature and subsequent thermal annealing. The α-Fe∕Nd2Fe14B nanocomposite magnets prepared by this approach possess homogeneously distributed nanocrystals with a small size, 15nm for α-Fe phase and 26nm for Nd2Fe14B, and therefore show enhanced magnetic properties as compared to those prepared by directly annealing amorphous Nd9Fe85B6.
Reduction of microtwin defects for high-electron-mobility InSb quantum wells
Authors: Mishima T. D. , Edirisooriya M. , Santos M. B.
Published: August 2007

The effect of structural defects on electron mobilities has been investigated in InSb quantum wells (QWs) grown on GaAs (001) substrates. The usefulness of a ⟨116⟩-directional transmission electron microscopy analysis for microtwins (MTs) in a plan-view specimen is demonstrated. MTs and threading dislocations reduce the room-temperature (RT) electron mobility in InSb QWs. It is found that the use of 2° off-axis GaAs (001) substrates is effective in reducing MT densities in InSb QWs. The electron mobility in InSb QW at RT, 4.0×104cm2∕Vs with an electron density of 4.6×1011∕cm2, is among the highest values reported in semiconductor QWs.
Influence of the compressive stress on the infrared absorption of sp2-bonded boron nitride in cubic boron nitride thin films
Authors: Yang Hangsheng , Zhang Yan , Zhang Xiaobin , Xu Yabo
Published: August 2007

Cubic BN films with a pure cubic phase upper layer were prepared by plasma-enhanced chemical vapor deposition. Infrared spectroscopy was applied to analyze the content of initial sp2-bonded BN layer in cubic BN thin films under compressive stress. It was found that the peak intensity near 1380cm−1 attributed to the B–N stretching vibration of sp2-bonded BN was suppressed by the compressive stress in cubic BN films. The deviation between the measured and calculated peak intensities was found to be linear with the compressive stress when the upper layer of the film is a pure cubic phase layer.
Current-induced magnetization switching in asymmetric necked wires
Authors: Lepadatu S. , Wu J. , Xu Y. B.
Published: August 2007

The authors have studied the current-induced domain wall movement mechanism in Ni80Fe20 wires patterned with a nanoconstriction and asymmetric arm widths using transport and focused magneto-optic Kerr effect (MOKE) measurements. Using dc current, the trapped domain wall is removed from the constriction at a current density greater than 1011A∕m2 and the direction of domain wall displacement is detected using focused MOKE measurements. At zero field, the current-induced domain wall displacement is in the direction of the current carriers while at the nucleation field of the domain wall the displacement direction is set by the direction of the applied field, independent of the current direction.
Displacement currents in semiconductor quantum dots embedded dielectric media: A method for room temperature photon detection
Authors: Jayaweera P. V. V. , Perera A. G. U. , Tennakone K.
Published: August 2007

It is shown that the high electronic polarizability of quantum dots can be utilized to devise photon detectors by embedding quantum dots in dielectric media to form capacitors. Modulated light generates displacement currents and an expression is obtained for responsivity in terms of the properties of the quantum dot, the dielectric, and the detector geometry. A model detector constituted of PbS quantum dots embedded in paraffin wax is devised to illustrate the principle, giving ∼0.6A∕W as an upper limit for the responsivity. As these systems sense only the variations of the light intensity, they could be operated at ambient temperature.
Strain-induced formation of carbon and boron clusters in boron carbide during dynamic indentation
Authors: Ghosh Dipankar , Subhash Ghatu , Lee Chee Huei , Yap Yoke Khin
Published: August 2007

The authors found that the level of amorphization or structural disorder in boron carbide is higher when induced by dynamic indentation compared to static indentation. Visible and uv Raman spectroscopies indicate that sp2-bonded aromatic carbon clusters were formed, consistent with the detected photoluminescence spectra. Infrared absorption shows that amorphous boron clusters were created by dynamic indentation which has strain rates ∼108 order higher than that introduced by static indentation. The decreased intensity of infrared stretching mode of carbon-boron-carbon (CBC) chains also suggests that amorphization is due to the collapse of B11C(CBC) unit cells, which reorganize into the energetically favorite carbon and boron clusters.
Immune complex-induced enhancement of bacterial antigen presentation requires Fcγ Receptor III expression on dendritic cells
Authors: Herrada Andrés A. , Contreras Francisco J. , Tobar Jaime A. , Pacheco Rodrigo , Kalergis Alexis M.
Published: August 2007

Dendritic cells (DCs) are capable of initiating adaptive immune responses against infectious agents by presenting pathogen-derived antigens on MHC molecules to naïve T cells. Because of their key role in priming adaptive immunity, it is expected that interfering with DC function would be advantageous to the pathogen. We have previously shown that
Salmonella enterica
serovar Typhimurium (ST), is able to survive inside DCs and interfere with their function by avoiding activation of bacteria-specific T cells. In contrast, when ST is targeted to Fcγ receptors on the DC surface, bacteria are degraded and their antigens presented to T cells. However, the specific Fcγ receptor responsible of restoring presentation of antigens remains unknown. Here, we show that IgG-coated ST was targeted to lysosomes and degraded and its antigens presented on MHC molecules only when the low-affinity activating FcγRIII was expressed on DCs. FcγRIII-mediated enhancement of Ag presentation led to a robust activation of T cells specific for bacteria-expressed antigens. Laser confocal and electron microscopy analyses revealed that IgG-coated ST was rerouted to the lysosomal pathway through an FcγRIII-dependent mechanism. PI-3K activity was required for this process, because specific inhibitors promoted the survival of IgG-coated ST inside DCs and prevented DCs from activating bacteria-specific T cells. Our data suggest that the DC capacity to efficiently activate T cells upon capturing IgG-coated virulent bacteria is mediated by FcγRIII and requires PI-3K activity.
Local initiation of caspase activation in
Drosophila
salivary gland programmed cell death
in vivo
Authors: Takemoto Kiwamu , Kuranaga Erina , Tonoki Ayako , Nagai Takeharu , Miyawaki Atsushi , Miura Masayuki
Published: August 2007

Programmed cell death, or apoptosis, is an essential event in animal development. Spatiotemporal analysis of caspase activation
in vivo
could provide new insights into programmed cell death occurring during development. Here, using the FRET-based caspase-3 indicator, SCAT3, we report the results of live-imaging analysis of caspase activation in developing
Drosophila in vivo
. In
Drosophila
, the salivary gland is sculpted by caspase-mediated programmed cell death initiated by the steroid hormone 20-hydroxyecdysone (ecdysone). Using a SCAT3 probe, we observed that caspase activation in the salivary glands begins in the anterior cells and is then propagated to the posterior cells
in vivo. In vitro
salivary gland culture experiments indicated that local exposure of ecdysone to the anterior salivary gland reproduces the caspase activation gradient as observed
in vivo
. In β
FTZ-F1
mutants, caspase activation was delayed and occurred in a random pattern
in vivo
. In contrast to the
in vivo
response, the salivary glands from β
FTZ-F1
mutants showed a normal
in vitro
response to ecdysone, suggesting that β
FTZ-F1
may be involved in ecdysteroid biosynthesis and secretion of ecdysone from the ring gland for local initiation of programmed cell death. These results imply a role of β
FTZ-F1
in coordinating the initiation of salivary gland apoptosis in development.
Three two-component transporters with channel-like properties have monovalent cation/proton antiport activity
Authors: Fujisawa Makoto , Ito Masahiro , Krulwich Terry A.
Published: August 2007

Properties of four two-component bacterial transport systems of the cation/proton antiporter-2 (CPA2) family led to suggestions that this CPA2 subset may use a channel rather than an antiport mechanism [see Booth IR, Edwards MD, Gunasekera B, Li C, Miller S (2005) in
Bacterial Ion Channels
, eds Kubalski A, Martinac B (Am Soc Microbiol, Washington, DC), pp 21–40]. The transporter subset includes the intensively studied glutathione-gated K
+
efflux systems from
Escherichia coli
, KefGB, and KefFC. KefG and KefF are ancillary proteins. They are peripheral membrane proteins that are encoded in operons with the respective transporter proteins, KefB and KefC, and are required for optimal efflux activity. The other two-component CPA2 transporters of the subset are AmhMT, an NH
4
+
(K
+
) efflux system from alkaliphilic
Bacillus pseudofirmus
OF4; and YhaTU, a K
+
efflux system from
Bacillus subtilis
. Here a K
+
/H
+
antiport capacity was demonstrated for YhaTU, AmhMT, and KefFC in membrane vesicles from antiporter-deficient
E. coli
KNabc. The apparent
K
m
for K
+
was in the low mM range. The peripheral protein was required for YhaU- and KefC-dependent antiport, whereas both AmhT and AmhMT exhibited antiport. KefFC had the broadest range of substrates, using Rb
+
≈K
+
>Li
+
>Na
+
. Glutathione significantly inhibited KefFC-mediated K
+
/H
+
antiport in vesicles. The inhibition was enhanced by NADH, which presumably binds to the KTN/RCK domain of KefC. The antiport mechanism accounts for the H
+
uptake involved in KefFC-mediated electrophile resistance
in vivo
. Because the physiological substrate of AmhMT in the alkaliphile is NH
4
+
, the results also imply that AmhMT catalyzes NH
4
+
/H
+
antiport, which would prevent net cytoplasmic H
+
loss during NH
4
+
efflux.
tRNA-modifying MiaE protein fromSalmonella typhimuriumis a nonheme diiron monooxygenase
Authors: Mathevon Carole , Pierrel Fabien , Oddou Jean-Louis , Garcia-Serres Ricardo , Blondin Geneviève , Latour Jean-Marc , Ménage Stéphane , Gambarelli Serge , Fontecave Marc , Atta Mohamed
Published: August 2007

MiaE catalyzes the posttranscriptional allylic hydroxylation of 2-methylthio-N-6-isopentenyl adenosine in tRNAs. TheSalmonella typhimuriumenzyme was heterologously expressed inEscherichia coli. The purified enzyme is a monomer with two iron atoms and displays activity inin vitroassays. The type and properties of the iron center were investigated by using a combination of UV-visible absorption, EPR, HYSCORE, and Mössbauer spectroscopies which demonstrated that the MiaE enzyme contains a nonheme dinuclear iron cluster, similar to that found in the hydroxylase component of methane monooxygenase. This is the first example of an enzyme from this important class of diiron monooxygenases to be involved in the hydroxylation of a biological macromolecule and the second example of a redox metalloenzyme participating in tRNA modification.
A Role for Eyebrows in Regulating the Visibility of Eye Gaze Direction
Authors: Watt Roger , Craven Ben , Quinn Sandra
Published: August 2007

The human eye is unique amongst those of primates in having white sclera against which the dark iris is clearly visible. This high-contrast structure makes the gaze direction of a human potentially easily perceptible to others. For a social creature such as a human, the ability to perceive the direction of another's gaze may be very useful, since gaze usually signals attention. We report data showing that the accuracy of gaze deviation detection is independent of viewing distance up to a certain critical distance, beyond which it collapses. This is, of itself, surprising since most visual tasks are performed better at closer viewing distances. Our data also show that the critical distance, but not accuracy, is affected by the position of the eyebrows so that lowering the eyebrows reduces the critical distance. These findings show that mechanisms exist by which humans could expand or restrict the availability of their gaze direction to others. A way to regulate the availability of the gaze direction signal could be an advantage. We show that an interpretation of eyebrow function in these terms provides a novel explanation for several well-known eyebrow actions, including the eyebrow flash.
Classification Accuracy across Multiple Tests following Item Method Directed Forgetting
Authors: Goernert Phillip N. , Widner Robert L. , Otani Hajime
Published: August 2007

We investigated recall of line-drawing pictures paired at study with an instruction either to remember (TBR items) or to forget (TBF items). Across three 7-minute tests, net recall (items reported independent of accuracy in instructional designation) and correctly classified recall (recall conditional on correct instructional designation) showed directed forgetting. That is, for both measures, recall of TBR items always exceeded recall of TBF items. Net recall for both item types increased across tests at comparable levels showing hypermnesia. However, across tests, correct classification of both item types decreased at comparable levels. Collectively, hypermnesia as measured by net recall is possible for items from multiple sets, but at the cost of accurate source information.
p32 is a novel mammalian Lgl binding protein that enhances the activity of protein kinase Cζ and regulates cell polarity
Authors: Bialucha Carl U. , Ferber Emma C. , Pichaud Franck , Peak-Chew Sew Y. , Fujita Yasuyuki
Published: August 2007

Lgl (lethal giant larvae) plays an important role in cell polarity. Atypical protein kinase C (aPKC) binds to and phosphorylates Lgl, and the phosphorylation negatively regulates Lgl activity. In this study, we identify p32 as a novel Lgl binding protein that directly binds to a domain on mammalian Lgl2 (mLgl2), which contains the aPKC phosphorylation site. p32 also binds to PKCζ, and the three proteins form a transient ternary complex. When p32 is bound, PKCζ is stimulated to phosphorylate mLgl2 more efficiently. p32 overexpression in Madin–Darby canine kidney cells cultured in a 3D matrix induces an expansion of the actin-enriched apical membrane domain and disrupts cell polarity. Addition of PKCζ inhibitor blocks apical actin accumulation, which is rescued by p32 overexpression. p32 knockdown by short hairpin RNA also induces cell polarity defects. Collectively, our data indicate that p32 is a novel regulator of cell polarity that forms a complex with mLgl2 and aPKC and enhances aPKC activity.
Activation of NMDA receptors promotes dendritic spine development through MMP-mediated ICAM-5 cleavage
Authors: Tian Li , Stefanidakis Michael , Ning Lin , Van Lint Philippe , Nyman-Huttunen Henrietta , Libert Claude , Itohara Shigeyoshi , Mishina Masayoshi , Rauvala Heikki , Gahmberg Carl G.
Published: August 2007

Matrix metalloproteinase (MMP)-2 and -9 are pivotal in remodeling many tissues. However, their functions and candidate substrates for brain development are poorly characterized. Intercellular adhesion molecule-5 (ICAM-5; Telencephalin) is a neuronal adhesion molecule that regulates dendritic elongation and spine maturation. We find that ICAM-5 is cleaved from hippocampal neurons when the cells are treated with N-methyl-d-aspartic acid (NMDA) or α-amino-3-hydroxy-5-methylisoxazole-propionic acid (AMPA). The cleavage is blocked by MMP-2 and -9 inhibitors and small interfering RNAs. Newborn MMP-2– and MMP-9–deficient mice brains contain more full-length ICAM-5 than wild-type mice. NMDA receptor activation disrupts the actin cytoskeletal association of ICAM-5, which promotes its cleavage. ICAM-5 is mainly located in dendritic filopodia and immature thin spines. MMP inhibitors block the NMDA-induced cleavage of ICAM-5 more efficiently in dendritic shafts than in thin spines. ICAM-5 deficiency causes retraction of thin spine heads in response to NMDA stimulation. Soluble ICAM-5 promotes elongation of dendritic filopodia from wild-type neurons, but not from ICAM-5–deficient neurons. Thus, MMPs are important for ICAM-5–mediated dendritic spine development.
Conformational changes in the GTPase modules of the signal reception particle and its receptor drive initiation of protein translocation
Authors: Shan Shu-ou , Chandrasekar Sowmya , Walter Peter
Published: August 2007

During cotranslational protein targeting, two guanosine triphosphatase (GTPase) in the signal recognition particle (SRP) and its receptor (SR) form a unique complex in which hydrolyses of both guanosine triphosphates (GTP) are activated in a shared active site. It was thought that GTP hydrolysis drives the recycling of SRP and SR, but is not crucial for protein targeting. Here, we examined the translocation efficiency of mutant GTPases that block the interaction between SRP and SR at specific stages. Surprisingly, mutants that allow SRP–SR complex assembly but block GTPase activation severely compromise protein translocation. These mutations map to the highly conserved insertion box domain loops that rearrange upon complex formation to form multiple catalytic interactions with the two GTPs. Thus, although GTP hydrolysis is not required, the molecular rearrangements that lead to GTPase activation are essential for protein targeting. Most importantly, our results show that an elaborate rearrangement within the SRP–SR GTPase complex is required to drive the unloading and initiate translocation of cargo proteins.
CD98hc (SLC3A2) participates in fibronectin matrix assembly by mediating integrin signaling
Authors: Féral Chloé C. , Zijlstra Andries , Tkachenko Eugene , Prager Gerald , Gardel Margaret L. , Slepak Marina , Ginsberg Mark H.
Published: August 2007

Integrin-dependent assembly of the fibronectin (Fn) matrix plays a central role in vertebrate development. We identify CD98hc, a membrane protein, as an important component of the matrix assembly machinery both in vitro and in vivo. CD98hc was not required for biosynthesis of cellular Fn or the maintenance of the repertoire or affinity of cellular Fn binding integrins, which are important contributors to Fn assembly. Instead, CD98hc was involved in the cell's ability to exert force on the matrix and did so by dint of its capacity to interact with integrins to support downstream signals that lead to activation of RhoA small GTPase. Thus, we identify CD98hc as a membrane protein that enables matrix assembly and establish that it functions by interacting with integrins to support RhoA-driven contractility. CD98hc expression can vary widely; our data show that these variations in CD98hc expression can control the capacity of cells to assemble an Fn matrix, a process important in development, wound healing, and tumorigenesis.
Principal stratification with predictors of compliance for randomized trials with 2 active treatments
Authors: Roy Jason , Hogan Joseph W. , Marcus Bess H.
Published: August 2007

In behavioral medicine trials, such as smoking cessation trials, 2 or more active treatments are often compared. Noncompliance by some subjects with their assigned treatment poses a challenge to the data analyst. The principal stratification framework permits inference about causal effects among subpopulations characterized by potential compliance. However, in the absence of prior information, there are 2 significant limitations: (1) the causal effects cannot be point identified for some strata and (2) individuals in the subpopulations (strata) cannot be identified. We propose to use additional information—compliance-predictive covariates—to help identify the causal effects and to help describe characteristics of the subpopulations. The probability of membership in each principal stratum is modeled as a function of these covariates. The model is constructed using marginal compliance models (which are identified) and a sensitivity parameter that captures the association between the 2 marginal distributions. We illustrate our methods in both a simulation study and an analysis of data from a smoking cessation trial.
Lentzea kentuckyensis sp. nov., of equine origin
Authors: Labeda D. P. , Donahue J. M. , Sells S. F. , Kroppenstedt R. M.
Published: August 2007

A novel actinomycete, designated strain LDDC 2876-05T, was isolated from an equine placenta during the course of routine diagnostic tests for nocardioform placentitis. In a preliminary study, the strain was observed to be phylogenetically distinct from the generaCrossiellaandAmycolatopsisand probably a member of the genusLentzea.A polyphasic study of strain LDDC 2876-05Tconfirmed its identification as a member ofLentzeaon the basis of its chemotaxonomic and morphological similarity to all of the known species of the genus. Moreover, the strain could be distinguished from other species with validly published names on the basis of its phylogenetic and physiological characteristics and its fatty acid profile. Therefore strain LDDC 2876-05Trepresents a novel species of the genusLentzea, for which the nameLentzea kentuckyensissp. nov. is proposed. The type strain is LDDC 2876-05T(=NRRL B-24416T=DSM 44909T).
Planifilum yunnanense sp. nov., a thermophilic thermoactinomycete isolated from a hot spring
Authors: Zhang Yan-xin , Dong Chen , Biao Shen
Published: August 2007

A thermophilic actinomycete, strain LA5T, was isolated from a hot spring in Yunnan province, People's Republic of China. The isolate grew aerobically at temperatures of 50–75 °C. Aerobic mycelia were not observed. Single spores were produced along the substrate hypha. Strain LA5T was characterized chemotaxonomically by having MK-7 as the predominant menaquinone and iso-C17 : 0 (27.7 %) and C16 : 0 (22.4 %) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. The DNA G+C content was 56.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain LA5T belongs to the genus Planifilum. Levels of DNA–DNA relatedness between strain LA5T and Planifilum fimeticola H0165T and Planifilum fulgidum 500275T were 43.6 and 52.7 %, respectively. On the basis of phenotypic properties and phylogeny, strain LA5T represents a novel species of the genus Planifilum, for which we propose the name Planifilum yunnanense sp. nov., with the type strain LA5T (=CCTCC AA206002T=KCTC 13052T).
Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group
Authors: Wang Li-Ting , Lee Fwu-Ling , Tai Chun-Ju , Kasai Hiroaki
Published: August 2007

TheBacillus subtilisgroup comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, thegyrBgene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whethergyrBgene sequence analysis could be used for phylogenetic analysis and species identification of members of theB. subtilisgroup, the congruence ofgyrBgrouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges ofgyrBnucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed thatgyrBgene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved bygyrBsequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that thegyrBgene may be an efficient alternative target for identification and taxonomic analysis of members of theB. subtilisgroup.
Streptomyces vietnamensis sp. nov., a streptomycete with violet–blue diffusible pigment isolated from soil in Vietnam
Authors: Zhu Hong-hui , Guo Jun , Yao Qing , Yang Song-zhen , Deng Ming-rong , Phuong Le Thi Bich , Hanh Vo Thi , Ryan Matthew J.
Published: August 2007

An actinomycete, designated strain GIMV4.0001T, was isolated from a forest soil sample in Vietnam. It produced white aerial mycelium and violet–blue diffusible pigment on Gause's synthetic agar. The substrate mycelium colour was not sensitive to pH. Micoscopic observations revealed that strain GIMV4.0001T produced long, straight chains of cylindrical spores, and chemotaxonomic data confirmed that it belongs to the genus Streptomyces. Melanin was produced, but no antibacterial activity was evident against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Candida albicans or Penicillium citrinum. Analysis of the 16S rRNA gene sequence of strain GIMV4.0001T revealed that the highest similarity (99.4 %) was to Streptomyces bikiniensis ATCC 11062T. However, the DNA–DNA relatedness between strain GIMV4.0001T and S. bikiniensis ATCC 11062T was found to be 50.3 %. Strain GIMV4.0001T could also be differentiated from S. bikiniensis ATCC 11062T and other Streptomyces species showing high 16S rRNA gene sequence similarity (98–99 %) based on morphological, physiological and biochemical characteristics. On the basis of its physiological and molecular properties, it is evident that strain GIMV4.0001T represents a novel species of the genus Streptomyces, for which the name Streptomyces vietnamensis sp. nov. is proposed. The type strain is GIMV4.0001T (=CCTCC M 205143T=IAM 15340T).
Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean
Authors: Shivaji S. , Bhadra Bhaskar , Rao R. Sreenivas , Chaturvedi Preeti , Pindi Pavan Kumar , Raghukumar Chandralata
Published: August 2007

Two bacterial strains, BBH6T and BBH9, were isolated from a deep-sea sediment sample collected from the Chagos Trench, Indian Ocean, at a depth of 5904 m. The two strains were closely related in their 16S rRNA gene sequences (99.7 %), belonged to one genomic species and were virtually identical at the phenotypic level. Microbacterium barkeri DSM 20145T was the nearest phylogenetic neighbour to the new isolates, with 16S rRNA gene sequence similarity levels of 97.2–97.4 %. The new isolates exhibited levels of DNA–DNA relatedness of 32–34 % to M. barkeri and differed from it in a number of phenotypic characteristics. Therefore, it is suggested that strains BBH6T and BBH9 represent a novel species of the genus Microbacterium, for which the name Microbacterium indicum sp. nov. is proposed. The type strain is BBH6T (=LMG 23459T=IAM 15355T).
Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea
Authors: An Dong-Shan , Lee Hyung-Gwan , Im Wan-Taek , Liu Qing-Mei , Lee Sung-Taik
Published: August 2007

A novel strain, designated Gsoil 664T, isolated from the soil of a ginseng field in South Korea, was characterized by a polyphasic approach to clarify its taxonomic position. The isolate was Gram-negative, strictly aerobic, heterotrophic, non-motile, non-spore-forming and possessed rod-shaped cells. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate formed a cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes. However, the isolate was clearly separated from these genera: the gene sequence similarities with respect to the type strains of recognized species from closely related genera ranged from 86.7 to 90.7 %. The G+C content of the genomic DNA was 40.4 mol%. The predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 and C16 : 1
ω5c. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 664T from recognized species of related genera. On the basis of the polyphasic evidence, Gsoil 664T represents a novel genus and species, for which the name Segetibacter koreensis gen. nov., sp. nov. is proposed. The type strain of S. koreensis is Gsoil 664T (=KCTC 12655T=DSM 18137T).
Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea
Authors: Ying Jiao-Yan , Wang Bao-Jun , Dai Xin , Yang Su-Sheng , Liu Shuang-Jiang , Liu Zhi-Pei
Published: August 2007

An aerobic and heterotrophic, Gram-negative bacterial isolate, strain HY34T, was isolated from sediment of an oilfield in the South China Sea, China. The taxonomy of strain HY34T was studied by phenotypic and phylogenetic methods. Strain HY34T formed faint-pink colonies on marine agar 2216. Cells of strain HY34T were non-motile, ovoid or short rods. Strain HY34T was positive for catalase and oxidase, and nitrate was reduced to nitrite. The nearly complete 16S rRNA gene sequence of strain HY34T was obtained and sequence analysis showed that it, together with the genus Rubellimicrobium, formed a distinct clade close to some members of the Roseobacter clade in the family Rhodobacteraceae, and it showed highest sequence similarities to Oceanicola granulosus HTCC2516T (93.8 %), Silicibacter lacuscaerulensis ITI-1157T (93.3 %), Dinoroseobacter shibae DFL 12T (93.3 %) and Rubellimicrobium thermophilum C-lvk-R2A-2T (92.2 %). Bacteriochlorophyll a was not detected. The ubiquinone system was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. The major fatty acids (>10 %) were C18 : 1
ω7c and C16 : 0. The DNA G+C content of this strain was 69.4 mol%. A polyphasic analysis supported the conclusion that this strain represents a novel genus and species, which we designated Wenxinia marina gen. nov., sp. nov. The type strain of Wenxinia marina is HY34T (=CGMCC 1.6105T =JCM 14017T).
Actinomadura alba sp. nov., isolated from soil in Yunnan, China
Authors: Wang Yong-Xia , Zhi Xiao-Yang , Chen Hua-Hong , Zhang Yu-Qin , Tang Shu-Kun , Jiang Cheng-Lin , Xu Li-Hua , Li Wen-Jun
Published: August 2007

A novel actinomycete, strain YIM 45681T, which was isolated from soil in a suburb of Kunming, Yunnan Province, China, was subjected to phenotypic and genotypic characterization. The micro-organism, which produces short spore chains arranged in spirals on the aerial mycelium, was shown to have meso-diaminopimelic acid in the cell wall. The sugars present in whole-cell hydrolysates were ribose, xylose, galactose, madurose and glucose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The phospholipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 1 H, C17 : 1
ω8c, 10-methyl C17 : 0 and C16 : 0. A comparative analysis of 16S rRNA gene sequences indicated that the organism formed a distinct clade within the evolutionary radiation of the family Thermomonosporaceae, and that it was closely associated with members of the genus Actinomadura. A broad range of phenotypic and genetic data supported the suggestion that this organism represents a novel species of the genus Actinomadura, for which the name Actinomadura alba sp. nov. is proposed, with YIM 45681T (=DSM 45045T =CCTCC AA206005T) as the type strain.
Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups
Authors: Wei Wei , Davis Robert E. , Lee Ing-Ming , Zhao Yan
Published: August 2007

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.
Aspergillus brasiliensis sp. nov., a biseriate black Aspergillus species with world-wide distribution
Authors: Varga János , Kocsubé Sándor , Tóth Beáta , Frisvad Jens C. , Perrone Giancarlo , Susca Antonia , Meijer Martin , Samson Robert A.
Published: August 2007

A novel species,Aspergillus brasiliensissp. nov., is described withinAspergillussectionNigri. This species can be distinguished from other black aspergilli based on intergenic transcribed region,β-tubulin and calmodulin gene sequences, by amplified fragment length polymorphism analysis and by extrolite profiles.A. brasiliensisisolates produced naphtho-γ-pyrones, tensidol A and B and pyrophen in common withAspergillus nigerandAspergillus tubingensis, but also several unique compounds, justifying their treatment as representing a separate species. None of the isolates were found to produce ochratoxin A, kotanins, funalenone or pyranonigrins. The novel species was most closely related toA. niger, and was isolated from soil from Brazil, Australia, USA and The Netherlands, and from grape berries from Portugal. The type strain ofAspergillus brasiliensissp. nov. is CBS 101740T(=IMI 381727T=IBT 21946T).
Aurantimonas ureilytica sp. nov., isolated from an air sample
Authors: Weon Hang-Yeon , Kim Byung-Yong , Yoo Seung-Hee , Joa Jae-Ho , Lee Ki Hwan , Zhang Yong-Seon , Kwon Soon-Wo , Koo Bon-Sung
Published: August 2007

A novel strain, designated 5715S-12T, was isolated from an air sample collected from Suwon region, Republic of Korea, using R2A medium. The cells were strictly aerobic, Gram-negative, motile, short rods. Comparison of the 16S rRNA gene sequence of strain 5715S-12T showed the highest sequence similarities to Aurantimonas altamirensis S21BT (95.9 %) and Aurantimonas coralicida WP1T (95.4 %). Phylogenetic trees indicated that the strain formed a cluster with members of the family Aurantimonadaceae (A.
altamirensis, A. coralicida and Fulvimarina pelagi). The major fatty acid was C18 : 1
ω7c. The predominant isoprenoid quinone was ubiquinone 10 (Q-10). Diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine and four unknown lipids were found as the polar lipid components. The DNA G+C content was 67.0 mol%. On the basis of the phenotypic and phylogenetic features studied, we propose that strain 5715S-12T be assigned to a novel species of the genus Aurantimonas, for which the name Aurantimonas ureilytica sp. nov. (type strain 5715S-12T =KACC 11607T =DSM 18598T) is proposed.
Chryseobacterium flavum sp. nov., isolated from polluted soil
Authors: Zhou Yu , Dong Jing , Wang Xu , Huang Xing , Zhang Ke-Yun , Zhang Yu-Qin , Guo Yu-Feng , Lai Ren , Li Wen-Jun
Published: August 2007

A Gram-negative, non-motile, rod-shaped bacterial strain, designated CW-E 2T, was isolated from a polluted soil sample collected from Jiangsu Province, China. A taxonomic study of the isolate, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was carried out. The predominant menaquinone was MK-6 and the major fatty acids were i-C15 : 0, i-C17 : 0 3-OH, i-C17 : 1
ω9c and summed feature 4. The G+C content of the DNA was 37.2 mol%. Based on phenotypic and genotypic characteristics, strain CW-E 2T represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium flavum sp. nov. is proposed. The type strain is CW-E 2T (=KCTC 12877T=CCTCC AB 206147T).
R156C mutation of keratin 10 causes mild form of epidermolytic hyperkeratosis
Authors: HARUNA Kunitaka , SUGA Yasushi , MIZUNO Yuki , HASEGAWA Toshio , KOUROU Kazuhiro , MATSUBA Shouichi , MURAMATSU Shigenori , IKEDA Shigaku
Published: August 2007

A 37‐year‐old Japanese male presented to us with persistent asteatotic skin with mild erythema on the trunk and extremities. Skin biopsy from the left knee showed marked epidermal acanthosis and hyperkeratosis, and milder granular degeneration. Ultrastructural analysis revealed clumping of the keratin filaments within suprabasal keratinocytes of the epidermis. Following direct sequencing, we found a single nucleotide substitution in one allele at the residue position 466 of the 1A rod domain segment (CGC to TGC, arginine to cysteine; R156C) in keratin 10. Clinical manifestations and molecular analysis indicated that R156C mutation in keratin 10 gene (KRT10) causes a mild form of epidermolytic hyperkeratosis (EHK) in the presented case.
Low‐grade myxofibrosarcoma invaded into the underlying skeletal muscle
Authors: MOTODA Natsuki , AKIYAMA Masashi , AOYAGI Satoru , SAWAMURA Daisuke , SHIMIZU Hiroshi
Published: August 2007

Myxofibrosarcoma is a rare, soft‐tissue sarcoma which is classified into three main subtypes according to cellularity and cell atypia: low, intermediate and high grade. A 44‐year‐old Japanese female presented with a low‐grade myxofibrosarcoma on the left forearm. The lesion was completely resected. Histopathologically, the tumor was remarkably hypocellular and exhibited only mild atypia. However, it rapidly invaded into the underlying brachioradial muscle. The present case clearly indicated that a low‐grade myxofibrosarcoma can invade into the deeper tissues including muscle even though its histological grade is very low.
Adverse skin reactions due to pegylated interferon alpha 2b plus ribavirin combination therapy in a patient with chronic hepatitis C virus
Authors: HASHIMOTO Yuki , KANTO Hiromi , ITOH Masatoshi
Published: August 2007

Pegylated interferon (IFN)‐α‐2b with ribavirin has recently replaced “standard” IFN‐α for the treatment of chronic hepatitis C. The most common side‐effect of pegylated IFN‐α‐2b plus ribavirin combination therapy is localized inflammatory skin lesions at the site of injection. A 66‐year‐old female treated with once‐weekly pegylated IFN‐α‐2b plus ribavirin for active chronic hepatitis C developed inflammatory skin lesions 2 months after starting antiviral treatment. The type of skin reactions observed were vesicle erythematous eruptions at the injection sites, and pruritic papular erythematous eruptions located on the face, neck, distal limbs, dorsa of the hands, trunk and buttocks away from the injection sites. Histological examination was performed on the pruritic papular erythematous eruption located on the left forearm, away from the injection sites. It showed epidermal spongiosis, a spongiotic microvesicle, and perivascular infiltration of the upper dermis with lymphocytes. The treatment was interrupted subsequently and the patient was rechallenged with pegylated IFN‐α‐2b plus ribavirin combination therapy, oral prednisolone with olopatadine hydrochloride and topical 0.1% diflucortolone valerate, which led to a significant improvement of skin lesions. Erythema with infiltration can occur at the injection sites of pegylated IFN‐α‐2b. However, the occurrence of vesicle erythematous eruptions away from the injection sites and autosensitization dermatitis apart from injection sites have not yet been frequently reported.
Case of acne conglobata successfully treated by CO2 laser combined with topical tretinoin therapy
Authors: HASEGAWA Toshio , MATSUKURA Tomoyuki , SUGA Yasushi , MURAMATSU Shigenori , MIZUNO Yuki , TSUCHIHASHI Hitoshi , HARUNA Kunitaka , OGAWA Hideoki , IKEDA Shigaku
Published: August 2007

Acne conglobata is an uncommon disorder characterized by the presence of nodulocystic lesions. Conservative therapy with oral and topical antibiotics is of limited efficacy in many cases, and surgical excision is often needed for removal of the cystic lesions. Treatment is particularly difficult in cases with lesions located in aesthetically sensitive areas, such as the face. We successfully treated a case of acne conglobata by CO2 laser ablation to remove the top of the sinuses and their tracts. In addition, topical tretinoin therapy was also initiated simultaneously to prevent the appearance of new acne lesions. Based on the results, we propose that the use of CO2 laser for opening the cysts, combined with topical tretinoin therapy to prevent the appearance of new lesions, is a powerful treatment option for acne conglobata.
Alternative pharmacokinetics of S‐1 components, 5‐fluorouracil, dihydrofluorouracil and α‐fluoro‐β‐alanine after oral administration of S‐1 following total gastrectomy
Authors: Kim Woo Young , Nakata Bunzo , Hirakawa Kosei
Published: August 2007

We studied whether total gastrectomy for gastric cancer would affect the pharmacokinetics of 5‐fluorouracil (5‐FU) and its degradation products, such as dihydrouracil (FUH2) and α‐fluoro‐β‐alanine (FBAL), after oral administration of the fluorouracil derivative S‐1, composed of tegafur, 5‐chloro‐2,4‐dihydroxypyridine (CDHP; a dihydropyrimidine dehydrogenase inhibitor) and potassium oxonate. Blood and urine samples were obtained, both preoperatively and at least 2 weeks postoperatively, from six patients with advanced gastric cancers who were undergoing total gastrectomy. Plasma levels of tegafur, 5‐FU, CDHP, potassium oxonate, FUH2and FBAL were measured prior to and at 1, 2, 4, 6 and 10 h after oral administration of 40 mg/m2S‐1. The total amounts of 5‐FU, FUH2and FBAL excreted into urine during the 24‐h period after S‐1 administration were also measured. Total gastrectomy significantly increased the maximum concentration and the area under the curve until 10 h after administration (AUC1–10h) of plasma 5‐FU. The plasma AUC1–10hof CDHP was significantly higher than the preoperative value. In terms of clinical efficacy, the higher AUC1–10hof 5‐FU after total gastrectomy may be beneficial to S‐1 administered as adjuvant chemotherapy, and might be caused by the higher postoperative AUC1–10hof CDHP relative to preoperative values. However, the dose of S‐1 for patients who have undergone total gastrectomy might be diminished to avoid severe adverse events and to continue the treatment for a long period. (Cancer Sci2007; 98: 1604–1608)