bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical sectioning microscope with a binary hologram based beam scanning
Authors: Das Abhijit , Boruah B. R.
Published: April 2011

We describe the development of a beam scanning microscope that can perform optical sectioning based on the principle of confocal microscopy. The scanning is performed by a laser beam diffracted from a dynamic binary hologram implemented using a liquid crystal spatial light modulator. Using the proposed scanning mechanism, unlike the conventional confocal microscopes, scanning over a two-dimensional area of the sample can be obtained without the use of a pair of galvo mirror scanners. The proposed microscope has a number of advantages, such as superior frame to frame repeatability, simpler optical arrangement, increased pixel dwell time relative to the time between two pixels, illumination of only the sample points without pulsing the laser, and absolute control over the amplitude and phase of the illumination beam on a pixel to pixel basis. The proposed microscope can be particularly useful for applications requiring very long exposure time or very large working distance objective lenses. In this paper we present experimental implementation of the setup using a nematic liquid crystal spatial light modulator and proof-of-concept experimental results.
Laser adiabatic manipulation of the bond length of diatomic molecules with a single chirped pulse
Authors: Chang Bo Y. , Shin Seokmin , Santamaria Jesus , Sola Ignacio R.
Published: April 2011

We propose and test numerically a scheme for controlling the bond distance in a diatomic molecule that requires the use of a single chirped pulse. The laser prepares a superposition state of both nuclear and electronic degrees of freedom, where the main character of the electronic wave function is that of an excited dissociative state. The main limitation of the scheme is the need of ultra broadband pulses, where the bandwidth must be of the order of the dissociation energy to achieve large bond elongations. The scheme can be used to deform the bond during the laser excitation to an arbitrary large and constant value, or to allow slow time-dependent bond elongations. Additionally, the scheme can be used to prepare highly excited vibrational wave packets in the ground potential after the pulse is switched off, at the expense of losing some population that dissociates. These wave packets are initially localized at the outer well of the potential, at energies controllable by the excitation process.
Riccati equation and the problem of decoherence II: Symmetry and the solution of the Riccati equation
Authors: Gardas Bartłomiej
Published: April 2011

In this paper we revisit the problem of decoherence by applying the block operator matrices analysis. The Riccati algebraic equation associated with the Hamiltonian describing the process of decoherence is studied. We prove that if the environment responsible for decoherence is invariant with respect to the antilinear transformation then the antilinear operator solves the Riccati equation in question. We also argue that this solution leads to neither a linear nor an antilinear operator similarity matrix. Therefore, we cannot use the standard procedure for solving a linear differential equation (e.g., Schrödinger equation). Furthermore, the explicit solution of the Riccati equation is found for the case where the environmental operators commute with each other. We discuss the connection between our results and the standard description of decoherence (one that uses the Kraus representation). We show that the reduced dynamics we obtain does not have the Kraus representation if the initial correlations between the system and its environment are present. However, for any initial state of the system (even when the correlations occur) reduced dynamics can be written in a manageable way.
Communication: Suppression of sintering of size-selected Pd clusters under realistic reaction conditions for catalysis
Authors: Yin Feng , Lee Sungsik , Abdela Ahmed , Vajda Stefan , Palmer Richard E.
Published: April 2011

The stability of model catalysts based on size-selected Pd clusters supported on graphite surfaces has been explored under realistic conditions for catalytic oxidation of methane at mild temperatures. The experimental results show that aggregated films of nanoparticles are highly unstable, but clusters pinned to the surface in the submonolayer coverage regime are much more stable against sintering. The degree of sintering of the pinned clusters, which does occur, proceeds by the release of clusters from their pinning sites. The suppression of sintering depends on the cluster deposition energy with respect to the pinning threshold.
He–ThO(1Σ+) interactions at low temperatures: Elastic and inelastic collisions, transport properties, and complex formation in cold 4He gas
Authors: Tscherbul T. V. , Sayfutyarova E. R. , Buchachenko A. A. , Dalgarno A.
Published: April 2011

We present an ab initio study of cold 4He + ThO(1Σ+) collisions based on an accurate potential energy surface (PES) evaluated by the coupled cluster method with single, double, and noniterative triple excitations using an extended basis set augmented by bond functions. Variational calculations of rovibrational energy levels show that the 4He–ThO van der Waals complex has a binding energy of 10.9 cm−1 in its ground J = 0 rotational state. The calculated energy levels are used to obtain the temperature dependence of the chemical equilibrium constant for the formation of the He–ThO complex. We find that complex formation is thermodynamically favored at temperatures below 1 K and predict the maximum abundance of free ground-state ThO(v = 0, j = 0) molecules between 2 and 3 K. The calculated cross sections for momentum transfer in elastic He + ThO collisions display a rich resonance structure below 5 cm−1 and decline monotonically above this collision energy. The cross sections for rotational relaxation accompanied by momentum transfer decline abruptly to zero at low collision energies (<0.1 cm−1). We find that Stark relaxation in He + ThO collisions can be enhanced by applying an external dc electric field of less than 100 kV/cm. Finally, we present calculations of thermally averaged diffusion cross sections for ThO in He gas, and find these to be insensitive to small variations of the PES at temperatures above 1 K.
Excitation of electronic states in tetrahydrofuran by electron impact
Authors: Do T. P. T. , Leung M. , Fuss M. , Garcia G. , Blanco F. , Ratnavelu K. , Brunger M. J.
Published: April 2011

We report on differential and integral cross section measurements for the electron impact excitation of the three lowest lying Rydberg bands of electronic states in tetrahydrofuran. The energy range of the present experiments was 15–50 eV with the angular range of the differential cross section measurements being 15°–90°. The important effects of the long-range target dipole moment and the target dipole polarizability, on the scattering dynamics of this system, are evident from the present results. To the best of our knowledge, there are no other theoretical or experimental data against which we can compare the cross section results from this study.
Compact tunable sub-terahertz oscillators based on Josephson junctions
Authors: Song Fengbin , Müller Franz , Scheller Thomas , Semenov Alexei , He Ming , Fang Lan , Hübers Heinz-Wilhelm , Klushin Alexander M.
Published: April 2011

Essential applications of terahertz technology are urgently in need of compact, tunable solid-state continuous wave radiation sources. However, no satisfactory solution is yet available for the frequency range of up to approximately 1.0 THz. Here, we present coherent radiation from large series arrays of Josephson junctions between 0.1 and 0.25 THz with off-chip radiation power of 7 μW. Niobium junctions oscillate at 4.2 K and the detection has been done at room temperature. The well-known obstacle to impedance matching is overcome by utilizing the excited resonances in the junction substrates serving as dielectric resonator antennae.
Effect of postgrowth hydrogen treatment on defects in GaNP
Authors: Dagnelund D. , Wang X. J. , Tu C. W. , Polimeni A. , Capizzi M. , Chen W. M. , Buyanova I. A.
Published: April 2011

Effect of postgrowth hydrogen treatment on defects and their role in carrier recombination in GaNP alloys is examined by photoluminescence (PL) and optically detected magnetic resonance. We present direct experimental evidence for effective activation of several defects by low-energy subthreshold hydrogen treatment (≤100 eV H ions). Among them, two defect complexes are identified to contain a Ga interstitial. Possible mechanisms for the H-induced defect activation and creation are discussed. Carrier recombination via these defects is shown to efficiently compete with the near band-edge PL, explaining the observed degraded optical quality of the alloys after the H treatment.
Electrode-contact enhancement in silicon nanowire-array-textured solar cells
Authors: Chen Chen , Jia Rui , Li Haofeng , Meng Yanlong , Liu Xinyu , Ye Tianchun , Kasai Seiya , Tamotsu Hashizume , Wu Nanjian , Wang Shanli , Chu Junhao
Published: April 2011

In the case of the silicon (Si) nanowire (NW)-array-textured solar cells, the electrode-contact enhancement has been achieved using a simple and convenient double-step diffusion process to form a highly doped N+ region at the tips of a Si-NW array. The series resistance can be effectively reduced, leading to an increase in the short-circuit current density in the cell. We have studied the physical mechanism of the impact of an increase in doping level at the tips of a Si-NW array on the electrode-contact property, which would benefit in realizing an improvement in cell performance in such a nanostructure solar cell.
Heat capacity in the glass transition range modeled on the basis of heterogeneous dynamics
Authors: Richert Ranko
Published: April 2011

A heterogeneous version of the Tool–Narayanaswamy–Moynihan (TNM) model is proposed, in which enthalpy relaxation is heterogeneous in the sense that the overall nonexponential relaxation originates from the superposition of independently and exponentially relaxing domains with individual time constants. Analogous to rate exchange at a constant temperature, there is only a single fictive temperature that controls the rate at which all time constants can change considerably during a temperature scan. The model is shown to be consistent with differential scanning calorimetry (DSC) data taken across the glass transition of polystyrene, propylene carbonate, and glycerol. In contrast to the standard homogeneous TNM model, the heterogeneous counterpart fits DSC up-scans for As2Se3 for cooling rates of 0.31, 2.5, and 20 K/min with a common set of parameters.
Canard explosion of limit cycles in templator models of self-replication mechanisms
Authors: Brøns Morten
Published: April 2011

Templators are differential equation models for self-replicating chemical systems. Beutel and Peacock-López [J. Chem. Phys. 126, 125104 (2007)]10.1063/1.2716396 have numerically analyzed a model for a cross-catalytic self-replicating system and found two cases of canard explosion, that is, a substantial change of amplitude of a limit cycle over a very short parameter interval. We show how the model can be reduced to a two-dimensional system and how canard theory for slow–fast equations can be applied to yield analytic information about the canard explosion. In particular, simple expressions for the parameter value where the canard explosion occurs are obtained. The connection to mixed-mode oscillations also observed in the model is briefly discussed.
Directed self-assembly of InAs quantum dots on nano-oxide templates
Authors: Dias N. L. , Garg A. , Reddy U. , Young J. D. , Verma V. B. , Mirin R. P. , Coleman J. J.
Published: April 2011

We describe the growth and characterization of InAs quantum dots on SiO2 patterned GaAs by metal organic chemical vapor deposition. Arrays of quantum dots with densities as high as 1.8×1010 cm−2 fabricated by electron beam lithography are demonstrated. A process consisting of dry and wet etching to minimize etch damage is developed. As the mask diameter increases, the nucleation transitions from single dots to multidot clusters. We achieve more uniform size and shape distributions of dots on patterned regions relative to unpatterned dots as revealed by structural characterization and room temperature photoluminescence emission spectra.
Magnetocaloric effect and magnetic cooling near a field-induced quantum-critical point
Authors: Wolf Bernd , Tsui Yeekin , Jaiswal-Nagar Deepshikha , Tutsch Ulrich , Honecker Andreas , Remović-Langer Katarina , Hofmann Georg , Prokofiev Andrey , Assmus Wolf , Donath Guido , Lang Michael
Published: April 2011

The presence of a quantum-critical point (QCP) can significantly affect the thermodynamic properties of a material at finite temperatures
T
. This is reflected, e.g., in the entropy landscape
S
(
T
,
r
) in the vicinity of a QCP, yielding particularly strong variations for varying the tuning parameter
r
such as pressure or magnetic field
B
. Here we report on the determination of the critical enhancement of ∂
S
/∂
B
near a
B
-induced QCP via absolute measurements of the magnetocaloric effect (MCE), (∂
T
/∂
B
)

S

and demonstrate that the accumulation of entropy around the QCP can be used for efficient low-temperature magnetic cooling. Our proof of principle is based on measurements and theoretical calculations of the MCE and the cooling performance for a Cu
2+
-containing coordination polymer, which is a very good realization of a spin-½ antiferromagnetic Heisenberg chain—one of the simplest quantum-critical systems.
Graphane sheets and crystals under pressure
Authors: Wen Xiao-Dong , Hand Louis , Labet Vanessa , Yang Tao , Hoffmann Roald , Ashcroft N. W. , Oganov Artem R. , Lyakhov Andriy O.
Published: April 2011

Eight isomeric two-dimensional graphane sheets are found in a theoretical study. Four of these nets—two built on chair cyclohexanes, two on boat—are more stable thermodynamically than the isomeric benzene, or polyacetylene. Three-dimensional crystals are built up from the two-dimensional sheets, and their hypothetical behavior under pressure (up to 300 GPa) is explored. While the three-dimensional graphanes remain, as expected, insulating or semiconducting in this pressure range, there is a remarkable inversion in stability of the five crystals studied. Two stacking polytypes that are not the most stable at ambient pressure (one based on an unusual chair cyclohexane net, the other on a boat) are significantly stabilized with increasing pressure relative to stackings of simple chair sheets. The explanation may lie in the balance on intra and intersheet contacts in the extended arrays.
Periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) is a disorder of innate immunity and Th1 activation responsive to IL-1 blockade
Authors: Stojanov Silvia , Lapidus Sivia , Chitkara Puja , Feder Henry , Salazar Juan C. , Fleisher Thomas A. , Brown Margaret R. , Edwards Kathryn M. , Ward Michael M. , Colbert Robert A. , Sun Hong-Wei , Wood Geryl M. , Barham Beverly K. , Jones Anne , Aksentijevich Ivona , Goldbach-Mansky Raphaela , Athreya Balu , Barron Karyl S. , Kastner Daniel L.
Published: April 2011

The syndrome of periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) is the most common periodic fever disease in children. However, the pathogenesis is unknown. Using a systems biology approach we analyzed blood samples from PFAPA patients whose genetic testing excluded hereditary periodic fevers (HPFs), and from healthy children and pediatric HPF patients. Gene expression profiling could clearly distinguish PFAPA flares from asymptomatic intervals, HPF flares, and healthy controls. During PFAPA attacks, complement (C1QB, C2, SERPING1), IL-1–related (IL-1B, IL-1RN, CASP1, IL18RAP), and IFN-induced (AIM2,IP-10/CXCL10) genes were significantly overexpressed, but T cell-associated transcripts (CD3, CD8B) were down-regulated. On the protein level, PFAPA flares were accompanied by significantly increased serum levels of chemokines for activated T lymphocytes (IP-10/CXCL10, MIG/CXCL9), G-CSF, and proinflammatory cytokines (IL-18, IL-6). PFAPA flares also manifested a relative lymphopenia. Activated CD4+/CD25+T-lymphocyte counts correlated negatively with serum concentrations of IP-10/CXCL10, whereas CD4+/HLA-DR+T lymphocyte counts correlated positively with serum concentrations of the counterregulatory IL-1 receptor antagonist. Based on the evidence for IL-1β activation in PFAPA flares, we treated five PFAPA patients with a recombinant IL-1 receptor antagonist. All patients showed a prompt clinical and IP-10/CXCL10 response. Our data suggest an environmentally triggered activation of complement and IL-1β/-18 during PFAPA flares, with induction of Th1-chemokines and subsequent retention of activated T cells in peripheral tissues. IL-1 inhibition may thus be beneficial for treatment of PFAPA attacks, with IP-10/CXCL10 serving as a potential biomarker.
KSTAR equilibrium operating space and projected stabilization at high normalized beta
Authors: Park Y.S. , Sabbagh S.A. , Berkery J.W. , Bialek J.M. , Jeon Y.M. , Hahn S.H. , Eidietis N. , Evans T.E. , Yoon S.W. , Ahn J.-W. , Kim J. , Yang H.L. , You K.-I. , Bae Y.S. , Chung J. , Kwon M. , Oh Y.K. , Kim W.-C. , Kim J.Y. , Lee S.G. , Park H.K. , Reimerdes H. , Leuer J. , Walker M.
Published: April 2011

Along with an expanded evaluation of the equilibrium operating space of the Korea Superconducting Tokamak Advanced Research, KSTAR, experimental equilibria of the most recent plasma discharges were reconstructed using the EFIT code. In near-circular plasmas created in 2009, equilibria reached a stored energy of 54 kJ with a maximum plasma current of 0.34 MA. Highly shaped plasmas with near double-null configuration in 2010 achieved H-mode with clear edge localized mode (ELM) activity, and transiently reached a stored energy of up to 257 kJ, elongation of 1.96 and normalized beta of 1.3. The plasma current reached 0.7 MA. Projecting active and passive stabilization of global MHD instabilities for operation above the ideal no-wall beta limit using the designed control hardware was also considered. Kinetic modification of the ideal MHD n = 1 stability criterion was computed by the MISK code on KSTAR theoretical equilibria with a plasma current of 2 MA, internal inductance of 0.7 and normalized beta of 4.0 with simple density, temperature and rotation profiles. The steep edge pressure gradient of this equilibrium resulted in the need for significant plasma toroidal rotation to allow thermal particle kinetic resonances to stabilize the resistive wall mode (RWM). The impact of various materials and electrical connections of the passive stabilizing plates on RWM growth rates was analysed, and copper plates reduced the RWM passive growth rate by a factor of 15 compared with stainless steel plates at a normalized beta of 4.4. Computations of active RWM control using the VALEN code showed that the n = 1 mode can be stabilized at normalized beta near the ideal wall limit via control fields produced by the midplane in-vessel control coils (IVCCs) with as low as 0.83 kW control power using ideal control system assumptions. The ELM mitigation potential of the IVCC, examined by evaluating the vacuum island overlap created by resonant magnetic perturbations, was analysed using the TRIP3D code. Using a combination of all IVCCs with dominant n = 2 field and upper/lower coils in an even parity configuration, a Chirikov parameter near unity at normalized poloidal flux 0.83, an empirically determined condition for ELM mitigation in DIII-D, was generated in theoretical high-beta equilibria. Chirikov profile optimization was addressed in terms of coil parity and safety factor profile.
Physical understanding of the instability spectrum and the feedback control of resistive wall modes in reversed field pinch
Authors: Wang Z.R. , Guo S.C.
Published: April 2011

The cylindrical MHD model integrated with a feedback system is applied to the study of resistive wall mode (RWM) in reversed field pinch (RFP) plasmas. The model takes into account the compressibility, longitudinal flow, viscosity and resistive wall with a finite thickness. The study, via both analytical and numerical analyses, provides a physical understanding on the following subjects: firstly, on the nature of the instability spectrum of the RWM observed in RFP plasmas; specifically, the growth rates of the two groups of the RWMs (internally non-resonant and externally non-resonant) have opposite dependence on the variation of the field reversal. Secondly, on the response of the unstable plasmas to the feedback control in RFPs, the mode behaviour in plasmas under the feedback is clarified and discussed in detail. Finally, the linear solutions of time evolution of RWM instability in various feedback scenarios are given. The effects of the wall proximity, the sensor location and the system response time are discussed, respectively.
Numerical calculations and RF characteristics measurement of complex-conjugate impedance antenna system for ICRF heating and current drive
Authors: Kumazawa Ryuhei , Kasahara Hiroshi , Saito Kenji , Seki Tetsuo , Mutoh Takashi , Shinpo Fujio , Nomura Goro , Zhao Yanping , Kwak Jong-Gu
Published: April 2011

Characteristics of a complex-conjugate impedance antenna system for ion cyclotron resonance frequency (ICRF) heating and current drive (H & CD) are discussed in this paper. Large RF power is reflected in such transitions as that of ELMy H–L mode due to the large change in plasma resistance during the ICRF H & CD. In such a case the RF power injection to the plasma must be ceased in order to protect the tetrode vacuum tubes. The idea of a complex-conjugate impedance antenna system to mitigate the large reflected RF power, referred to as ELM tolerance, has recently been proposed. It has been proved that the reflected RF power fraction can be reduced even during a large change in plasma resistance. But it is not reduced to the level allowable for the tetrode tubes. Therefore, an improved system adding a single stub tuner is proposed. Using it, the reflected RF power fraction can be reduced to the allowable level. Numerical calculations and experiments are carried out for this system. It is found that the experimental data agree with numerical calculations.
Analytic dispersion relation for resistive wall modes in rotating plasmas by generalized matching theory
Authors: Shiraishi J. , Tokuda S.
Published: April 2011

Analytic dispersion relation is derived for resistive wall modes (RWMs) in rotating plasmas, which gives the growth rate and the real frequency. The given parameters are wall information (radius, thickness and volume resistivity) and equilibrium quantities at a plasma surface and at a singular point of the generalized Newcomb equation, which is an inertia-less linearized ideal magnetohydrodynamic equation with equilibrium rotation. Derivation of the dispersion relation is based on the generalized matching theory proposed by the present authors, which exploits the inner ‘region’ with finite width. It is found that the RWM stability is strongly affected by rotation shear, not at the rational surface, but at the singular point of the generalized Newcomb equation.
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
Authors: Mu Fangping , Unkefer Clifford J. , Unkefer Pat J. , Hlavacek William S.
Published: April 2011

Motivation: Our knowledge of the metabolites in cells and their reactions is far from complete as revealed by metabolomic measurements that detect many more small molecules than are documented in metabolic databases. Here, we develop an approach for predicting the reactivity of small-molecule metabolites in enzyme-catalyzed reactions that combines expert knowledge, computational chemistry and machine learning.

Results: We classified 4843 reactions documented in the KEGG database, from all six Enzyme Commission classes (EC 1–6), into 80 reaction classes, each of which is marked by a characteristic functional group transformation. Reaction centers and surrounding local structures in substrates and products of these reactions were represented using SMARTS. We found that each of the SMARTS-defined chemical substructures is widely distributed among metabolites, but only a fraction of the functional groups in these substructures are reactive. Using atomic properties of atoms in a putative reaction center and molecular properties as features, we trained support vector machine (SVM) classifiers to discriminate between functional groups that are reactive and non-reactive. Classifier accuracy was assessed by cross-validation analysis. A typical sensitivity [TP/(TP+FN)] or specificity [TN/(TN+FP)] is ≈0.8. Our results suggest that metabolic reactivity of small-molecule compounds can be predicted with reasonable accuracy based on the presence of a potentially reactive functional group and the chemical features of its local environment.

Availability: The classifiers presented here can be used to predict reactions via a web site (http://cellsignaling.lanl.gov/Reactivity/). The web site is freely available.

Contact:  fmu@lanl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks
Authors: Audenaert Pieter , Van Parys Thomas , Brondel Florian , Pickavet Mario , Demeester Piet , Van de Peer Yves , Michoel Tom
Published: April 2011

Summary: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm.

Availability: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.

Contact:  tom.michoel@frias.uni-freiburg.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov., isolated from marine sediment
Authors: Zhang Dong-Sheng , Huo Ying-Yi , Xu Xue-Wei , Wu Yue-Hong , Wang Chun-Sheng , Xu Xue-Feng , Wu Min
Published: April 2011

Two Gram-negative, aerobic strains, Y215T and Y226T, were isolated from sediment from Yueqing Bay, Zhejiang Province, China. The two novel strains were both positive for oxidase activity, nitrate reduction, and aesculin and casein decomposition, but negative for gelatin and tyrosine decomposition. Catalase activity, and starch and Tween 80 decomposition differed between the two strains. Cells of both novel strains were rod-shaped in young cultures and ovoid in older cultures. Optimum NaCl concentration and pH range for growth of both strains were 2.0–3.0 % (w/v) and 7.0–8.0, respectively, whereas the optimum growth temperature for strain Y215T (25–30 °C) was lower than that for strain Y226T (30–37 °C). The genomic DNA G+C contents of strains Y215T and Y226T were 54.0 and 56.7 mol%, respectively. The major fatty acids in both isolates were iso-C15 : 0 and iso-C17 : 1ω9c, which was also the case in the reference strains apart from Microbulbifer salipaludis, which possessed C18 : 1ω7c as the predominant fatty acid. The predominant isoprenoid quinone was Q-8 and the major polar lipids of both strains were phosphatidylethanolamine, phosphatidylglycerol and an unknown glycolipid. Both strains had highest 16S rRNA gene sequence similarity to members of the genus Microbulbifer. Strain Y215T was closely related to the type strains of Microbulbifer maritimus (97.6 %) and Microbulbifer donghaiensis (97.5 %), whereas strain Y226T was closely related to the type strain of M. salipaludis (97.6 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y215T and Y226T fell into two separate clusters. The DNA–DNA relatedness values of strain Y215T with M. maritimus TF-17T and M. donghaiensis CN85T were 34.1 and 32.8 %, respectively, whereas that between strain Y226T and M. salipaludis SM-1T was 38.0 %; these values are significantly lower than the threshold value for the delineation of bacterial species. On the basis of their distinct taxonomic characteristics, the two isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov. are proposed; the type strains are Y215T ( = CGMCC 1.10657T = JCM 17211T) and Y226T ( = CGMCC 1.10658T = JCM 17212T), respectively.
Kangiella geojedonensis sp. nov., isolated from seawater
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Soo-Young , Lee Jung-Sook , Oh Tae-Kwang
Published: April 2011

A Gram-stain-negative, non-motile, non-spore-forming bacterial strain, YCS-5T, was isolated from seawater off the southern coast of Korea. Strain YCS-5T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YCS-5T fell within the clade comprising Kangiella species. Strain YCS-5T exhibited 16S rRNA gene sequence similarity values of 96.6, 95.7 and 97.9 % to the type strains of Kangiella koreensis, Kangiella aquimarina and Kangiella japonica, respectively, and less than 89.8 % to strains of other species used in the phylogenetic analysis. Strain YCS-5T contained Q-8 as the predominant ubiquinone and iso-C17 : 0, iso-C15 : 0, iso-C11 : 0 3-OH and iso-C17 : 1ω9c as the major fatty acids. The polar lipid profile of strain YCS-5T was similar to that of K. koreensis SW-125T, with phosphatidylglycerol and an unidentified aminolipid as major polar lipids. The DNA G+C content was 47 mol%. The mean DNA–DNA relatedness value between strain YCS-5T and K. japonica JCM 16211T was 12 %. Differential phenotypic properties and the phylogenetic and genetic distinctiveness of strain YCS-5T demonstrated that this strain is distinguishable from other Kangiella species. On the basis of the data presented, strain YCS-5T is considered to represent a novel species of the genus Kangiella, for which the name Kangiella geojedonensis sp. nov. is proposed; the type strain is YCS-5T ( = KCTC 23420T = CCUG 60526T).
Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium
Authors: Zhang Jun , Chen Shu-An , Zheng Jin-Wei , Cai Shu , Hang Bao-Jian , He Jian , Li Shun-Peng
Published: April 2011

A novel facultatively anaerobic, non-spore-forming, non-motile, catalase- and oxidase-positive, Gram-negative and rod-shaped bacterial strain, designated Y12T, was isolated from activated sludge of a wastewater bio-treatment facility. The strain was able to degrade about 90 % of added propanil (100 mg l−1) within 3 days of incubation. Growth occurred in the presence of 0–4.5 % (w/v) NaCl (optimum 0.5 %), at 10–40 °C (optimum 28 °C) and at pH 5.5–10.0 (optimum pH 7.0). Vesicular internal membrane structures and photoheterotrophic growth were not observed. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acid was summed feature 8 (C18 : 1ω6cand/or C18 : 1ω7c). The genomic DNA G+C content of strain Y12Twas 63.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain Y12Twas a member of the genusCatellibacterium, as it showed highest sequence similarities toCatellibacterium caeniDCA-1T(99.1 %) and <96.0 % similarities with other species of the genusCatellibacterium. Strain Y12Tshowed low DNA–DNA relatedness values withC. caeniDCA-1T. Based on phenotypic, genotypic and phylogenetic properties, strain Y12Trepresents a novel species of the genusCatellibacterium, for which the nameCatellibacterium nanjingensesp. nov. is proposed. The type strain is Y12T( = CCTCC AB 2010218T = KCTC 23298T). An emended description of the genusCatellibacteriumis also presented.
Mucilaginibacter lutimaris sp. nov., isolated from a tidal flat sediment
Authors: Kim Ji-Hoon , Kang So-Jung , Jung Yong-Taek , Oh Tae-Kwang , Yoon Jung-Hoon
Published: April 2011

A Gram-staining-negative, non-spore-forming, facultatively aerobic, non-motile, rod-shaped bacterial strain, BR-3T, was isolated from a tidal flat on the western coast of Korea, and subjected to a polyphasic study. Strain BR-3T grew optimally at 25 °C, at pH 6.5–7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BR-3T fell within the clade comprising species of the genus Mucilaginibacter, joining the type strain of Mucilaginibacter rigui, with which it exhibited highest 16S rRNA gene sequence similarity (98.2 %). 16S rRNA gene sequence similarity values between strain BR-3T and the type strains of the other species of the genus Mucilaginibacter were in the range 93.8–95.9 %. A mean DNA–DNA relatedness value between strain BR-3T and M. rigui KCTC 12534T was 21 %. Strain BR-3T contained MK-7 as the predominant menaquinone and C16 : 1ω7c and/or iso-C15 : 0 2-OH and iso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The DNA G+C content was 49.8 mol%. Differential phenotypic properties and phylogenetic and genetic distinctiveness of strain BR-3T demonstrated that this strain is separate from M. rigui as well as the other species of the genus Mucilaginibacter. On the basis of the data presented, strain BR-3T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter lutimaris sp. nov. is proposed. The type strain is BR-3T ( = KCTC 23461T  = CCUG 60742T).
Wickerhamiella pagnoccae sp. nov. and Candida tocantinsensis sp. nov., two ascomycetous yeasts from flower bracts of Heliconia psittacorum (Heliconiaceae)
Authors: Barbosa Anne C. , Morais Camila G. , Morais Paula B. , Rosa Luiz H. , Pimenta Raphael S. , Lachance Marc-André , Rosa Carlos A.
Published: April 2011

Two novel yeast species were isolated from nectar of flower bracts ofHeliconia psittacorum(Heliconiaceae) collected in a Cerrado ecosystem in the state of Tocantins, northern Brazil.Wickerhamiella pagnoccaesp. nov., which is closely related toCandida jalapaonensis, is heterothallic and produces one spheroid ascospore per ascus.Candida tocantinsensissp. nov. belongs to the Metschnikowiaceae clade and its nearest relative isCandida ubatubensis, but the sequence identity (%) in the D1/D2 domains of the rRNA gene is low. The type strain ofW. pagnoccaeis UFMG-F18C1T( = CBS 12178T = NRRL Y-48735T) and the type strain ofC. tocantinsensisis UFMG-F16D1T( = CBS 12177T = NRRL Y-48734T).
Dietzia aurantiaca sp. nov., isolated from a human clinical specimen
Authors: Kämpfer P. , Falsen E. , Frischmann A. , Busse H.-J.
Published: April 2011

A Gram-positive, coccoid, non-endospore-forming actinobacterium (strain CCUG 35676T) was isolated from cerebrospinal fluid from a 24-year-old woman in Gothenborg, Sweden. Based on pairwise 16S rRNA gene sequence similarity studies, strain CCUG 35676T was shown to belong to the genus Dietzia and was most closely related to the type strains of Dietzia aerolata (99.3 %), Dietzia lutea (98.8 %), Dietzia schimae (98.5 %), Dietzia maris (98.5 %), Dietzia alimentaria (98.3 %) and Dietzia cercidiphylli (98.0 %). The major menaquinone was MK-8(H2). Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid (APL1), an unidentified phospholipid (PL1) and unidentified glycolipids (GL1 and GL3). Numerous other lipids were also detected. The fatty acid profile, comprising C16 : 0, C17 : 0, C18 : 1ω9c and 10-methyl-C18 : 0 as major fatty acids, supported the affiliation of strain CCUG 35676T to the genus Dietzia. On the basis of the results of physiological and biochemical tests and DNA–DNA hybridizations, a clear phenotypic and genotypic differentiation of strain CCUG 35676T from the most closely related Dietzia species is possible. Strain CCUG 35676T represents a novel species, for which the name Dietzia aurantiaca sp. nov. is proposed, with CCUG 35676T ( = JCM 17645T) as the type strain.
Endogenous Myc maintains the tumor microenvironment
Authors: Sodir Nicole M. , Swigart Lamorna Brown , Karnezis Anthony N. , Hanahan Douglas , Evan Gerard I. , Soucek Laura
Published: April 2011

The ubiquitous deregulation of Myc in human cancers makes it an intriguing therapeutic target, a notion supported by recent studies in Ras-driven lung tumors showing that inhibiting endogenous Myc triggers ubiquitous tumor regression. However, neither the therapeutic mechanism nor the applicability of Myc inhibition to other tumor types driven by other oncogenic mechanisms is established. Here, we show that inhibition of endogenous Myc also triggers ubiquitous regression of tumors in a simian virus 40 (SV40)-driven pancreatic islet tumor model. Such regression is presaged by collapse of the tumor microenvironment and involution of tumor vasculature. Hence, in addition to its diverse intracellular roles, endogenous Myc serves an essential and nonredundant role in coupling diverse intracellular oncogenic pathways to the tumor microenvironment, further bolstering its credentials as a pharmacological target.
Hierarchy and Roles of Pathogen-Associated Molecular Pattern-Induced Responses in Nicotiana benthamiana
Authors: Segonzac Cécile , Feike Doreen , Gimenez-Ibanez Selena , Hann Dagmar R. , Zipfel Cyril , Rathjen John P.
Published: April 2011

Our current understanding of pathogen-associated molecular pattern (PAMP)-triggered immunity signaling pathways in plants is limited due to the redundancy of several components or the lethality of mutants in Arabidopsis (Arabidopsis thaliana). To overcome this, we used a virus-induced gene silencing-based approach in combination with pharmacological studies to decipher links between early PAMP-triggered immunity events and their roles in immunity following PAMP perception in Nicotiana benthamiana. Two different calcium influx inhibitors suppressed the reactive oxygen species (ROS) burst: activation of the mitogen-activated protein kinases (MAPKs) and PAMP-induced gene expression. The calcium burst was unaffected in plants specifically silenced for components involved in ROS generation or for MAPKs activated by PAMP treatment. Importantly, the ROS burst still occurred in plants silenced for the two major defense-associated MAPK genes NbSIPK (for salicylic acid-induced protein kinase) and NbWIPK (for wound-induced protein kinase) or for both genes simultaneously, demonstrating that these MAPKs are dispensable for ROS production. We further show that NbSIPK silencing is sufficient to prevent PAMP-induced gene expression but that both MAPKs are required for bacterial immunity against two virulent strains of Pseudomonas syringae and their respective nonpathogenic mutants. These results suggest that the PAMP-triggered calcium burst is upstream of separate signaling branches, one leading to MAPK activation and then gene expression and the other to ROS production. In addition, this study highlights the essential roles of NbSIPK and NbWIPK in antibacterial immunity. Unexpectedly, negative regulatory mechanisms controlling the intensity of the PAMP-triggered calcium and ROS bursts were also revealed by this work.
The Arabidopsis RING Finger E3 Ligase RHA2b Acts Additively with RHA2a in Regulating Abscisic Acid Signaling and Drought Response
Authors: Li Hongmei , Jiang Hongling , Bu Qingyun , Zhao Qingzhen , Sun Jiaqiang , Xie Qi , Li Chuanyou
Published: April 2011

We have previously shown that the Arabidopsis (Arabidopsis thaliana) RING-H2 E3 ligase RHA2a positively regulates abscisic acid (ABA) signaling during seed germination and postgerminative growth. Here, we report that RHA2b, the closest homolog of RHA2a, is also an active E3 ligase and plays an important role in ABA signaling. We show that RHA2b expression is induced by ABA and that overexpression of RHA2b leads to ABA-associated phenotypes such as ABA hypersensitivity in seed germination and seedling growth, enhanced stomatal closure, reduced water loss, and, therefore, increased drought tolerance. On the contrary, the rha2b-1 mutant shows ABA-insensitive phenotypes and reduced drought tolerance. We provide evidence showing that a rha2a rha2b-1 double mutant generally enhances ABA insensitivity of rha2b-1 in seed germination, seedling growth, and stomatal closure, suggesting that RHA2b and RHA2a act redundantly in regulating ABA responses. Genetic analyses support that, like RHA2a, the RHA2b action in ABA signaling is downstream of a protein phosphatase 2C, ABA-INSENSITIVE2 (ABI2), and in parallel with that of the ABI transcription factors ABI3/4/5. We speculate that RHA2b and RHA2a may have redundant yet distinguishable functions in the regulation of ABA responses.
The DNA Damage Response Signaling Cascade Regulates Proliferation of the Phytopathogenic FungusUstilago maydisin Planta
Authors: de Sena-Tomás Carmen , Fernández-Álvarez Alfonso , Holloman William K. , Pérez-Martín José
Published: April 2011

In the phytopathogenic fungus Ustilago maydis, the dikaryotic state dominates the period of growth occurring during the infectious phase. Dikaryons are cells in which two nuclei, one from each parent cell, share a single cytoplasm for a period of time without undergoing nuclear fusion. In fungal cells, maintenance of the dikaryotic state requires an intricate cell division process that often involves the formation of a structure known as the clamp connection as well as the sorting of one of the nuclei to this structure to ensure that each daughter dikaryon inherits a balance of each parental genome. Here, we describe an atypical role of the DNA damage checkpoint kinases Chk1 and Atr1 during pathogenic growth of U. maydis. We found that Chk1 and Atr1 collaborate to control cell cycle arrest during the induction of the virulence program in U. maydis and that Chk1 and Atr1 work together to control the dikaryon formation. These findings uncover a link between a widely conserved signaling cascade and the virulence program in a phytopathogen. We propose a model in which adjustment of the cell cycle by the Atr1-Chk1 axis controls fidelity in dikaryon formation. Therefore, Chk1 and Atr1 emerge as critical cell type regulators in addition to their roles in the DNA damage response.
A DELLA in Disguise: SPATULA Restrains the Growth of the DevelopingArabidopsisSeedling
Authors: Josse Eve-Marie , Gan Yinbo , Bou-Torrent Jordi , Stewart Kelly L. , Gilday Alison D. , Jeffree Christopher E. , Vaistij Fabián E. , Martínez-García Jaime F. , Nagy Ferenc , Graham Ian A. , Halliday Karen J.
Published: April 2011

The period following seedling emergence is a particularly vulnerable stage in the plant life cycle. In Arabidopsis thaliana, the phytochrome-interacting factor (PIF) subgroup of basic-helix-loop-helix transcription factors has a pivotal role in regulating growth during this early phase, integrating environmental and hormonal signals. We previously showed that SPATULA (SPT), a PIF homolog, regulates seed dormancy. In this article, we establish that unlike PIFs, which mainly promote hypocotyl elongation, SPT is a potent regulator of cotyledon expansion. Here, SPT acts in an analogous manner to the gibberellin-dependent DELLAs, REPRESSOR OF GA1-3 and GIBBERELLIC ACID INSENSITIVE, which restrain cotyledon expansion alongside SPT. However, although DELLAs are not required for SPT action, we demonstrate that SPT is subject to negative regulation by DELLAs. Cross-regulation of SPT by DELLAs ensures that SPT protein levels are limited when DELLAs are abundant but rise following DELLA depletion. This regulation provides a means to prevent excessive growth suppression that would result from the dual activity of SPT and DELLAs, yet maintain growth restraint under DELLA-depleted conditions. We present evidence that SPT and DELLAs regulate common gene targets and illustrate that the balance of SPT and DELLA action depends on light quality signals in the natural environment.
RAC/ROP GTPases and Auxin Signaling
Authors: Wu Hen-ming , Hazak Ora , Cheung Alice Y. , Yalovsky Shaul
Published: April 2011

Auxin functions as a key morphogen in regulating plant growth and development. Studies on auxin-regulated gene expression and on the mechanism of polar auxin transport and its asymmetric distribution within tissues have provided the basis for realizing the molecular mechanisms underlying auxin function. In eukaryotes, members of the Ras and Rho subfamilies of the Ras superfamily of small GTPases function as molecular switches in many signaling cascades that regulate growth and development. Plants do not have Ras proteins, but they contain Rho-like small G proteins called RACs or ROPs that, like fungal and metazoan Rhos, are regulators of cell polarity and may also undertake some Ras functions. Here, we discuss the advances made over the last decade that implicate RAC/ROPs as mediators for auxin-regulated gene expression, rapid cell surface-located auxin signaling, and directional auxin transport. We also describe experimental data indicating that auxin–RAC/ROP crosstalk may form regulatory feedback loops and theoretical modeling that attempts to connect local auxin gradients with RAC/ROP regulation of cell polarity. We hope that by discussing these experimental and modeling studies, this perspective will stimulate efforts to further refine our understanding of auxin signaling via the RAC/ROP molecular switch.
Effect of germination and probiotic fermentation on nutrient profile of pearl millet based food blends
Authors: Arora Sonia , Jood Sudesh , Khetarpaul N.
Published: April 2011

Purpose

Probiotic fermented foods are fast being recognized as health foods. Most of such foods are based on dairy products but little research work is available on coarse cereals and millets, which constitute the staple foods in developing countries. This paper aims to determine the effect of germination and fementation on nutrient composition of pearl millet based food blends.

Design/methodology/approach

Indigenously developed pearl millet based food blends containing raw and germinated pearl millet flour, whey powder and tomato pulp (2:1:1w/w) were autoclaved, cooled and fermented with 5 percent Lactobacillus acidophilus curd which supplied 106cells/ml to the slurry at 37°C for 12 h. The unfermented blends, after autoclaving, served as controls. The developed food blends were subjected to nutritional evaluation by using the standard methods of analysis. The data were statistically analysed.

Findings

Pearl millet based, germinated, autoclaved and fermented, food blend maintained adequate cell viability (8.64 cfu g‐1) as compared to non‐germinated food blend. Germination and probiotic fermentation caused significant improvement in the contents of thiamine, niacin, total lysine, protein fractions, sugars, soluble dietary fibre and in vitro availability of Ca, Fe and Zn of food blends.

Practical implications

Research is currently aimed at developing probiotic millet based food mixture, which had enhanced nutrient profile. Hence, it can be considered for commercialization after establishing its health/therapeutic implications among the population.

Originality/value

Dairy foods have preferentially been used as the carrier medium for probiotics. This paper explores the possibility of using staple foods as the carrier medium. The consumption of such food mixtures containing viable probiotic bacteria should be enhanced among consumers in term of their role in health maintenance and disease prevention.