bluuebunny/crossref_metadata_2025 huggingface dataset:
STRUGGLES UNDER AUTHORITARIANISM: REGIMES, STATES, AND PROFESSIONAL ASSOCIATIONS IN THE ARAB WORLD
Authors: Moore Pete W. , Salloukh Bassel F.
Published: March 2007

Scholars interested in the variation of Third Wave democratization have utilized cross–regional frameworks in which a single outcome characterizes the Arab world: no democratization. A number of social scientists working on Arab cases have shifted the investigation away from why democratization failed to how authoritarianism endured and changed over the past two decades. This article joins these efforts by examining the importance of professional associations, which refers to professional representatives and private economic groups, and their relations with regimes and states. The paper examines how three nondemocratic Arab regimes in Jordan, Syria, and Kuwait weathered economic and political crises in the 1980s and 1990s through contested or coordinated relations with professional associations. Outcomes are explained by focusing on (1) the respective social bases of regimes and associations influencing state intervention in associational life and (2) how state intervention shaped the capacity of associations either to contest state policy or to coordinate toward implementation.
Free-flying robots in space: an overview of dynamics modeling, planning and control
Authors: Moosavian S. Ali A. , Papadopoulos Evangelos
Published: March 2007

Free-flying space manipulator systems, in which robotic manipulators are mounted on a free-flying spacecraft, are envisioned for assembling, maintenance, repair, and contingency operations in space. Nevertheless, even for fixed-base systems, control of mechanical manipulators is a challenging task. This is due to strong nonlinearities in the equations of motion, and consequently different algorithms have been suggested to control end-effector motion or force, since the early research in robotic systems. In this paper, first a brief review of basic concepts of various algorithms in controlling robotic manipulators is introduced. Then, specific problems related to application of such systems in space and a microgravity environment is highlighted. Basic issues of kinematics and dynamics modeling of such systems, trajectory planning and control strategies, cooperation of multiple arm space free-flying robots, and finally, experimental studies and technological aspects of such systems with their specific limitations are discussed.
A NEW FERN AND TWO FLORISTIC RECORDS FROM THE KARIUS LIMESTONE OF PAPUA NEW GUINEA
Authors: TAKEUCHI W.
Published: March 2007

Plesioneuron crassum subsp. chromeanum Takeuchi (Thelypteridaceae) is described as a new subspecies from one of Papuasia's most isolated karst districts. The subspecies is distinguished by bifacially glabrous pinnae with revolute lobes, conspicuously raised aerophores, and glandular-setiferous sporangia. Distributional records for Helicia acutifolia (Proteaceae) and Loranthus odoratus (Loranthaceae) are also reported with the new fern.
REVISION OF ANEMONE SECT. HIMALAYICAE (RANUNCULACEAE) WITH THREE NEW SERIES
Authors: ZIMAN S. N. , EHRENDORFER F. , KEENER C. S. , WANG W. T. , MOSYAKIN S. L. , BULAKH E. V. , TSARENKO O. N. , DUTTON B. E. , CHAUDHARY R. P. , KADOTA Y.
Published: March 2007

The members of Anemone L. sect. Himalayicae (Ulbr.) Juz. (Ranunculaceae) are mainly distributed in the Himalaya of North India, Nepal and Bhutan and the neighbouring mountains of SW China at elevations between 1850 and 4800 m. Their taxonomy is re-evaluated on the basis of a critical morphological analysis of extensive herbarium material. The section is placed in Anemone subgen. Omalocarpus and differentiated into three new series: ser. Obtusilobae, ser. Trullifoliae and ser. Rupestres. A conspectus, keys to species, subspecies and varieties, descriptions of taxa, illustrations and distribution maps are presented. Eleven species with several infraspecific taxa are recognized and their synonymy, variability and relationships are discussed. In addition to the generally accepted species Anemone obtusiloba, A. trullifolia and A. rupestris, we recognize the following: A. polycarpa, A. rockii, A. geum and A. coelestina and four Chinese endemics, A. yulongshanica, A. patula, A. subpinnata and A. subindivisa. Anemone imbricata and A. fuscopurpurea are described but excluded from the section. The origins, morphological differentiations and eco-geographical radiations of Anemone sect. Himalayicae are discussed.
BEGONIA CLADOTRICHA (BEGONIACEAE): A NEW SPECIES FROM LAOS
Authors: HUGHES M.
Published: March 2007

A new species of Begonia (Begoniaceae) is described from Khammouan Province in Laos. The new species, Begonia cladotricha M.Hughes, belongs in Begonia sect. Diploclinium, and is unusual amongst Asian Begonia in having basally branched hairs on all vegetative parts of the plant.
The Development of Social Care Online
Authors: Gwynne-Smith Diane
Published: March 2007

Diane Gwynne-Smith writes about the project, which she managed, to create the most comprehensive and freely available online database of materials on social care. It can be found at: www.scie-socialcareonline.org.uk
Free Legal Databases at IALS Library
Authors: Griffiths Laura
Published: March 2007

Laura Griffiths provides information about the portals or gateways of qualitatively evaluated links to legal information on the internet, including FLAG, INTUTE: Law and eagle-I, and repositories of information produced by IALS and its partners such as FLARE and the Current Legal Research Topics database.
Molecular microbial community structure of the Regenerative Enclosed Life Support Module Simulator air system
Authors: Moissl Christine , Hosoya Naofumi , Bruckner James , Stuecker Tara , Roman Monsi , Venkateswaran Kasthuri
Published: March 2007

The Regenerative Enclosed Life Support Module Simulator (REMS) was designed to simulate the conditions aboard the International Space Station (ISS). This unique terrestrial, encapsulated environment for humans and their associated organisms allowed investigations into the microbial communities within an enclosed habitat system, primarily with respect to diversity, phylogeny and the possible impact on human health. To assess time- and/or condition-dependent changes in microbial diversity within REMS, a total of 27 air samples were collected during three consecutive months. The microbial burden and diversity were elucidated using culture-dependent and culture-independent molecular methods. The results indicate that during controlled conditions the total microbial burden detected by culture-dependent techniques (below a detectable level to 102 cells m−3of air) and intracellular ATP assay was significantly low (102–103 cells m−3of air), but increased during the uncontrolled post-operation phase (∼104 cells m−3of air). Only Gram-positive and α-proteobacteria grew under tested culture conditions, with a predominant occurrence ofMethylobacterium radiotolerans, andSphingomonas yanoikuyae. Direct DNA extraction and 16S rDNA sequencing methodology revealed a broader diversity of microbes present in the REMS air (51 species). Unlike culture-dependent analysis, both Gram-positive and proteobacteria were equally represented, while members of a few proteobaterial groups dominated (Rhodopseudomonas,Sphingomonas,Acidovorax,Ralstonia,Acinetobacter,Pseudomonas, andPsychrobacter). Although the presence of several opportunistic pathogens warrants further investigation, the results demonstrated that routine maintenance such as controlling the humidity, crew’s daily cleaning, and air filtration were effective in reducing the microbial burden in the REMS.
Unexpected consequences of increasing CO2 and ocean acidity on marine production of DMS and CH2ClI: Potential climate impacts
Authors: Wingenter Oliver W. , Haase Karl B. , Zeigler Max , Blake Donald R. , Rowland F. Sherwood , Sive Barkley C. , Paulino Ana , Thyrhaug Runar , Larsen Aud , Schulz Kai , Meyerhöfer Michael , Riebesell Ulf
Published: March 2007

Increasing atmospheric mixing ratios of CO2 have already lowered surface ocean pH by 0.1 units compared to preindustrial values and pH is expected to decrease an additional 0.3 units by the end of this century. Pronounced physiological changes in some phytoplankton have been observed during previous CO2 perturbation experiments. Marine microorganisms are known to consume and produce climate‐relevant organic gases. Concentrations of (CH3)2S (DMS) and CH2ClI were quantified during the Third Pelagic Ecosystem CO2 Enrichment Study. Positive feedbacks were observed between control mesocosms and those simulating future CO2. Dimethyl sulfide was 26% (±10%) greater than the controls in the 2x ambient CO2 treatments, and 18% (±10%) higher in the 3xCO2 mesocosms. For CH2ClI the 2xCO2 treatments were 46% (±4%) greater than the controls and the 3xCO2 mesocosms were 131% (±11%) higher. These processes may help contribute to the homeostasis of the planet.
Water properties and circulation in Arctic Ocean models
Authors: Holloway G. , Dupont F. , Golubeva E. , Häkkinen S. , Hunke E. , Jin M. , Karcher M. , Kauker F. , Maltrud M. , Morales Maqueda M. A. , Maslowski W. , Platov G. , Stark D. , Steele M. , Suzuki T. , Wang J. , Zhang J.
Published: March 2007

As a part of the Arctic Ocean Model Intercomparison Project, results from 10 Arctic ocean/ice models are intercompared over the period 1970 through 1999. Models' monthly mean outputs are laterally integrated over two subdomains (Amerasian and Eurasian basins), then examined as functions of depth and time. Differences in such fields as averaged temperature and salinity arise from models' differences in parameterizations and numerical methods and from different domain sizes, with anomalies that develop at lower latitudes carried into the Arctic. A systematic deficiency is seen as AOMIP models tend to produce thermally stratified upper layers rather than the “cold halocline”, suggesting missing physics perhaps related to vertical mixing or to shelf‐basin exchanges. Flow fields pose a challenge for intercomparison. We introduce topostrophy, the vertical component of V×∇D where V is monthly mean velocity and ∇D is the gradient of total depth, characterizing the tendency to follow topographic slopes. Positive topostrophy expresses a tendency for cyclonic “rim currents”. Systematic differences of models' circulations are found to depend strongly upon assumed roles of unresolved eddies.
Influence of an extended source on goniopolarimetry (or direction finding) with Cassini and Solar Terrestrial Relations Observatory radio receivers
Authors: Cecconi B.
Published: March 2007

In a recent paper, Cecconi and Zarka (2005) provided analytical goniopolarimetric inversions, which allow us to retrieve the direction of arrival of an incoming electromagnetic wave, its flux, and its polarization state, also referred as direction finding inversions, to be used with measurements acquired with a system of electric dipole antennas on a three‐axis stabilized spacecraft such as the Cassini/Radio and Plasma Wave Science/High Frequency Receiver or the Solar Terrestrial Relations Observatory/Waves receivers. In the present study, we establish the expressions of the measurements (autocorrelations and cross correlations) in the case of an extended source. We also analyze the effect of an extended source on the outputs of the analytical inversions presented in the former paper, which are supposing a point radio source. We show that for a source with an angular half width smaller than 5°, the induced biases are not significant.
Computer simulation of nucleation in a gas-saturated liquid
Authors: Protsenko S. P. , Baidakov V. G. , Teterin A. S. , Zhdanov E. R.
Published: March 2007

Molecular dynamics methods have been used to investigate the kinetics of the liquid-gas phase transition in a two-component Lennard-Jones system at negative pressures and elastic stretches of the liquid to values close to spinodal ones. The molecular dynamics system consists of 2048 interacting particles with parameters of the Lennard-Jones potential for argon and neon. Density dependences of pressure and internal energy have been calculated for stable and metastable states of the mixture at a temperature T*≈0.7±0.01 and three values of the concentration. The location of mechanical and the diffusion spinodals has been determined. It has been established that a gas-saturated mixture retains its stability against finite variations of state variables up to stretches close to the values near the diffusion spinodal. The statistic laws of the process of destruction of the metastable state have been investigated. The lifetimes of the metastable phase have been determined. It is shown that owing to the small height of the potential barrier that separates the microheterogeneous from the homogeneous state a system of finite size has a possibility to make the reverse transition from the microheterogeneous into the homogeneous state. The lifetimes of the system in the microheterogeneous state, as well as the expectation times of the occurrence of a critical nucleus, are described by Poissonian distributions.
The effect of oxygen adsorption on Cu{111} thin film growth stresses
Authors: Kennedy J. K. , Friesen C.
Published: March 2007

Thin film stress evolution during physical vapor deposition is highly sensitive to the exact nature of the growth environment. It has been previously observed that during the growth of Cu films, stress evolution is acutely affected by oxygen partial pressure. However, changes in partial pressure imply a number of changes to the growth environment and to the condition of the growth surface. To specifically examine the role of adsorption on growth stresses, in this work we have grown Cu Volmer-Weber films, adsorbed a known quantity of oxygen, and continued growth once ultrahigh vacuum conditions were again achieved. This enabled the study of stress evolution as a function of adsorbate coverage, independent of background pressure. We found that even at low coverages, adsorbed oxygen has a profound impact on stress evolution. Additionally, we found that the adsorbed oxygen is consumed by the growing film over a significant thickness of growth and we have extracted the rate of oxygen consumption. We also observed an epitaxial stress associated with the continued growth of Cu on the underlying strained O-dosed Cu film, and show that the reversible stress is apparently unaffected by the oxygen adsorption step.
Analysis of electron beam induced deposition (EBID) of residual hydrocarbons in electron microscopy
Authors: Rykaczewski Konrad , White William B. , Fedorov Andrei G.
Published: March 2007

In this work we have developed a comprehensive dynamic model of electron beam induced deposition (EBID) of residual hydrocarbon coupling mass transport, electron transport and scattering, and species decomposition to predict the deposition of carbon nanopillars. The simulations predict the local species and electron density distributions, as well as the three-demensional morphology and the growth rate of the deposit. Since the process occurs in a high vacuum environment, surface diffusion is considered as the primary transport mode of surface-adsorbed hydrocarbon precursor. The governing surface transport equation (STE) of the adsorbed species is derived and solved numerically. The transport, scattering, and absorption of primary electron as well as secondary electron generation are treated using the Monte Carlo method. Low energy secondary electrons are the major contributors to hydrocarbon decomposition due to their energy range matching peak dissociation reaction cross section energies for precursor molecules. The deposit and substrate are treated as a continuous entity allowing the simulation of the growth of a realistically sized deposit rather than a large number of cells representing each individual atom as in previously published simulations [Mitsuishi et al., Ultramicroscopy 103, 17 (2005); Silvis-Cividjian, Ph.D. thesis, University of Delft, 2002]. Such formulation allows for simple coupling of the STE with the dynamic growth of the nanopillar. Three different growth regimes occurring in EBID are identified using scaling analysis, and simulations are used to describe the deposit morphology and precursor surface concentration specific for each growth regime.
Brownian dynamics algorithm for entangled wormlike threads
Authors: Ramanathan Shriram , Morse David C.
Published: March 2007

The authors present a hybrid Brownian dynamics/Monte Carlo algorithm for simulating solutions of highly entangled semiflexible polymers or filaments. The algorithm combines a Brownian dynamics time-stepping approach with an efficient scheme for rejecting moves that cause chains to cross or that lead to excluded volume overlaps. The algorithm allows simulation of the limit of infinitely thin but uncrossable threads, and is suitable for simulating the conditions obtained in experiments on solutions of long actin protein filaments.
Simple density functional approach to adsorption of biomolecules on solid surfaces
Authors: Bucior K. , Fischer J. , Patrykiejew A. , Tscheliessnig R. , Sokolowski S.
Published: March 2007

A simple density functional approach for modeling the adsorption of biomolecules is considered. The model comprises a three-component mixture consisting of spherical and differently charged ions and chain molecules. Spherical ions can form associative bonds with selected segments of a chain. To enable the formation of bonds between chain segments and spherical ions, the statistical associating fluid theory is applied. The present theory is used to study the structure of adsorbed layers, the excess adsorption isotherms, and the capacitance of the double layer.
Ellipsometric study of percolation in electroless deposited silver films
Authors: de Vries Anna Jo , Kooij E. Stefan , Wormeester Herbert , Mewe Agnes A. , Poelsema Bene
Published: March 2007

Using spectroscopic ellipsometry in the visible and near-infrared spectral range we investigate the optical properties of a growing silver film starting from predeposited gold nanoparticles. The effective pseudodielectric functions, obtained by direct inversion of the ellipsometry spectra, reveal a surface plasmon resonance for the nanoparticulate films. Upon prolonged electroless silver deposition, the resonance shifts to lower energies. The redshift is due the longer electron mean free path in larger silver structures and is analyzed by describing the optical response of the developing silver film in terms of a Lorentz line shape. The position of the oscillator, i.e., its resonance energy, is discussed in relation to the transition from isolated nanoparticles to an interconnected, eventually continuous metal film. This transition is also observed in the optical conductivity which exhibits an abrupt, stepwise increase at the same energy where the aforementioned resonance energy becomes zero. For longer deposition times, the optical spectra can be described in terms of a Drude-like free-electron metal. The development of the Drude–Lorentz parameters, i.e., the relaxation time and electron density, are compared to values for bulk silver; the latter were obtained from an optical measurement on a thick bulk silver sample. The saturation values for the relaxation time and thus the conductivity amount to approximately 40% of the bulk value, in agreement with direct current conductivity measurements on these films.
Field-effect transistors on molecular beam epitaxy GaP
Authors: Chen A. , Woodall J. M.
Published: March 2007

Field-effect transistors (FETs) were fabricated on epitaxial GaP grown using molecular beam epitaxy. Both metal-semiconductor junctions and p-n junctions were tested as gate structures for metal-semiconductor FET and junction FET, respectively. The fabricated FETs demonstrate typical transistor characteristics with low gate leakage that is desirable for low-noise applications. The measured device characteristics match the theoretical expectation based on the material properties of epitaxial GaP and suggest directions for improvement.
Photon-induced conduction modulation in SiO2 thin films embedded with Ge nanocrystals
Authors: Ding L. , Chen T. P. , Yang M. , Wong J. I. , Liu Y. , Yu S. F. , Zhu F. R. , Tan M. C. , Fung S. , Tung C. H. , Trigg A. D.
Published: March 2007

The authors report the photon-induced conduction modulation in SiO2 thin films embedded with germanium nanocrystals (nc-Ge). The conduction of the oxide could be switched to a higher- or lower-conductance state by a ultraviolet (UV) illumination. The conduction modulation is caused by charging and discharging in the nc-Ge due to the UV illumination. If the charging process is dominant, the oxide conductance is reduced; however, if the discharging process is dominant, the oxide conductance is increased. As the conduction can be modulated by UV illumination, it could have potential applications in silicon-based optical memory devices.
From spinel Mn3O4 to layered nanoarchitectures using electrochemical cycling and the distinctive pseudocapacitive behavior
Authors: Dai Yang , Wang Ke , Xie Jingying
Published: March 2007

In this letter the authors show the structure transformation from distorted spinel Mn3O4 to layered structure birnessite by cyclic voltammetry (CV) cycling in aqueous Na2SO4 using the high temperature (900°C) treated manganese oxide film as the electrode. The process is a dynamic-potential activated procedure, which causes the formation of sheet-shaped nanoarchitectures. During the cycling process, the specific capacitance of manganese oxide increases by more than 20 times, and the resulting film after 1000 CV cycles shows good power capability.
Understanding of the excess channel noise in InAlAs∕InGaAs∕InP high electron mobility transistors in impact ionization regime
Authors: Wang Hong , Liu Yuwei , Zeng Rong , Tan Chee Leong
Published: March 2007

The characterization and analysis of high frequency noise of InP-based high electron mobility transistors in the impact ionization regime reveal that different physical mechanisms are responsible for the excess channel noise at different frequency ranges. The excess noise at frequencies below 10GHz is mainly due to the hole recombination in the channel. However, excess channel noise at higher frequencies could be dominated by the fluctuation of impact ionization which has a much smaller time constant and therefore a much higher cutoff frequency.
First-order conformation transition of single poly(2-vinylpyridine) molecules in aqueous solutions
Authors: Wang Shengqin , Zhao Jiang
Published: March 2007

By measuring diffusion rate, the conformation change of single poly(2-vinylpyridine) chain in aqueous solution was studied by fluorescence correlation spectroscopy. The data showed a stepwise change of hydrodynamic radius when pH value was tuned, reflecting a sign of first-order conformation transition, and a continuous change was found at varying salt concentration.
Solar influence on climate during the past millennium: Results from transient simulations with the NCAR Climate System Model
Authors: Ammann Caspar M. , Joos Fortunat , Schimel David S. , Otto-Bliesner Bette L. , Tomas Robert A.
Published: March 2007

The potential role of solar variations in modulating recent climate has been debated for many decades and recent papers suggest that solar forcing may be less than previously believed. Because solar variability before the satellite period must be scaled from proxy data, large uncertainty exists about phase and magnitude of the forcing. We used a coupled climate system model to determine whether proxy-based irradiance series are capable of inducing climatic variations that resemble variations found in climate reconstructions, and if part of the previously estimated large range of past solar irradiance changes could be excluded. Transient simulations, covering the published range of solar irradiance estimates, were integrated from 850 AD to the present. Solar forcing as well as volcanic and anthropogenic forcing are detectable in the model results despite internal variability. The resulting climates are generally consistent with temperature reconstructions. Smaller, rather than larger, long-term trends in solar irradiance appear more plausible and produced modeled climates in better agreement with the range of Northern Hemisphere temperature proxy records both with respect to phase and magnitude. Despite the direct response of the model to solar forcing, even large solar irradiance change combined with realistic volcanic forcing over past centuries could not explain the late 20th century warming without inclusion of greenhouse gas forcing. Although solar and volcanic effects appear to dominate most of the slow climate variations within the past thousand years, the impacts of greenhouse gases have dominated since the second half of the last century.
Modeling sporadic loss of heterozygosity in mice by using mosaic analysis with double markers (MADM)
Authors: Muzumdar Mandar Deepak , Luo Liqun , Zong Hui
Published: March 2007

The initiation and progression of many human cancers involve either somatic activation of protooncogenes or inactivation of tumor-suppressor genes (TSGs) in sporadic cells. Although sporadic gain-of-function of protooncogenes has been successfully modeled in mice [e.g., Johnson L, Mercer K, Greenbaum D, Bronson RT, Crowley D, Tuveson DA, Jacks T (2001)
Nature
410:1111–1116], generating a similar degree of sparseness of TSG loss-of-function remains a challenge. Here, we use mosaic analysis with double markers (MADM) to achieve TSG inactivation and concurrent labeling in sporadic somatic cells of mice, closely mimicking loss of heterozygosity as occurs in human cancers. As proof of principle, we studied the consequence of sporadic loss of p27kip1, a cyclin-dependent kinase inhibitor. MADM-mediated loss of p27kip1 results in mutant cell expansion markedly greater than that observed in conventional
p27kip1
knockouts. Moreover, the direct comparison of WT and mutant cells at single-cell resolution afforded by MADM reveals that p27kip1 regulates organ size
in vivo
by cell-autonomous control of cell cycle exit timing. These studies establish MADM as a high-resolution method for modeling sporadic loss of heterozygosity in mice, providing insights into TSG function.
Intranasal immunization with heterologously expressed polysaccharide protects against multiple
Pseudomonas aeruginosa
infections
Authors: DiGiandomenico Antonio , Rao Jayasimha , Harcher Katie , Zaidi Tanweer S. , Gardner Jason , Neely Alice N. , Pier Gerald B. , Goldberg Joanna B.
Published: March 2007

Surface-expressed bacterial polysaccharides are often immunodominant, protective antigens. However, these antigens are chemically and serologically highly heterogeneous, and conjugation to protein carriers is often necessary to enhance their immunogenicity. Here we show the efficacy of intranasal immunization of mice with attenuated
Salmonella enterica
serovar Typhimurium expressing the O antigen portion of
Pseudomonas aeruginosa
lipopolysaccharide.
P. aeruginosa
is an ideal model system because it can cause a myriad of localized and systemic infections. In particular, this bacterium is a leading cause of hospital-acquired pneumonia and is responsible for infections after burns and after eye injury. In addition, there are mouse models of infection that mimic the clinical manifestations of
P. aeruginosa
infections. Immunized mice were highly protected against infection, with long-lasting immunity to acute
P. aeruginosa
pneumonia, whereas mice immunized with
Salmonella
containing only the cloning vector or PBS were not. Prophylactic and therapeutic administration of sera from vaccinated animals protected naive mice. Intranasal vaccination also provided complete protection from infections after burns and reduced pathology after corneal abrasions. These results indicate that intranasal delivery of heterologously expressed polysaccharide antigens provides protection at distinct sites of infection. This approach for the expression and delivery of polysaccharide antigens as recombinant immunogens could be easily adapted to develop vaccines for many infectious agents, without the need for complicated purification and conjugation procedures.
Structure and function of a hexameric copper-containing nitrite reductase
Authors: Nojiri Masaki , Xie Yong , Inoue Tsuyoshi , Yamamoto Takahiko , Matsumura Hiroyoshi , Kataoka Kunishige , Deligeer  , Yamaguchi Kazuya , Kai Yasushi , Suzuki Shinnichiro
Published: March 2007

Dissimilatory nitrite reductase (NIR) is a key enzyme in denitrification, catalyzing the first step that leads to gaseous products (NO, N
2
O, and N
2
). We have determined the crystal structure of a Cu-containing NIR from a methylotrophic denitrifying bacterium,
Hyphomicrobium denitrificans
, at 2.2-Å resolution. The overall structure of this
H. denitrificans
NIR reveals a trigonal prism-shaped molecule in which a monomer consisting of 447 residues and three Cu atoms is organized into a unique hexamer (i.e., a tightly associated dimer of trimers). Each monomer is composed of an N-terminal region containing a Greek key β-barrel folding domain, cupredoxin domain I, and a C-terminal region containing cupredoxin domains II and III. Both cupredoxin domains I and II bind one type 1 Cu and are combined with a long loop comprising 31 amino acid residues. The type 2 Cu is ligated at the interface between domain II of one monomer and domain III of an adjacent monomer. Between the two trimeric C-terminal regions are three interfaces formed by an interaction between the domains I, and the type 1 Cu in the domain is required for dimerization of the trimer. The type 1 Cu in domain II functions as an electron acceptor from an electron donor protein and then transfers an electron to the type 2 Cu, binding the substrate to reduce nitrite to NO. The discussion of the intermolecular electron transfer process from cytochrome
c
550
to the
H. denitrificans
NIR is based on x-ray crystallographic and kinetic results.
High-throughput synergy screening identifies microbial metabolites as combination agents for the treatment of fungal infections
Authors: Zhang Lixin , Yan Kezhi , Zhang Yu , Huang Ren , Bian Jiang , Zheng Chuansen , Sun Haixiang , Chen Zhihui , Sun Nuo , An Rong , Min Fangui , Zhao Weibo , Zhuo Ying , You Jianlan , Song Yongjie , Yu Zhenyan , Liu Zhiheng , Yang Keqian , Gao Hong , Dai Huanqin , Zhang Xiaoli , Wang Jian , Fu Chengzhang , Pei Gang , Liu Jintao , Zhang Si , Goodfellow Michael , Jiang Yuanying , Kuai Jun , Zhou Guochun , Chen Xiaoping
Published: March 2007

The high mortality rate of immunocompromised patients with fungal infections and the limited availability of highly efficacious and safe agents demand the development of new antifungal therapeutics. To rapidly discover such agents, we developed a high-throughput synergy screening (HTSS) strategy for novel microbial natural products. Specifically, a microbial natural product library was screened for hits that synergize the effect of a low dosage of ketoconazole (KTC) that alone shows little detectable fungicidal activity. Through screening of ≈20,000 microbial extracts, 12 hits were identified with broad-spectrum antifungal activity. Seven of them showed little cytotoxicity against human hepatoma cells. Fractionation of the active extracts revealed beauvericin (BEA) as the most potent component, because it dramatically synergized KTC activity against diverse fungal pathogens by a checkerboard assay. Significantly, in our immunocompromised mouse model, combinations of BEA (0.5 mg/kg) and KTC (0.5 mg/kg) prolonged survival of the host infected with
Candida parapsilosis
and reduced fungal colony counts in animal organs including kidneys, lungs, and brains. Such an effect was not achieved even with the high dose of 50 mg/kg KTC. These data support synergism between BEA and KTC and thereby a prospective strategy for antifungal therapy.
The metabolic signature related to high plant growth rate in
Arabidopsis thaliana
Authors: Meyer Rhonda C. , Steinfath Matthias , Lisec Jan , Becher Martina , Witucka-Wall Hanna , Törjék Ottó , Fiehn Oliver , Eckardt Änne , Willmitzer Lothar , Selbig Joachim , Altmann Thomas
Published: March 2007

The decline of available fossil fuel reserves has triggered world-wide efforts to develop alternative energy sources based on plant biomass. Detailed knowledge of the relations of metabolism and biomass accumulation can be expected to yield powerful novel tools to accelerate and enhance energy plant breeding programs. We used metabolic profiling in the model
Arabidopsis
to study the relation between biomass and metabolic composition using a recombinant inbred line (RIL) population. A highly significant canonical correlation (0.73) was observed, revealing a close link between biomass and a specific combination of metabolites. Dividing the entire data set into training and test sets resulted in a median correlation between predicted and true biomass of 0.58. The demonstrated high predictive power of metabolic composition for biomass features this composite measure as an excellent biomarker and opens new opportunities to enhance plant breeding specifically in the context of renewable resources.
Retaliatory mafia behavior by a parasitic cowbird favors host acceptance of parasitic eggs
Authors: Hoover Jeffrey P. , Robinson Scott K.
Published: March 2007

Why do many hosts accept costly avian brood parasitism even when parasitic eggs and nestlings differ dramatically in appearance from their own? Scientists argue that evolutionary lag or equilibrium can explain this evolutionary enigma. Few, however, consider the potential of parasitic birds to enforce acceptance by destroying eggs or nestlings of hosts that eject parasitic eggs and thereby reject parasitism. This retaliatory “mafia” behavior has been reported in one species of parasitic cuckoo but never in parasitic cowbirds. Here we present experimental evidence of mafia behavior in the brown-headed cowbird (Molothrus ater), a widely distributed North American brood parasite. We manipulated ejection of cowbird eggs and cowbird access to predator-proof nests in a common host to test experimentally for mafia behavior. When cowbird access was allowed, 56% of “ejector” nests were depredated compared with only 6% of “accepter” nests. No nests were destroyed when cowbird access was always denied or when access was denied after we removed cowbird eggs, indicating that cowbirds were responsible. Nonparasitized nests were depredated at an intermediate rate (20%) when cowbirds were allowed access, suggesting that cowbirds may occasionally “farm” hosts to create additional opportunities for parasitism. Cowbirds parasitized most (85%) renests of the hosts whose nests were depredated. Ejector nests produced 60% fewer host offspring than accepter nests because of the predatory behavior attributed to cowbirds. Widespread predatory behaviors in cowbirds could slow the evolution of rejection behaviors and further threaten populations of some of the >100 species of regular cowbird hosts.
Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages
Authors: Timmons James A. , Wennmalm Kristian , Larsson Ola , Walden Tomas B. , Lassmann Timo , Petrovic Natasa , Hamilton D. Lee , Gimeno Ruth E. , Wahlestedt Claes , Baar Keith , Nedergaard Jan , Cannon Barbara
Published: March 2007

Attainment of a brown adipocyte cell phenotype in white adipocytes, with their abundant mitochondria and increased energy expenditure potential, is a legitimate strategy for combating obesity. The unique transcriptional regulators of the primary brown adipocyte phenotype are unknown, limiting our ability to promote brown adipogenesis over white. In the present work, we used microarray analysis strategies to study primary preadipocytes, and we made the striking discovery that brown preadipocytes demonstrate a myogenic transcriptional signature, whereas both brown and white primary preadipocytes demonstrate signatures distinct from those found in immortalized adipogenic models. We found a plausible SIRT1-related transcriptional signature during brown adipocyte differentiation that may contribute to silencing the myogenic signature. In contrast to brown preadipocytes or skeletal muscle cells, white preadipocytes express Tcf21, a transcription factor that has been shown to suppress myogenesis and nuclear receptor activity. In addition, we identified a number of developmental genes that are differentially expressed between brown and white preadipocytes and that have recently been implicated in human obesity. The interlinkage between the myocyte and the brown preadipocyte confirms the distinct origin for brown versus white adipose tissue and also represents a plausible explanation as to why brown adipocytes ultimately specialize in lipid catabolism rather than storage, much like oxidative skeletal muscle tissue.
Usherin is required for maintenance of retinal photoreceptors and normal development of cochlear hair cells
Authors: Liu Xiaoqing , Bulgakov Oleg V. , Darrow Keith N. , Pawlyk Basil , Adamian Michael , Liberman M. Charles , Li Tiansen
Published: March 2007

Usher syndrome type IIA (USH2A), characterized by progressive photoreceptor degeneration and congenital moderate hearing loss, is the most common subtype of Usher syndrome. In this article, we show that the USH2A protein, also known as usherin, is an exceptionally large (≈600-kDa) matrix protein expressed specifically in retinal photoreceptors and developing cochlear hair cells. In mammalian photoreceptors, usherin is localized to a spatially restricted membrane microdomain at the apical inner segment recess that wraps around the connecting cilia, corresponding to the periciliary ridge complex described for amphibian photoreceptors. In sensory hair cells of the cochlea, it is associated transiently with the hair bundles during postnatal development. Targeted disruption of the
Ush2a
gene in mice leads to progressive photoreceptor degeneration and a moderate but nonprogressive hearing impairment, mimicking the visual and hearing deficits in USH2A patients. These data suggest that usherin is required for the long-term maintenance of retinal photoreceptors and for the development of cochlear hair cells. We propose a model in which usherin in photoreceptors is tethered via its C terminus to the plasma membrane and its large extracellular domain projecting into the periciliary matrix, where they may interact with the connecting cilium to fulfill important structural or signaling roles.
Importance of culturing primary lymphocytes at physiological oxygen levels
Authors: Atkuri Kondala R. , Herzenberg Leonard A. , Niemi Anna-Kaisa , Cowan Tina , Herzenberg Leonore A.
Published: March 2007

Although studies with primary lymphocytes are almost always conducted in CO
2
incubators maintained at atmospheric oxygen levels (atmosO
2
; 20%), the physiological oxygen levels (physO
2
; 5%) that cells encounter
in vivo
are 2–4 times lower. We show here that culturing primary T cells at atmosO
2
significantly alters the intracellular redox state (decreases intracellular glutathione, increases oxidized intracellular glutathione), whereas culturing at physO
2
maintains the intracellular redox environment (intracellular glutathione/oxidized intracellular glutathione) close to its
in vivo
status. Furthermore, we show that CD3/CD28-induced T cell proliferation (based on proliferation index and cell yield) is higher at atmosO
2
than at physO
2
. This apparently paradoxical finding, we suggest, may be explained by two additional findings with CD3/CD28-stimulated T cells: (
i
) the intracellular NO (iNO) levels are higher at physO
2
than at atmosO
2
; and (
ii
) the peak expression of CD69 is significantly delayed and more sustained at physO
2
that at atmosO
2
. Because high levels of intracellular NO and sustained CD69 tend to down-regulate T cell responses
in vivo
, the lower proliferative T cell responses at physO
2
likely reflect the
in vitro
operation of the natural
in vivo
regulatory mechanisms. Thus, we suggest caution in culturing primary lymphocytes at atmosO
2
because the requisite adaptation to nonphysiological oxygen levels may seriously skew T cell responses, particularly after several days in culture.
Studies of nucleotide binding to the catalytic sites of
Escherichia coli
βY331W-F
1
-ATPase using fluorescence quenching
Authors: Bulygin Vladimir V. , Milgrom Yakov M.
Published: March 2007

Most studies of nucleotide binding to catalytic sites of
Escherichia coli
βY331W-F
1
-ATPase by the quenching of the βY331W fluorescence have been conducted in the presence of ≈20 mM sulfate. We find that, in the absence of sulfate, the nucleotide concentration dependence of fluorescence quenching induced by ADP, ATP, and MgADP is biphasic, revealing two classes of binding sites, each contributing about equally to the overall extent of quenching. For the high-affinity catalytic site, the
K
d
values for MgADP, ADP, and ATP equal 10, 43, and 185 nM, respectively. For the second class of sites, the
K
d
values for these ligands are ≈1,000× larger at 8.1, 37, and 200 μM, respectively. The presence of sulfate or phosphate during assay results in a marked increase in the apparent
K
d
values for the high-affinity catalytic site. The results show, contrary to earlier reports, that Mg
2+
is not required for expression of different affinities for a nucleotide by the three catalytic sites. In addition, they demonstrate that the fluorescence of the introduced tryptophans is nearly completely quenched when only two sites bind nucleotide. Binding of ADP to the third site with a
K
d
near mM gives little fluorescence change. Many previous results of fluorescence quenching of introduced tryptophans appear to require reinterpretation. Our findings support a bi-site catalytic mechanism for F
1
-ATPase.
Dose-dependent cross-talk between the transforming growth factor-β and interleukin-1 signaling pathways
Authors: Lu Tao , Tian Liping , Han Yulong , Vogelbaum Michael , Stark George R.
Published: March 2007

Some tumor cell lines secrete high concentrations of TGFβ or IL-1. Similarly high concentrations of each of these cytokines cross-activate the other pathway: TGFβ activates NFκB, and IL-1β activates Smads. The IL-1 signaling components IRAK, MyD88, TRAF6, and TAK1 are all required for cross-activation of NFκB by TGFβ. Knockdown experiments revealed that both TGFβ receptor subunits are required for IL-1β to activate Smads, and the IL-1 receptor is required for TGFβ to activate NFκB. Coimmunoprecipitations showed that either TGFβ or IL-1β stimulate ligand-dependent association of all three receptor subunits. Furthermore, cross-talk between the TGFβ and IL-1 signaling pathways leads to dose-dependent cross-control of gene expression. These interactions provide new insight into biological responses to IL-1 and TGFβ in the proximity of tumors that secrete high concentrations of these factors and probably also at sites of inflammation, where the local concentrations of these cytokines are likely to be high.
MRI detection of glycogen
in vivo
by using chemical exchange saturation transfer imaging (glycoCEST)
Authors: van Zijl Peter C. M. , Jones Craig K. , Ren Jimin , Malloy Craig R. , Sherry A. Dean
Published: March 2007

Detection of glycogen
in vivo
would have utility in the study of normal physiology and many disorders. Presently, the only magnetic resonance (MR) method available to study glycogen metabolism
in vivo
is
13
C MR spectroscopy, but this technology is not routinely available on standard clinical scanners. Here, we show that glycogen can be detected indirectly through the water signal by using selective radio frequency (RF) saturation of the hydroxyl protons in the 0.5- to 1.5-ppm frequency range downfield from water. The resulting saturated spins are rapidly transferred to water protons via chemical exchange, leading to partial saturation of the water signal, a process now known as chemical exchange saturation transfer. This effect is demonstrated in glycogen phantoms at magnetic field strengths of 4.7 and 9.4 T, showing improved detection at higher field in adherence with MR exchange theory. Difference images obtained during RF irradiation at 1.0 ppm upfield and downfield of the water signal showed that glycogen metabolism could be followed in isolated, perfused mouse livers at 4.7 T before and after administration of glucagon. Glycogen breakdown was confirmed by measuring effluent glucose and, in separate experiments, by
13
C NMR spectroscopy. This approach opens the way to image the distribution of tissue glycogen
in vivo
and to monitor its metabolism rapidly and noninvasively with MRI.
Modulation of
Drosophila
male behavioral choice
Authors: Certel Sarah J. , Savella Mary Grace , Schlegel Dana C. F. , Kravitz Edward A.
Published: March 2007

The reproductive and defensive behaviors that are initiated in response to specific sensory cues can provide insight into how choices are made between different social behaviors. We manipulated both the activity and sex of a subset of neurons and found significant changes in male social behavior. Results from aggression assays indicate that the neuromodulator octopamine (OCT) is necessary for
Drosophila
males to coordinate sensory cue information presented by a second male and respond with the appropriate behavior: aggression rather than courtship. In competitive male courtship assays, males with no OCT or with low OCT levels do not adapt to changing sensory cues and court both males and females. We identified a small subset of neurons in the suboesophageal ganglion region of the adult male brain that coexpress OCT and male forms of the neural sex determination factor, Fruitless (Fru
M
). A single Fru
M
-positive OCT neuron sends extensive bilateral arborizations to the suboesophageal ganglion, the lateral accessory lobe, and possibly the posterior antennal lobe, suggesting a mechanism for integrating multiple sensory modalities. Furthermore, eliminating the expression of Fru
M
by
transformer
expression in OCT/tyramine neurons changes the aggression versus courtship response behavior. These results provide insight into how complex social behaviors are coordinated in the nervous system and suggest a role for neuromodulators in the functioning of male-specific circuitry relating to behavioral choice.
Exo70p mediates the secretion of specific exocytic vesicles at early stages of the cell cycle for polarized cell growth
Authors: He Bing , Xi Fengong , Zhang Jian , TerBush Daniel , Zhang Xiaoyu , Guo Wei
Published: March 2007

In budding yeast, two classes of post-Golgi secretory vesicles carrying different sets of cargoes typified by Bgl2p and invertase are delivered to the plasma membrane for secretion. The exocyst is implicated in tethering these vesicles to the daughter cell membrane for exocytosis. In this study, we report that mutations in the exocyst component Exo70p predominantly block secretion of the Bgl2p vesicles. Furthermore, a defect in invertase vesicle trafficking caused by vps1Δ or pep12Δ in the exo70 mutant background is detrimental to the cell. The secretion defect in exo70 mutants was most pronounced during the early budding stage, which affected daughter cell growth. The selective secretion block does not occur at the vesicle formation or sorting stage because the exocytic vesicles are properly generated and protein processing is normal in the exo70 mutants. Our study suggests that Exo70p functions primarily at early stages of the cell cycle in Bgl2p vesicle secretion, which is critical for polarized cell growth.