bluuebunny/crossref_metadata_2025 huggingface dataset:
Schottky-quantum dot photovoltaics for efficient infrared power conversion
Authors: Johnston Keith W. , Pattantyus-Abraham Andras G. , Clifford Jason P. , Myrskog Stefan H. , MacNeil Dean D. , Levina Larissa , Sargent Edward H.
Published: April 2008

Planar Schottky photovoltaic devices were prepared from solution-processed PbS nanocrystal quantum dot films with aluminum and indium tin oxide contacts. These devices exhibited up to 4.2% infrared power conversion efficiency, which is a threefold improvement over previous results. Solar power conversion efficiency reached 1.8%. The simple, optimized architecture allows for direct implementation in multijunction photovoltaic device configurations.
Effective passivation of slow interface states at the interface of single crystalline Gd2O3 and Si(100)
Authors: Sun Qing-Qing , Laha Apurba , Ding Shi-Jin , Zhang David Wei , Osten H. Jörg , Fissel A.
Published: April 2008

The as-grown single crystalline Gd2O3 thin film on Si(100) substrate suffers from flatband voltage instability and large hysteresis which are possibly due to the intrinsic dangling bonds induced by the existing binding mismatch at the Gd2O3∕Si(100) interface. The instability of flatband voltage and hysteresis of Pt∕Gd2O3∕Si and W∕Gd2O3∕Si structures can be fully eliminated by the introduction of traditional forming gas annealing with proper process optimization. Both optimized metal-oxide-semiconductor structures show negligible hysteresis with the interface state at the magnitude order of 1011∕cm2eV at the midgap of silicon and can be considered for the future of complementary metal oxide semiconductor devices.
Electron heating and huge positive magnetoresistance in an AlGaAs∕GaAs high electron mobility transistor structure at high temperatures
Authors: Liang C.-T. , Li Yu-Ru , Lin Li-Hung , Lin Po-Tsun , Yang Chun-Kai , Tseng Yen Shung , Chen Kuang Yao , Cooper N. R. , Simmons M. Y. , Ritchie D. A.
Published: April 2008

We have performed magnetoresistivity measurements ρxx(B) on an AlGaAs∕GaAs high electron mobility transistor (HEMT) structure at high temperatures T. The observed positive magnetoresistance (MR) in the HEMT structure can be greatly enhanced simply by increasing the driving current. At T=80K and B=6T, the MR value can be increased from ∼150% to 4000%, almost a 30-fold increase when a large current of 40μA is applied. Such results are due to electron heating effects and our data lay the foundation for practical magnetic device applications which can be readily combined with high-speed electronics, high-frequency amplifiers, and radar using the mature GaAs-based HEMT technology.
Composition dependence of the hole mobility in GaSbxAs1−x
Authors: Alberi K. , Dubon O. D. , Walukiewicz W. , Yu K. M. , Gupta J. A. , Baribeau J.-M.
Published: April 2008

The unusually low hole mobility observed in heavily p-type doped dilute GaSbxAs1−x alloys is explained in the context of the valence band anticrossing model. The anticrossing interaction between the localized p-states of the Sb atoms and the extended states of the GaAs host leads to a significant reconfiguration of the valence band structure and results in a greatly enhanced scattering of holes by state broadening effects in As-rich alloys. These results suggest that the mobility drop is fundamental in nature and indicate that the valence band anticrossing model is capable of describing the electronic transport properties of highly mismatched alloys.
Integer charge transfer at the tetrakis(dimethylamino)ethylene/Au interface
Authors: Lindell Linda , Unge Mikael , Osikowicz Wojciech , Stafström Sven , Salaneck William R. , Crispin Xavier , de Jong Michel P.
Published: April 2008

In organic-based electronics, interfacial properties have a profound impact on device performance. The lineup of energy levels is usually dependent on interface dipoles, which may arise from charge transfer reactions. In many applications, metal-organic junctions are prepared under ambient conditions, where direct overlap of the organic π system from the metal bands is prevented due to presence of oxides and/or hydrocarbons. We present direct experimental and theoretical evidence showing that the interface energetic for such systems is governed by exchange of an integer amount of electrons.
Atomically flat single-terminated SrTiO3 (111) surface
Authors: Chang Jaewan , Park Yoon-Seok , Kim Sang-Koog
Published: April 2008

The authors have reproducibly obtained an atomically well-defined SrTiO3 (111) surface by a combined chemical etching and thermal annealing process. Although thermodynamic mixed termination is preferred as a means of suppressing the surface dipole, the kinetics-driven etching process, via selective etching of SrO34−, enables a single-terminated surface to be obtained. Subsequent O2 annealing of the etched surface produces a clear step-and-terrace structure. Atomically flat terraces and only one-unit-cell-high step edges are observed, signifying a single-terminated surface. This study might pave the way for constructing (111)-oriented perovskite oxide superlattices, which would be expected to demonstrate new and better physical phenomena and functionalities.
Low-loss terahertz transmission through curved metallic slit waveguides fabricated by spark erosion
Authors: Wächter Markus , Nagel Michael , Kurz Heinrich
Published: April 2008

Propagation characteristics of broadband terahertz pulses in straight and curved metallic slit (MS) waveguides fabricated using spark erosion technique are investigated in the 0.1–1.0THz frequency range. As the straight MS waveguides, the curved MS waveguides, having radii of curvature as small as 5mm, exhibit comparably undistorted terahertz pulse transmission. The observed bending loss is unexpectedly low, giving rise to the assumption that surface oxidization and roughness generated by the fabrication process are responsible for the improved signal routing behavior. Experimental results are compared with theoretical data from numerical field simulations incorporating the influence of a thin dielectric cover layer.
Exciton decay dynamics in individual carbon nanotubes at room temperature
Authors: Gokus Tobias , Hartschuh Achim , Harutyunyan Hayk , Allegrini Maria , Hennrich Frank , Kappes Manfred , Green Alexander A. , Hersam Mark C. , Araújo Paulo T. , Jorio Ado
Published: April 2008

We studied the exciton decay dynamics of individual semiconducting single-walled carbon nanotubes at room temperature using time-resolved photoluminescence spectroscopy. The photoluminescence decay from nanotubes of the same (n,m) type follows a single exponential decay function, however, with lifetimes varying between about 1 and 40ps from nanotube to nanotube. A correlation between broad photoluminescence spectra and short lifetimes was found and explained by defects promoting both nonradiative decay and vibronic dephasing.
Effects of cation size on infiltration and defiltration pressures of a MCM-41
Authors: Han Aijie , Punyamurtula Venkata K. , Qiao Yu
Published: April 2008

With the nanopore structure, ionic charge, solvent, and testing condition being kept the same, the cation size effects on liquid motion in a MCM-41 are investigated by using chloride salts. As the cation becomes larger, both infiltration and defiltration pressures decrease. The variation in infiltration pressure is more pronounced.
Defect structure of highly Zn-doped LiNbO3 single crystal revealed by extended x-ray absorption spectra
Authors: Tsai P.-C. , Sun M.-L. , Chia C.-T. , Lu H.-F. , Lin S.-H. , Hu M.-L. , Lee J.-F.
Published: April 2008

To determine the defect structure of ZnO-doped LiNbO3 single crystals with high doping concentrations, we obtain the measurements using the extended x-ray absorption fine structure (EXAFS) at room temperature. It indicates Zn atom is directly substituted on the Li site of the LiNbO3 crystal after Zn doping. EXAFS simulation by way of analyzing the scattering amplitudes also shows that the Zn atom does not substitute the Nb site at highly Zn-doped LiNbO3. Finally, we confirm that VNb5−, a strong charged vacancy, should be considered as an important factors in influencing the physical properties of LiNbO3 beyond 7.5mol% Zn-doped doping concentration.
The evidence of the glassy behavior in the layered cobaltites
Authors: Ang R. , Sun Y. P. , Luo X. , Hao C. Y. , Zhu X. B. , Song W. H.
Published: April 2008

In this letter, we demonstrate that the origin of the glassy behavior in the phase-separated layered cobaltites cannot be simply ascribed to intercluster interactions as the phase-separated manganites can. Instead, our result indicates that both the intercluster interactions and a spin glass phase contribute to the glassy behaviors. Thus, this study distinguishes the picture of phase separation between cobaltites and manganites. We also observe training effect of the exchange bias, which can be interpreted by a spin configurational relaxation model.
Long-range surface plasmon polaritons on asymmetric double-electrode structures
Authors: Joo Yang Hyun , Jung Myoung Jin , Yoon Jaewoong , Song Seok Ho , Won Hyong Sik , Park Suntak , Ju Jung Jin
Published: April 2008

An asymmetric double-electrode structure composed of metal strips separated by a dielectric core layer, all on a metal slab, is proposed as a long-range surface plasmon-polariton (LR-SPP) waveguide. LR-SPP modes on asymmetric structures, including straight, S-bended, and Y-branched strips, are found by far-field measurement to be consistent with theoretical estimates. The proposed structure is inherently free from a symmetry requirement on dielectric constants between the core and cladding materials, therefore, an asymmetric double-electrode waveguide which substitutes a nonlinear medium or biofluid for the core dielectric may be essential to realization of SPP nonlinear devices or biosensors in a long-range manner.
Growth of high-uniformity InAs∕GaAs quantum dots with ultralow density below 107cm−2 and emission above 1.3μm
Authors: Guimard Denis , Lee Hearin , Nishioka Masao , Arakawa Yasuhiko
Published: April 2008

We report the growth of high-uniformity large coherent InAs∕GaAs quantum dots (QDs) by metal organic chemical vapor deposition, with density between 106 and 1010cm−2, emission close to 1.4μm at room temperature with only GaAs capping, and temperature-independent peak linewidth as low as 14meV. It is shown that the QD density can be controlled by the InAs coverage, while the QD size remains remarkably constant. The observed decrease of the emission wavelength with coverage is explained by a density-dependent alloying. Microphotoluminescence measurement was performed on bare samples at 5K and single dot emission was observed.
Improvement of orientation of planar cholesteric liquid crystal by rapid thermal processing
Authors: Ozaki Ryotaro , Shinpo Toshikazu , Moritake Hiroshi
Published: April 2008

We demonstrate the improvement of the orientation of a planar cholesteric liquid crystal (CLC) by rapid thermal processing. Rapid thermal annealing and cooling reduce the number of orientation defects in the planar CLC. The annealing temperature strongly affects the number of treatment cycles required for improved orientation and the effective annealing temperature range is very narrow. In a treated cell, scattering is reduced and sharp band edges appear in the transmission spectrum. The proposed method is applicable to chiral dopants having various thermal properties. Through this method, a uniform planar CLC cell with a thickness greater than 100μm is achieved.
Intraband emission at λ≈1.48μm from GaN∕AlN quantum dots at room temperature
Authors: Nevou L. , Julien F. H. , Tchernycheva M. , Guillot F. , Monroy E. , Sarigiannidou E.
Published: April 2008

We report on the intraband emission at room temperature from GaN∕AlN quantum dots grown by plasma-assisted molecular-beam epitaxy. The dots exhibit TM-polarized absorption ascribed to the intraband transition from the s to the pz shells. The pz-s intraband luminescence is observed at λ=1.48μm under optical excitation at λ=1.34μm perpendicular to the [0001] growth axis. The population of the pz state arises from Raman scattering by GaN A1 longitudinal optical phonons. Based on the emission spectral shape, we estimate that the homogeneous linewidth of the s-pz intraband transition is less than 4meV.
Unpinning of the Fermi level and tunneling in metal oxide semiconductors
Authors: Malagù C. , Martinelli G. , Ponce M. A. , Aldao C. M.
Published: April 2008

The widely accepted expression for conductance in polycrystalline metal oxides cannot take into account of the observed decrease in conductance of nanostructured materials with respect to their larger counterpart. We provide here an explanation for this phenomenon suggesting that tunneling through the Schottky barrier has a comparable importance to thermionic crossing in ruling the electron transport in these materials.
Enhanced light emission in photonic crystal nanocavities with Erbium-doped silicon nanocrystals
Authors: Makarova Maria , Sih Vanessa , Warga Joe , Li Rui , Dal Negro Luca , Vuckovic Jelena
Published: April 2008

Photonic crystal nanocavities are fabricated in silicon membranes covered by thermally annealed silicon-rich nitride films with Erbium-doped silicon nanocrystals. Silicon nitride films were deposited by sputtering on top of silicon on insulator wafers. The nanocavities were carefully designed in order to enhance emission from the nanocrystal sensitized Erbium at the 1540nm wavelength. Experimentally measured quality factors of ∼6000 were found to be consistent theoretical predictions. The Purcell factor of 1.4 was estimated from the observed 20-fold enhancement of Erbium luminescence.
Control of the perpendicular magnetic anisotropy of FePd films via Pd capping deposition
Authors: Clavero C. , Skuza J. R. , Choi Y. , Haskel D. , García-Martín J. M. , Cebollada A. , Lukaszew R. A.
Published: April 2008

We have investigated the influence of two capping layers (MgO and Pd) on the magnetic anisotropy of highly anisotropic L10 FePd films. While we mainly found perpendicular magnetic anisotropy in MgO capped films, we observed that the Pd capping layer induces formation of an additional new phase near the FePd∕Pd interface that exhibits in-plane magnetic anisotropy. The combined effect of these two anisotropies results in global canted magnetic anisotropy. Thus, our findings illustrate a mechanism to influence the magnetic anisotropy in FePd highly ordered alloys via adequate choice of capping layer materials.
Silicon light emitting diodes emitting over the 1.2–1.4μm wavelength region in the extended optical communication band
Authors: Lourenço M. A. , Gwilliam R. M. , Homewood K. P.
Published: April 2008

Here, we demonstrate bulk silicon light emitting diodes operating over the 1.2–1.35μm range. This is achieved by the implantation of the rare earth thulium, incorporated in the trivalent Tm3+ state, into silicon p-n junctions. Light emitting diodes operating under forward bias have been obtained by codoping of boron to reduce the thermal quenching. Seven sharp lines are observed, corresponding to known internal Tm3+ transitions in the manifold from the H53 to the H63 ground states. This center, together with the basic 1.15μm silicon emitters and Si:Er devices operating at 1.54μm, now enables significant coverage of the extended (1.1–1.8μm) optical communications band in silicon.
Modulating emission polarization of semiconductor quantum dots through surface plasmon of metal nanorod
Authors: Cheng Mu-Tian , Liu Shao-Ding , Wang Qu-Quan
Published: April 2008

We theoretically investigated the dynamics of exciton populations [ρyy(t) and ρxx(t)] on two orthogonal polarization eigenstates (∣x⟩ and ∣y⟩) and the polarization ratio P(t)=[ρyy(t)−ρxx(t)]∕[ρyy(t)+ρxx(t)] of an anisotropic InGaAs quantum dot modulated by the surface plasmon of an Au nanorod (NR). In the resonance of longitudinal surface plasmon of AuNR, the polarization ratio P(t) increases from 0.22 to 0.99 during the excitation due to the efficient enhancement of Rabi frequency of the transition between the ∣y⟩ and vacuum states, and decreases from 0.02 to −0.92 after the excitation pulse due to the enhancement of decay rate of the ∣y⟩ state. This offers an approach to modulate the dynamic polarization ratio of radiative emissions.
The sensitivity of photosynthesis to phosphorus deficiency differs between C3 and C4 tropical grasses
Authors: Ghannoum Oula , Paul Matthew J. , Ward Jane L. , Beale Michael H. , Corol Delia-Irina , Conroy Jann P.
Published: April 2008

Phosphorus (P) is an important determinant of plant productivity, particularly in the tropical grasslands of Australia, which contain both C3 and C4 species. Few studies have compared the responses of such species to P deficiency. Previous work led us to hypothesise that C3 photosynthesis and the three subtypes of C4 photosynthesis have different sensitivities to P deficiency. To examine their dynamic response to P deficiency in more detail, four taxonomically related tropical grasses (Panicum laxum (C3) and Panicum coloratum, Cenchrus ciliaris and Panicum maximum belonging to the C4 subtypes NAD-ME, NADP-ME and PCK, respectively) were grown under contrasting P supplies, including P withdrawal from the growing medium. Changes in photosynthesis and growth were compared with leaf carbohydrate contents and metabolic fingerprints obtained using high-resolution proton nuclear magnetic resonance (1H-NMR). The response of CO2 assimilation rates to leaf contents of inorganic phosphate ([Pi]) was linear in the C3 grass, but asymptotic for the three C4 grasses. Relative growth rate was affected most by low P in the C3 species and was correlated with the leaf content of glucose 6-phosphate more than with carbohydrates. Principal component analysis of the 1H-NMR spectra revealed distinctive profiles of carbohydrates and amino acids for the four species. Overall, the data showed that photosynthesis of the three C4 subtypes behaved similarly. Compared with the C3 counterpart, photosynthesis of the three C4 grasses had a higher P use efficiency and lower Pi requirement, and responded to a narrower range of [Pi]. Although each of the four grass species showed distinctive 1H-NMR fingerprints, there were no differences in response that could be attributed to the C4 subtypes.
Improvement of Torenia fournieri salinity tolerance by expression of Arabidopsis AtNHX5
Authors: Shi Le-Yi , Li Hong-Qing , Pan Xiao-Ping , Wu Guo-Jiang , Li Mei-Ru
Published: April 2008

In this paper, transgenic torenia plants expressing the AtNHX5 gene from Arabidopsis in sense and antisense orientations were produced to examine the potential role of AtNHX5 in plant salt tolerance and development. We found that torenia plants overexpressing AtNHX5 showed markedly enhanced tolerance to salt stress compared with both wild-type and antisense AtNHX5 transgenic plants upon salt stress. Measurements of ion levels indicated that Na+ and K+ contents were all higher in AtNHX5 overexpressing shoots than in those of both wild-type and antisense AtNHX5 shoots treated with 50 mm NaCl. This indicated that overexpression of AtNHX5 could improve the salt tolerance of transgenic torenia via accumulation of both Na+ and K+ in shoots, in which overall ion homeostasis and osmotic adjustment was changed to sustain the increase in shoot salt tolerance. Further, we found that overexpression of AtNHX5 in torenia significantly improved the shoot regeneration frequency in leaf explants and increased the plantlet survival rate when transferring the regenerated plants to soil. In addition, the AtNHX5 expressing plants produced flowers earlier than both wild-type and the antisense AtNHX5 plants. Taken together, the results indicated that AtNHX5 functions not only in plant salt tolerance but also in plant growth and development.
Higher effect of plant species diversity on productivity in natural than artificial ecosystems
Authors: Flombaum Pedro , Sala Osvaldo E.
Published: April 2008

Current and expected changes in biodiversity have motivated major experiments, which reported a positive relationship between plant species diversity and primary production. As a first step in addressing this relationship, these manipulative experiments controlled as many potential confounding covariables as possible and assembled artificial ecosystems for the purpose of the experiments. As a new step in this endeavor, we asked how plant species richness relates to productivity in a natural ecosystem. Here, we report on an experiment conducted in a natural ecosystem in the Patagonian steppe, in which we assessed the biodiversity effect on primary production. Using a plant species diversity gradient generated by removing species while maintaining constant biomass, we found that aboveground net primary production increased with the number of plant species. We also found that the biodiversity effect was larger in natural than in artificial ecosystems. This result supports previous findings and also suggests that the effect of biodiversity in natural ecosystems may be much larger than currently thought.
A dry ligand-binding cavity in a solvated protein
Authors: Qvist Johan , Davidovic Monika , Hamelberg Donald , Halle Bertil
Published: April 2008

Ligands usually bind to proteins by displacing water from the binding site. The affinity and kinetics of binding therefore depend on the hydration characteristics of the site. Here, we show that the extreme case of a completely dehydrated free binding site is realized for the large nonpolar binding cavity in bovine β-lactoglobulin. Because spatially delocalized water molecules may escape detection by x-ray diffraction, we use water
17
O and
2
H magnetic relaxation dispersion (MRD),
13
C NMR spectroscopy, molecular dynamics simulations, and free energy calculations to establish the absence of water from the binding cavity. Whereas carbon nanotubes of the same diameter are filled by a hydrogen-bonded water chain, the MRD data show that the binding pore in the apo protein is either empty or contains water molecules with subnanosecond residence times. However, the latter possibility is ruled out by the computed hydration free energies, so we conclude that the 315 Å
3
binding pore is completely empty. The apo protein is thus poised for efficient binding of fatty acids and other nonpolar ligands. The qualitatively different hydration of the β-lactoglobulin pore and carbon nanotubes is caused by subtle differences in water–wall interactions and water entropy.
Bromodomain 4
activation predicts breast cancer survival
Authors: Crawford Nigel P. S. , Alsarraj Jude , Lukes Luanne , Walker Renard C. , Officewala Jennifer S. , Yang Howard H. , Lee Maxwell P. , Ozato Keiko , Hunter Kent W.
Published: April 2008

Previous work identified the Rap1 GTPase-activating protein Sipa1 as a germ-line-encoded metastasis modifier. The bromodomain protein Brd4 physically interacts with and modulates the enzymatic activity of Sipa1.
In vitro
analysis of a highly metastatic mouse mammary tumor cell line ectopically expressing
Brd4
demonstrates significant reduction of invasiveness without altering intrinsic growth rate. However, a dramatic reduction of tumor growth and pulmonary metastasis was observed after s.c. implantation into mice, implying that activation of
Brd4
may somehow be manipulating response to tumor microenvironment in the
in vivo
setting. Further
in vitro
analysis shows that
Brd4
modulates extracellular matrix gene expression, a class of genes frequently present in metastasis-predictive gene signatures. Microarray analysis of the mammary tumor cell lines identified a
Brd4
activation signature that robustly predicted progression and/or survival in multiple human breast cancer datasets analyzed on different microarray platforms. Intriguingly, the
Brd4
signature also almost perfectly matches a molecular classifier of low-grade tumors. Taken together, these data suggest that dysregulation of
Brd4
-associated pathways may play an important role in breast cancer progression and underlies multiple common prognostic signatures.
Protein exchange dynamics at chemoreceptor clusters in
Escherichia coli
Authors: Schulmeister Sonja , Ruttorf Michaela , Thiem Sebastian , Kentner David , Lebiedz Dirk , Sourjik Victor
Published: April 2008

Signal processing in bacterial chemotaxis relies on large sensory complexes consisting of thousands of protein molecules. These clusters create a scaffold that increases the efficiency of pathway reactions and amplifies and integrates chemotactic signals. The cluster core in
Escherichia coli
comprises a ternary complex composed of receptors, kinase CheA, and adaptor protein CheW. All other chemotaxis proteins localize to clusters by binding either directly to receptors or to CheA. Here, we used fluorescence recovery after photobleaching (FRAP) to investigate the turnover of chemotaxis proteins at the cluster and their mobility in the cytoplasm. We found that cluster exchange kinetics were protein-specific and took place on several characteristic time scales that correspond to excitation, adaptation, and cell division, respectively. We further applied analytical and numerical data fitting to analyze intracellular protein diffusion and to estimate the rate constants of cluster equilibration
in vivo
. Our results indicate that the rates of protein turnover at the cluster have evolved to ensure optimal performance of the chemotaxis pathway.
Neural correlates of mentalizing-related computations during strategic interactions in humans
Authors: Hampton Alan N. , Bossaerts Peter , O'Doherty John P.
Published: April 2008

Competing successfully against an intelligent adversary requires the ability to mentalize an opponent's state of mind to anticipate his/her future behavior. Although much is known about what brain regions are activated during mentalizing, the question of how this function is implemented has received little attention to date. Here we formulated a computational model describing the capacity to mentalize in games. We scanned human subjects with functional MRI while they participated in a simple two-player strategy game and correlated our model against the functional MRI data. Different model components captured activity in distinct parts of the mentalizing network. While medial prefrontal cortex tracked an individual's expectations given the degree of model-predicted influence, posterior superior temporal sulcus was found to correspond to an influence update signal, capturing the difference between expected and actual influence exerted. These results suggest dissociable contributions of different parts of the mentalizing network to the computations underlying higher-order strategizing in humans.
Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria
Authors: Gefen Orit , Gabay Chana , Mumcuoglu Michael , Engel Giora , Balaban Nathalie Q.
Published: April 2008

Phenotypic variability in populations of cells has been linked to evolutionary robustness to stressful conditions. A remarkable example of the importance of cell-to-cell variability is found in bacterial persistence, where subpopulations of dormant bacteria, termed persisters, were shown to be responsible for the persistence of the population to antibiotic treatments. Here, we use microfluidic devices to monitor the induction of fluorescent proteins under synthetic promoters and characterize the dormant state of single persister bacteria. Surprisingly, we observe that protein production does take place in supposedly dormant bacteria, over a narrow time window after the exit from stationary phase. Only thereafter does protein production stop, suggesting that differentiation into persisters fully develops over this time window and not during starvation, as previously believed. In effect, we observe that exposure of bacteria to antibiotics during this time window significantly reduces persistence. Our results point to new strategies to fight persistent bacterial infections. The quantitative measurement of single-cell induction presented in this study should shed light on the processes leading to the dormancy of subpopulations in different systems, such as in subpopulations of viable but nonculturable bacteria, or those of quiescent cancer cells.
Strong human association with plant invasion success for
Trifolium
introductions to New Zealand
Authors: Gravuer Kelly , Sullivan Jon J. , Williams Peter A. , Duncan Richard P.
Published: April 2008

It has proven difficult, when focused only on biological determinants, to explain why some plant species become naturalized in or invade new locations, whereas others fail. We analyzed the invasion of
Trifolium
(true clover) species into New Zealand, assessing a range of human, biogeographic, and biological influences at three key invasion stages: introduction, naturalization, and spread. We used sparse principal component analysis (SPCA) to define suites of related attributes and aggregated boosted trees to model relationships with invasion outcomes. Human and biogeographic attributes were strongly associated with success at all stages. Whereas biogeographic attributes, notably large native range, were consistently associated with success, different human factors appeared to favor success at different stages, such as presence in early trade/immigration hotspots (introduction), intentional large-scale planting (naturalization), and frequent presence as a seed contaminant (relative spread rate). Biological traits were less strongly associated with success for introduction and spread and little if at all for naturalization; we found that tall perennials with long flowering periods were more frequently selected for introduction, whereas species with extended flowering in New Zealand spread more rapidly. In addition to causal relationships, the importance of human factors may reflect indirect associations, including ecological traits associated with both human use and invasion. Nevertheless, our results highlight key roles that humans can play in facilitating plant invasion via two pathways: (
i
) commercial introduction leading to widespread planting and concomitant naturalization and spread and (
ii
) unintentional introduction and spread of species associated with human activities, such as seed contaminants.
Antiinflammatory cAMP signaling and cell migration genes co-opted by the anthrax bacillus
Authors: Kim Chun , Wilcox-Adelman Sarah , Sano Yasuyo , Tang Wei-Jen , Collier R. John , Park Jin Mo
Published: April 2008

Bacillus anthracis, the etiologic agent of anthrax, avoids immune surveillance and commandeers host macrophages as a vehicle for lymphatic spreading. Here, we show thatB. anthracisedema toxin (ET), via its adenylyl cyclase activity, dramatically increases the motility of infected macrophages and the expression of vascular endothelial growth factor. The transcription factor CREB and the syndecan-1 gene, a CREB target, play crucial roles in ET-induced macrophage migration. These molecular and cellular responses occur in macrophages engaged in antiinflammatory G protein-coupled receptor activation, thus illustrating a common signaling circuitry controlling resolution of inflammation and host cell hijacking byB. anthracis.
The molecular and cellular basis of olfactory-driven behavior inAnopheles gambiaelarvae
Authors: Xia Yuanfeng , Wang Guirong , Buscariollo Daniela , Pitts R. Jason , Wenger Heidi , Zwiebel Laurence J.
Published: April 2008

The mosquitoAnopheles gambiaeis the principal Afrotropical vector for human malaria. A central component of its vectorial capacity is the ability to maintain sufficient populations of adults. During both adult and preadult (larval) stages, the mosquitoes depend on the ability to recognize and respond to chemical cues that mediate feeding and survival. In this study, we used a behavioral assay to identify a range of odorant-specific responses ofAn. gambiaelarvae that are dependent on the integrity of the larval antennae. Parallel molecular analyses have identified a subset of theAn. gambiaeodorant receptors (AgOrs) that are localized to discrete neurons within the larval antennae and facilitate odor-evoked responses inXenopusoocytes that are consistent with the larval behavioral spectrum. These studies shed light on chemosensory-driven behaviors and represent molecular and cellular characterization of olfactory processes in mosquito larvae. These advances may ultimately enhance the development of vector control strategies, targeting olfactory pathways in larval-stage mosquitoes to reduce the catastrophic effects of malaria and other diseases.
Dendritic cells in islets of Langerhans constitutively present β cell-derived peptides bound to their class II MHC molecules
Authors: Calderon Boris , Suri Anish , Miller Mark J. , Unanue Emil R.
Published: April 2008

Islets of Langerhans from normal mice contained dendritic cells (DCs) in the range of 8–10 per islet. DCs were found in several mouse strains, including those from lymphocyte-deficient mice. DCs were absent in islets from colony stimulating factor-1 deficient mice and this absence correlated with small size islets. Most DCs were found next to blood vessels and resided in islets for several days. Some DCs contained insulin-like granules, and most expressed peptide–MHC complexes derived from β cell proteins. Islet DCs were highly effective in presenting β cell antigens to CD4 T cellsex vivo. Presentation of β cell-derived peptide–MHC complexes by DCs neither depended on islet inflammation nor correlated with the extent of spontaneous β cell death. Periislet stroma DCs did not contain β cell peptide–MHC complexes; however, 50% of DCs in pancreatic node were positive. Hence, presentation of high levels of β cell antigens normally takes place by islet DCs, a finding that has to be placed in the perspective of autoimmune diabetes.
Notch signaling mediates hypoxia-induced tumor cell migration and invasion
Authors: Sahlgren Cecilia , Gustafsson Maria V. , Jin Shaobo , Poellinger Lorenz , Lendahl Urban
Published: April 2008

Tumor hypoxia is linked to increased metastatic potential, but the molecular mechanisms coupling hypoxia to metastasis are poorly understood. Here, we show that Notch signaling is required to convert the hypoxic stimulus into epithelial–mesenchymal transition (EMT), increased motility, and invasiveness. Inhibition of Notch signaling abrogated hypoxia-induced EMT and invasion, and, conversely, an activated form of Notch could substitute for hypoxia to induce these processes. Notch signaling deploys two distinct mechanisms that act in synergy to control the expression of Snail-1, a critical regulator of EMT. First, Notch directly up-regulated
Snail-1
expression by recruitment of the Notch intracellular domain to the
Snail-1
promoter, and second, Notch potentiated hypoxia-inducible factor 1α (HIF-1α) recruitment to the
lysyl oxidase
(
LOX
) promoter and elevated the hypoxia-induced up-regulation of LOX, which stabilizes the Snail-1 protein. In sum, these data demonstrate a complex integration of the hypoxia and Notch signaling pathways in regulation of EMT and open up perspectives for pharmacological intervention with hypoxiainduced EMT and cell invasiveness in tumors.
The highly conserved nuclear lamin Ig-fold binds to PCNA: its role in DNA replication
Authors: Shumaker Dale K. , Solimando Liliana , Sengupta Kaushik , Shimi Takeshi , Adam Stephen A. , Grunwald Antje , Strelkov Sergei V. , Aebi Ueli , Cardoso M. Cristina , Goldman Robert D.
Published: April 2008

This study provides insights into the role of nuclear lamins in DNA replication. Our data demonstrate that the Ig-fold motif located in the lamin C terminus binds directly to proliferating cell nuclear antigen (PCNA), the processivity factor necessary for the chain elongation phase of DNA replication. We find that the introduction of a mutation in the Ig-fold, which alters its structure and causes human muscular dystrophy, inhibits PCNA binding. Studies of nuclear assembly and DNA replication show that lamins, PCNA, and chromatin are closely associated in situ. Exposure of replicating nuclei to an excess of the lamin domain containing the Ig-fold inhibits DNA replication in a concentration-dependent fashion. This inhibitory effect is significantly diminished in nuclei exposed to the same domain bearing the Ig-fold mutation. Using the crystal structures of the lamin Ig-fold and PCNA, molecular docking simulations suggest probable interaction sites. These findings also provide insights into the mechanisms underlying the numerous disease-causing mutations located within the lamin Ig-fold.
Genome-wide analysis of signaling networks regulating fatty acid–induced gene expression and organelle biogenesis
Authors: Saleem Ramsey A. , Knoblach Barbara , Mast Fred D. , Smith Jennifer J. , Boyle John , Dobson C. Melissa , Long-O'Donnell Rose , Rachubinski Richard A. , Aitchison John D.
Published: April 2008

Reversible phosphorylation is the most common posttranslational modification used in the regulation of cellular processes. This study of phosphatases and kinases required for peroxisome biogenesis is the first genome-wide analysis of phosphorylation events controlling organelle biogenesis. We evaluate signaling molecule deletion strains of the yeast Saccharomyces cerevisiae for presence of a green fluorescent protein chimera of peroxisomal thiolase, formation of peroxisomes, and peroxisome functionality. We find that distinct signaling networks involving glucose-mediated gene repression, derepression, oleate-mediated induction, and peroxisome formation promote stages of the biogenesis pathway. Additionally, separate classes of signaling proteins are responsible for the regulation of peroxisome number and size. These signaling networks specify the requirements of early and late events of peroxisome biogenesis. Among the numerous signaling proteins involved, Pho85p is exceptional, with functional involvements in both gene expression and peroxisome formation. Our study represents the first global study of signaling networks regulating the biogenesis of an organelle.
Aurora B kinase and protein phosphatase 1 have opposing roles in modulating kinetochore assembly
Authors: Emanuele Michael J. , Lan Weijie , Jwa Miri , Miller Stephanie A. , Chan Clarence S.M. , Stukenberg P. Todd
Published: April 2008

The outer kinetochore binds microtubules to control chromosome movement. Outer kinetochore assembly is restricted to mitosis, whereas the inner kinetochore remains tethered to centromeres throughout the cell cycle. The cues that regulate this transient assembly are unknown. We find that inhibition of Aurora B kinase significantly reduces outer kinetochore assembly in Xenopus laevis and human tissue culture cells, frog egg extracts, and budding yeast. In X. leavis M phase extracts, preassembled kinetochores disassemble after inhibiting Aurora B activity with either drugs or antibodies. Kinetochore disassembly, induced by Aurora B inhibition, is rescued by restraining protein phosphatase 1 (PP1) activity. PP1 is necessary for kinetochores to disassemble at the exit from M phase, and purified enzyme is sufficient to cause disassembly on isolated mitotic nuclei. These data demonstrate that Aurora B activity is required for kinetochore maintenance and that PP1 is necessary and sufficient to disassemble kinetochores. We suggest that Aurora B and PP1 coordinate cell cycle–dependent changes in kinetochore assembly though phosphorylation of kinetochore substrates.
IL-6–dependent spontaneous proliferation is required for the induction of colitogenic IL-17–producing CD8+ T cells
Authors: Tajima Masaki , Wakita Daiko , Noguchi Daisuke , Chamoto Kenji , Yue Zhang , Fugo Kazunori , Ishigame Harumichi , Iwakura Yoichiro , Kitamura Hidemitsu , Nishimura Takashi
Published: April 2008

We propose a novel role for interleukin (IL) 6 in inducing rapid spontaneous proliferation (SP) of naive CD8+ T cells, which is a crucial step in the differentiation of colitogenic CD8+ T cells. Homeostasis of T cells is regulated by two distinct modes of cell proliferation: major histocompatibility complex/antigen–driven rapid SP and IL-7/IL-15–dependent slow homeostatic proliferation. Using our novel model of CD8+ T cell–dependent colitis, we found that SP of naive CD8+ T cells is essential for inducing pathogenic cytokine-producing effector T cells. The rapid SP was predominantly induced in mesenteric lymph nodes (LNs) but not in peripheral LNs under the influence of intestinal flora and IL-6. Indeed, this SP was markedly inhibited by treatment with anti–IL-6 receptor monoclonal antibody (IL-6R mAb) or antibiotic-induced flora depletion, but not by anti–IL-7R mAb and/or in IL-15–deficient conditions. Concomitantly with the inhibition of SP, anti–IL-6R mAb significantly inhibited the induction of CD8+ T cell–dependent autoimmune colitis. Notably, the transfer of naive CD8+ T cells derived from IL-17−/− mice did not induce autoimmune colitis. Thus, we conclude that IL-6 signaling is crucial for SP under lymphopenic conditions, which subsequently caused severe IL-17–producing CD8+ T cell–mediated autoimmune colitis. We suggest that anti–IL-6R mAb may become a promising strategy for the therapy of colitis.
C5 deficiency and C5a or C5aR blockade protects against cerebral malaria
Authors: Patel Samir N. , Berghout Joanne , Lovegrove Fiona E. , Ayi Kodjo , Conroy Andrea , Serghides Lena , Min-oo Gundula , Gowda D. Channe , Sarma J. Vidya , Rittirsch Daniel , Ward Peter A. , Liles W. Conrad , Gros Philippe , Kain Kevin C.
Published: April 2008

Experimental infection of mice with Plasmodium berghei ANKA (PbA) provides a powerful model to define genetic determinants that regulate the development of cerebral malaria (CM). Based on the hypothesis that excessive activation of the complement system may confer susceptibility to CM, we investigated the role of C5/C5a in the development of CM. We show a spectrum of susceptibility to PbA in a panel of inbred mice; all CM-susceptible mice examined were found to be C5 sufficient, whereas all C5-deficient strains were resistant to CM. Transfer of the C5-defective allele from an A/J (CM resistant) onto a C57BL/6 (CM-susceptible) genetic background in a congenic strain conferred increased resistance to CM; conversely, transfer of the C5-sufficient allele from the C57BL/6 onto the A/J background recapitulated the CM-susceptible phenotype. The role of C5 was further explored in B10.D2 mice, which are identical for all loci other than C5. C5-deficient B10.D2 mice were protected from CM, whereas C5-sufficient B10.D2 mice were susceptible. Antibody blockade of C5a or C5a receptor (C5aR) rescued susceptible mice from CM. In vitro studies showed that C5a-potentiated cytokine secretion induced by the malaria product P. falciparum glycosylphosphatidylinositol and C5aR blockade abrogated these amplified responses. These data provide evidence implicating C5/C5a in the pathogenesis of CM.
Comparative conservation analysis of the human mitotic phosphoproteome
Authors: Malik Rainer , Nigg Erich A. , Körner Roman
Published: April 2008

Motivation: A key challenge in phosphoproteomic studies is to distinguish functionally relevant phosphorylation sites from potentially ‘silent’ phosphorylation. Considering that relevant phosphorylation sites are expected to be better conserved during evolution than overall Serine, Threonine and Tyrosine (S/ T/ Y) residues, we asked whether this can be directly demonstrated through statistic analysis, using a large experimental dataset.

Results: Analyzing phosphoproteomic data derived from the human mitotic spindle apparatus, we found that 95.2% of 1744 phosphorylation sites are conserved in at least one of six other vertebrate species. Using a new score, termed conservation Z-score (CZ-score), we demonstrate that phosphorylation sites are significantly better conserved than other S/T/Y sites, a conclusion validated from several kinase consensus motifs. Most importantly, phosphorylation sites with experimentally verified biological functions were significantly better conserved than other phosphorylation sites, indicating that analysis utilizing evolutionary conservation may constitute a powerful basis for the development of improved phosphorylation site predictors.

Contact:  malik@biochem.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Eukaryotic transcription factor binding sites—modeling and integrative search methods
Authors: Hannenhalli Sridhar
Published: April 2008

A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks. Because the DNA motif recognized by a transcription factor is typically short and degenerate, computational approaches for identifying binding sites based only on the sequence motif inevitably suffer from high error rates. Current state-of-the-art techniques for improving computational identification of binding sites can be broadly categorized into two classes: (1) approaches that aim to improve binding motif models by extracting maximal sequence information from experimentally determined binding sites and (2) approaches that supplement binding motif models with additional genomic or other attributes (such as evolutionary conservation). In this review we will discuss recent attempts to improve computational identification of TFBS through these two types of approaches and conclude with thoughts on future development.

Contact:  sridharh@pcbi.upenn.edu
Genetic assignment identifies farm of origin for Atlantic salmon Salmo salar escapees in a Norwegian fjord
Authors: Glover K. A. , Skilbrei O. T. , Skaala Ø.
Published: April 2008

Glover, K. A., Skilbrei, O. T., and Skaala, Ø. 2008. Genetic assignment identifies farm of origin for Atlantic salmon Salmo salar escapees in a Norwegian fjord. – ICES Journal of Marine Science, 65: 912–920. This study represents the first example of genetic assignment being used to identify the farm of origin for escaped Atlantic salmon. Following reports by local fishers of escaped farmed salmon in Romsdalfjord, western Norway, baseline samples were collected from 16 cages located on seven operational farms. The baseline samples, in addition to 29 escapees, were screened for 15 microsatellite loci. Pairwise FST values between baseline samples varied from <0.001 to 0.154, indicating variable but significant genetic differences among them. Direct assignment of the escapees (data from 13 informative loci) demonstrated that the most likely origin of 21 of them was from a single baseline sample (5I) collected at one farm. At a probability of 0.01, between 25 and 29 of the escapees were rejected in 12 baseline samples, 19–21 escapees were rejected from another three baseline samples, and only seven of the escapees were rejected from baseline sample 5I. Consequently, these data demonstrate that most of the escapees most likely originated from a single farm, and importantly, that 15 of the 16 baseline samples could with high probability be excluded as donors for most of the escapees recaptured in the area.
Testing the hypothesis that amphiphilic antineoplastic lipid analogues act through reduction of membrane curvature elastic stress
Authors: Dymond Marcus , Attard George , Postle Anthony D
Published: April 2008

The alkyllysophospholipid (ALP) analogues Mitelfosine and Edelfosine are anticancer drugs whose mode of action is still the subject of debate. It is agreed that the primary interaction of these compounds is with cellular membranes. Furthermore, the membrane-associated protein CTP: phosphocholine cytidylyltransferase (CCT) has been proposed as the critical target. We present the evaluation of our hypothesis that ALP analogues disrupt membrane curvature elastic stress and inhibit membrane-associated protein activity (e.g. CCT), ultimately resulting in apoptosis. This hypothesis was tested by evaluating structure–activity relationships of ALPs from the literature. In addition we characterized the lipid typology, cytotoxicity and critical micelle concentration of novel ALP analogues that we synthesized. Overall we find the literature data and our experimental data provide excellent support for the hypothesis, which predicts that the most potent ALP analogues will be type I lipids.