bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic characterization of micropatterned Nd–Fe–B hard magnetic films using scanning Hall probe microscopy
Authors: Kustov M. , Laczkowski P. , Hykel D. , Hasselbach K. , Dumas-Bouchiat F. , O’Brien D. , Kauffmann P. , Grechishkin R. , Givord D. , Reyne G. , Cugat O. , Dempsey N. M.
Published: September 2010

Scanning Hall probe microscopy has been used for the quantitative measurement of the z-component (out-of-plane) of the stray magnetic fields produced by Nd–Fe–B hard magnetic films patterned at the micron scale using both topographic and thermomagnetic methods. Peak-to-peak field values in the range 20–120 mT have been measured at scan heights of 25–30 μm above the samples. Quantitative comparison between calculated and measured field profiles gives nondestructive access to the micromagnets’ internal magnetic structure. In the case of topographically patterned films the average value of remanent magnetization is extracted; in the case of thermomagnetically patterned films the depth of magnetization reversal is estimated. The measured field profiles are used to derive the spatial variation in the field and field gradient values at distances in the range 0.1–10 μm above the micromagnet arrays. These length-scales are relevant to the application of the micromagnet arrays for lab-on-chip applications (trapping and confinement of magnetic particles). Very large field and field gradient values as high as 1.1 T and 4.1×106 T/m, respectively, are estimated.
A robust approach for the growth of epitaxial spinel ferrite films
Authors: Ma J. X. , Mazumdar D. , Kim G. , Sato H. , Bao N. Z. , Gupta A.
Published: September 2010

Heteroepitaxial spinel ferrites NiFe2O4 and CoFe2O4 films have been prepared by pulsed laser deposition at various temperatures (175–690 °C) under ozone/oxygen pressure of 10 mTorr. Due to enhanced kinetic energy of ablated species at low pressure and enhanced oxidation power of ozone, epitaxy has been achieved at significantly lower temperatures than previously reported. Films grown at temperature below 550 °C show a novel growth mode, which we term “vertical step-flow” growth mode. Epitaxial spinel ferrite films with atomically flat surface over large areas and enhanced magnetic moment can be routinely obtained. Interestingly, the growth mode is independent of the nature of substrate (spinel MgAl2O4, perovskite SrTiO3, and rock-salt MgO) and film thickness. The underlying growth mechanism is discussed.
Solitons, Bäcklund transformation, and Lax pair for the (2+1)-dimensional Boiti–Leon–Pempinelli equation for the water waves
Authors: Jiang Yan , Tian Bo , Liu Wen-Jun , Li Min , Wang Pan , Sun Kun
Published: September 2010

Under investigation in this paper is the (2+1)-dimensional Boiti–Leon–Pempinelli (BLP) equation for the water waves. By virtue of the binary Bell polynomials and symbolic computation, the bilinear form for the BLP equation is obtained. Furthermore, soliton solutions are presented, and soliton interaction properties including the elastic, inelastic, and elastic-inelastic collisions are discussed by the graphical analysis. Besides, the Bäcklund transformation in the form of the binary Bell polynomials is derived. Via the Bäcklund transformation, the shock-wave solutions and Lax pair are both constructed.
The spaces Hn(osp(1∣2),M) for some modules M
Authors: Arnal Didier , Ben Ammar Mabrouk , Dali Bechir
Published: September 2010

We first generalize a result by Bavula on the sl(2) cohomology to the osp(1∣2) cohomology and then we entirely compute the cohomology for a natural class of osp(1∣2) modules M. We study the restriction to the sl(2) cohomology of M and apply our results to the module M=Dλ,μ of differential operators on the superline acting on densities.
(
7
×
7
)
reconstruction as barrier for Schottky-barrier formation at the Ga/Si(111) interface
Authors: Kumar Praveen , Kumar Mahesh , Shivaprasad S. M.
Published: September 2010

We report the change in electronic properties of the Ga/Si interface by monitoring the Ga(3d) core-level photoelectron spectra and electron diffraction induced by submonolayer Ga adsorption on Si(111)-7×7 surface. The spectra shows a flat band for submonolayer coverages, attributed to the metallic nature of the Si(111)-7×7 reconstruction and a premetallic band structure of two-dimensional Ga islands. At 1 ML, electron diffraction pattern shows metallic (7×7) to semiconducting (1×1) phase-transition and the spin-orbit split branching ratio of Ga(2p) core level attain the metallic bulk value, and the barrier assumes the Schottky–Mott value while full width half maxima and branching ratio attain bulk values.
Flux-mediated diffuse mismatch model
Authors: Loh G. C. , Tay B. K. , Teo E. H. T.
Published: September 2010

The diffuse mismatch model (DMM) is modified to account for the effect of thermal flux on phonon transmission at interfaces. This new model, the flux-mediated diffuse mismatch model (FMDMM) takes a slightly different approach in its formulation, and does not employ the principle of detailed balance. Two competing processes—an increase in the flux coefficient, and a decrease in the rest of the transmission term, may result in either a rise or fall in thermal boundary resistance when thermal flux is increased. This might partially explain the large disparities between experimental, theoretical, and simulated results of thermal boundary resistance.
Microwave annealing of polymer solar cells with various transparent anode materials
Authors: Flügge H. , Schmidt H. , Riedl T. , Schmale S. , Rabe T. , Fahlbusch J. , Danilov M. , Spieker H. , Schöbel J. , Kowalsky W.
Published: September 2010

Efficient organic solar cells were produced through annealing with microwave radiation (2.45 GHz) within only 8 s. Efficiencies of up to 3% were obtained, similar to those of devices annealed with a hot plate for 300 s. We examined the effect of microwave irradiation on the individual layers of the solar cell architecture. Microwave absorption was found to be related exclusively to the sheet resistance of the layers. As a result, in a polymer solar cell comprising an electrode based on a transparent conducting oxide (TCO) the microwave annealing is evidenced to be directly linked to the microwave absorption in the TCO layer.
CdSe quantum dot-sensitized solar cell employing TiO2 nanotube working-electrode and Cu2S counter-electrode
Authors: Shen Qing , Yamada Akari , Tamura Satoru , Toyoda Taro
Published: September 2010

We proposed a CdSe quantum dot (QD)-sensitized solar cell (QDSSC), which is constructed with a CdSe QD adsorbed TiO2 nanotube working electrode on a Ti substrate, a ring shaped Cu2S counter electrode, prepared on a brass substrate having a glass window, and polysulfide electrolyte. The light was incident from the counter electrode. An incident photon to current conversion efficiency as high as 65% and a photovoltaic conversion efficiency as high as 1.8% under one sun have been achieved. We have demonstrated less costly QDSSC, without the requirement for both a transparent conductive electrode or a platinum film.
Negative refraction of zero order flexural Lamb waves through a two-dimensional phononic crystal
Authors: Pierre J. , Boyko O. , Belliard L. , Vasseur J. O. , Bonello B.
Published: September 2010

We investigate experimentally the refraction of antisymmetric Lamb waves at frequencies in the second band of a two-dimensional phononic crystal. The heterostructure is made of a square lattice of air inclusions in a silicon plate. Our experimental scheme is based on the selective generation of narrow band elastic waves at a few megahertz. Both positive and negative refractions are observed. The comparison of our data with computed dispersion curves shows very good agreement.
Electronic states of InAs/GaAs quantum dots by scanning tunneling spectroscopy
Authors: Gaan S. , He Guowei , Feenstra R. M. , Walker J. , Towe E.
Published: September 2010

InAs/GaAs quantum-dot (QD) heterostructures grown by molecular-beam epitaxy are studied using cross-sectional scanning tunneling microscopy and spectroscopy. Individual InAs QDs are resolved in the images. Tunneling spectra acquired 3–4 nm from the QDs show a peak located in the upper part of the GaAs band gap originating from the lowest electron confined state, together with a tail extending out from the valence band from hole confined states. A line-shape analysis is used to deduce the binding energies of the electron and hole QD states.
Analytical solution to sine-Gordon equation
Authors: Eleuch H. , Rostovtsev Y. V.
Published: September 2010

We present an analytical solution for the sine-Gordon equation using the arctan-transformation and without restriction to any set of parameters.
Phase diagram and electrostrictive properties of Bi0.5Na0.5TiO3–BaTiO3–K0.5Na0.5NbO3 ceramics
Authors: Zhang Shan-Tao , Yan Feng , Yang Bin , Cao Wenwu
Published: September 2010

Phase diagram of Bi0.5Na0.5TiO3–BaTiO3–K0.5Na0.5NbO3 ternary system has been analyzed and (0.94−x)BNT–0.06BT–xKNN (0.15≤x≤0.30) ceramics have been prepared and investigated. Pseudocubic structures were confirmed by x-ray diffractions and its preliminary Rietveld refinements. P-E, S-E, and S-P2 profiles (where P, E, and S denote polarization, electric field, and strain, respectively) indicate electrostrictive behavior of all ceramics. The compositions with x=0.20 and 0.25 show pure electrostrictive characteristics. The dissipation energy, electrostrictive strain, and electrostrictive coefficient have been determined and compared with other lead-free and lead-containing electrostrictors. The electrostrictive coefficient can reach as high as 0.026 m4/C2, about 1.5 times of the value of traditional Pb-based electrostrictors.
A theoretical framework to obtain interface’s shapes during the high-temperature annealing of high-aspect-ratio gratings
Authors: Castez Marcos F. , Salvarezza Roberto C. , Nakamura Jun , Sudoh Koichi
Published: September 2010

High-temperature annealing applied to solid samples produces important morphological modifications on their surfaces, particularly in high-aspect-ratio gratings. We show, how by means of a framework based in a nonlinear analysis of the Mullins’ equation [J. Appl. Phys. 28, 333 (1957)], we can mathematically reproduce surface’s shapes just by measuring a few characteristic features of the interfaces (essentially pattern’s amplitudes and wavelengths). We compared our results with experimental data on silicon samples, finding a close agreement between experimental shapes and those theoretically predicted. The introduced framework could be particularly useful in those situations where no cross-sectional information were available.
Aperiodic conductivity oscillations in quasiballistic graphene heterojunctions
Authors: Begliarbekov Milan , Sul Onejae , Ai Nan , Yang Eui-Hyeok , Strauf Stefan
Published: September 2010

We observe conductivity oscillations with aperiodic spacing to only one side of the tunneling current in a dual-gated graphene field effect transistor with an n-p-n type potential barrier. The spacing and width of these oscillations were found to be inconsistent with pure Fabry–Perot-type interferences, but are in quantitative agreement with theoretical predictions that attribute them to resonant tunneling through quasibound impurity states. This observation may be understood as another signature of Klein tunneling in graphene heterojunctions and is of importance for future development and modeling of graphene based nanoelectronic devices.
Effects of root restriction on growth and associated cytokinin levels in cotton (Gossypium hirsutum)
Authors: Yong Jean W. H. , Letham D. Stuart , Wong S. Chin , Farquhar Graham D.
Published: September 2010

Root restriction experiments on cotton plants were conducted under conditions where water and nitrogen supplies were not limiting. Xylem sap and leaf tissues were obtained before significant biomass reduction as a result of root restriction. Xylem-derived cytokinins (CTKs) entering a leaf and the CTK levels in the same excised leaf were measured, thus, enabling xylem sap and foliar CTKs to be compared concurrently under root-restrictive and control conditions. Abscisic acid (ABA) was also measured simultaneously in the same xylem sap samples. Root restriction reduced photosynthesis and δ18O of leaf matter showed that leaves of root-restricted plants generally had lower stomatal conductances. Root-restriction significantly decreased (37%) the delivery rate per unit leaf area of CTK bases (dihydrozeatin (DZ) and N6-(2-isopentenyl)adenine (iP)) to the leaf but did not alter the export of CTK O-glucosides and ABA from the roots to leaf 4. Root-restriction also did not alter significantly the levels of total CTK bases in the leaves but increased (54–57% higher) the CTK O-glucosides (especially zeatin O-glucosides). Root restriction also slowed down the apparent CTK turnover rates in the leaves. The slow down in CTK turnover rate can be interpreted as a reduction in leaf CTK metabolism during root restriction.
Comparative and functional morphology of hierarchically structured anti-adhesive surfaces in carnivorous plants and kettle trap flowers
Authors: Poppinga Simon , Koch Kerstin , Bohn Holger Florian , Barthlott Wilhelm
Published: September 2010

Plant surfaces that are slippery for insects have evolved independently several times in the plant kingdom, mainly in the groups of carnivorous plants and kettle trap flowers. The surface morphologies of 53 species from both groups were investigated by scanning electron microscopy. It was found that the surfaces possess highly diverse topographical structures. We present a classification of 12 types of anti-adhesive surfaces, in regard to the assembly and hierarchy of their structural elements. The observed structural elements are different combinations of epidermal cell curvatures with cuticular folds or 3D epicuticular wax crystals and idioblastic elements.
In situ detection of Esr proteins secretion during maize microspore embryogenesis and their secretion blockage show effects on the culture progression
Authors: Testillano Pilar S. , Coronado María-José , Thierry Anne-Marie , Matthys-Rochon Elisabeth , Risueño María C.
Published: September 2010

In vitro plant cells in culture release proteins and carbohydrates, but the active molecules responsible for sustaining the switch in embryogenic development and progression have not yet been identified. In maize (Zea mays L.), the Esr genes encode for small hydrophilic proteins and are expressed in the restricted region of maize endosperm surrounding the embryo: the embryo surrounding region (ESR). In the present work, the possible influence of secreted molecules in the liquid medium during microspore-derived embryo development and specifically, the presence of Esr proteins, has been analysed in maize microspore cultures. The study has been conducted with in situ monitoring of the structural and cellular organisation of developing embryos and the subcellular localisation of the Esr proteins by immunofluorescence and immunogold labelling. The results obtained using confocal and electron microscopy revealed that Esr proteins were localised in elements of the secretory pathway and cell walls in microspore-derived embryo cells during early embryogenesis. Esr proteins were also detected in the liquid medium of maize microspore cultures and accumulated at 20 days of culture. Tunicamycin treatment to block protein glycosilation and, therefore, secretion inhibited microspore-derived embryo development, which was subsequently recovered by supplementation with medium containing all the secreted factors from a well developed microspore culture. Esr labelling was not present in non-developing microspore embryos of cultures treated with tunicamycin, whereas labelling was present again in the Golgi elements and secretory vesicles of embryo cells when development was restored. The results indicate that Esr proteins are part of the secreted proteins, which show a nursing or signalling role during in vitro embryo development in maize microspore embryogenesis cultures and provide new evidence for an endosperm-like function of microspore-derived embryo structures during the early stages.
Proteinaceous necrotrophic effectors in fungal virulence
Authors: Tan Kar-Chun , Oliver Richard P. , Solomon Peter S. , Moffat Caroline S.
Published: September 2010

The host–pathogen interface can be considered as a biological battlefront. Molecules produced by both the pathogen and the host are critical factors determining the outcome of the interaction. Recent studies have revealed that an increasing number of necrotrophic fungal pathogens produce small proteinaceous effectors that are able to function as virulence factors. These molecules can cause tissue death in host plants that possess dominant sensitivity genes, leading to subsequent pathogen colonisation. Such effectors are only found in necrotrophic fungi, yet their roles in virulence are poorly understood. However, several recent key studies of necrotrophic effectors from two wheat (Triticum aestivum L.) pathogens, Pyrenophora tritici-repentis (Died.) Drechs. and Stagonospora nodorum (Berk.) Castell. & Germano, have shed light upon how these effector proteins serve to disable the host from the inside out.
Effectors of plant parasitic nematodes that re-program root cell development
Authors: Hassan Samira , Behm Carolyn A. , Mathesius Ulrike
Published: September 2010

Plant parasitic nematodes infect the roots of a wide range of host plants. Migratory endo- or ectoparasites feed off the roots temporarily, but sedentary endoparasites are biotrophic parasites that invade roots and establish a permanent feeding site by re-directing root cell development. Feeding sites develop after injection of nematode effectors into plant cells through a stylet. In this review, we concentrate on several recently-identified effectors and discuss their possible functions in re-directing root cell development. We give examples of effectors that regulate host gene expression, interact with specific host proteins or mimic plant signalling molecules.
Benthic community composition influences within-habitat variation in macroalgal browsing on the Great Barrier Reef
Authors: Cvitanovic C. , Hoey A. S.
Published: September 2010

The removal of macroalgae by herbivores is fundamental to the long-term persistence of coral reefs. Variation in macroalgal browsing has been documented across a range of spatial scales on coral reefs; however, few studies have examined the factors that influence within-habitat rates of herbivory. The aim of the present study was to quantify herbivory on two species of Sargassum across three bays on an inshore island in the central Great Barrier Reef (GBR), and to determine whether these removal rates were related to the benthic composition or herbivorous fish communities. Removal rates of Sargassum differed significantly among bays, with removal rates in the southern bay (66.9–83.0% per 3 h) being approximately double that of the two other bays (29.2–38.5% per 3 h). The removal rates displayed a direct relationship with the benthic community structure, in particular the cover of macroalgae and live plate corals. Although it is difficult to determine whether these relationships are related to the availability of food resources or the structural complexity of the substratum, they highlight the potential influence of benthic composition on ecological processes. Quantifying and understanding the drivers of herbivory across a range of spatial scales is essential to the future management of coral reefs.
Sorption and desorption dynamics of bulk dissolved organic matter and amino acids in the Mississippi River plume - a microcosm study
Authors: Grace Bryan L. , Bianchi Thomas S.
Published: September 2010

Particulate and dissolved carbon, nitrogen and amino acids were analysed in a microcosm experiment where particulate material from the Mississippi River was mixed with surface waters of different salinities (2.0, 20.4 and 28.9) collected from the Mississippi River plume. There was evidence for the partitioning of amino acids in different salinity treatments during a 24-h period. Dissolved amino acids in the productive mid-salinity region of the plume had higher binding efficiencies than did amino acids from non-productive waters, indicative of the relative importance of phytoplankton sources of reactive amino acids. Basic amino acids were adsorbed more readily to particles, whereas acidic amino acids remained in the dissolved pool, indicating that electrostatic mechanisms affected amino-acid partitioning. Neutral amino-acid enrichment onto the particles was proportional to their respective hydrophobicity. Because riverine particles enter the higher salinity-shelf waters of the Mississippi River plume, changing ionic strength is a key in controlling amino-acid sorption and desorption kinetics. We propose that the short-term partitioning of amino acids between dissolved and particulate amino-acid pools across salinity gradients in the plume were affected by (1) electrostatic characteristics of suspended riverine sediment surfaces, (2) the availability of ‘freshly’ produced amino acids from phytoplankton and (3) the functional groups of amino acids.
Age and growth of the great hammerhead shark, Sphyrna mokarran, in the north-western Atlantic Ocean and Gulf of Mexico
Authors: Piercy Andrew N. , Carlson John K. , Passerotti Michelle S.
Published: September 2010

The great hammerhead shark, Sphyrna mokarran, is a cosmopolitan species that is caught in a variety of fisheries throughout much of its range. The apparent decline of great hammerhead shark populations has reinforced the need for accurate biological data to enhance fishery management plans. To this end, age and growth estimates for the great hammerhead were determined from sharks (n = 216) ranging in size from 54- to 315-cm fork length (FL), captured in the Gulf of Mexico and north-western Atlantic Ocean. Growth curves were fitted using multiple models and evaluated using Akaike’s information criterion. The von Bertalanffy growth model was the best fitting model, with resulting growth parameters of L∞ = 264.2-cm FL, k = 0.16 year–1, t0 = –1.99 year for males, and L∞ = 307.8-cm FL, k = 0.11 year–1, t0 = –2.86 year for females. Annual band pair deposition was confirmed through marginal-increment analysis and a concurrent bomb radiocarbon validation study. Great hammerheads have one of the oldest reported ages for any elasmobranch (44 years) but grow at relatively similar rates (on the basis of von Bertalanffy k value) to other large hammerhead species from this region. The present study is the first to provide vertebral ages for great hammerheads.
Applying paleolimnological techniques in estuaries: a cautionary case study from Moreton Bay, Australia
Authors: Logan Brendan , Taffs Kathryn H. , Cunningham Laura
Published: September 2010

Paleoecological techniques are useful tools to identify restoration targets and natural variability for natural resource management programs. However, despite recent advances, caution is required when employing paleoecological techniques in estuaries, due to their dynamic nature relative to lake environments where these techniques were pioneered. This study used a novel combination of chronological, diatom, geochemical and isotopic data to assess the effectiveness of using these techniques in estuaries, and to develop an understanding of environmental changes within Moreton Bay, an open estuarine environment in subtropical east Australia. Results indicated mixed success, with 210Pb results indicating only background unsupported 210Pb levels, 14C results indicating sediment deposition from mixed sources, no diatom preservation and inconsistencies between geochemical and isotope proxies. Evidence did exist that the Moreton Bay sediments have been derived from different sources over the past 10 000 years. However, isotope records were not able to identify the likely sources of these sediments. Problems with diatom preservation were most probably due to the high salinity and temperatures associated with subtropical open embayment estuaries. Future studies attempting to identify environmental histories of estuaries should incorporate river-influenced locations rather than marine-dominated sites to ensure better diatom preservation and more definitive geochemical signals.
Demographic analysis of the pelagic thresher shark, Alopias pelagicus, in the north-western Pacific using a stochastic stage-based model
Authors: Tsai Wen-Pei , Liu Kwang-Ming , Joung Shoou-Jeng
Published: September 2010

The pelagic thresher shark, Alopias pelagicus, like most large sharks produces a low number of offspring (two embryos per litter). However, there is no accurate information on its population status. To improve the accuracy of population simulations, a stochastic stage-based birth-flow model was constructed to assess the stock status of the pelagic thresher in the north-western Pacific. Based on the best biological information available, its life history was represented as four stages: neonates, juveniles, subadults, and adults. Results indicated that, without mortality from fishing, the stock would clearly increase (mean annual population growth rate (λ) = 1.058 year–1, 95% CI = 1.014–1.102 year–1). When current fishing mortality was taken into account, a decrease in population was indicated (λ = 0.979 year–1, 95% CI = 0.921–1.030 year–1) with a projected reduction of 34.3% over 20 years. These results suggest that the stock is overexploited. Simulations using various management measures showed that the population will remain steady under these protection options. However, this species is extremely vulnerable to overexploitation and is especially sensitive at the juvenile and adult stages, implying that nursery closures or size limit management measures are urgently needed to ensure the sustainable utilisation of the stock.
Scanning electron microscopy of the operculum of Garra lamta (Hamilton) (Cyprinidae:Cypriniformes), an Indian hill stream fish
Authors: Mittal Swati , Kumari Usha , Tripathi Pinky , Mittal Ajay Kumar
Published: September 2010

The surface architecture of the epidermis on the outer surface of the operculum (OE) and the epithelium on the inner surface of the operculum (EISO) of Garra lamta was examined by scanning electron microscopy. The surface appeared smooth on the OE and wavy on the EISO. A wavy epithelium is considered to facilitate an increase in its stretchability, during the expansion of the branchial chamber. The OE and the EISO were covered by a mosaic pavement of epithelial cells with characteristic patterns of microridges and microbridges. Interspersed between the epithelial cells were mucous goblet cell pores, which were not significantly different in number in the OE and the EISO. Nevertheless, their surface area in the EISO was significantly higher than in the OE. This could be an adaptation to secrete higher amounts of mucus on the EISO for keeping the branchial chamber lining clean, avoiding clogging, the increased slipperiness reducing friction from water flow and increased efficiency in protecting against microbial attachments. Rounded bulges on the OE and the EISO were associated with mucous goblet cells. The absence of the taste buds in the EISO, in contrast to the OE, suggests that their function in the branchial chamber may not be of much significance in this fish. Breeding tubercles on the OE are believed to facilitate better contact between the male and female during breeding.
Phylogeography of the Australian sugar glider (Petaurus breviceps): evidence for a new divergent lineage in eastern Australia
Authors: Malekian Mansoureh , Cooper Steven J. B. , Carthew Susan M.
Published: September 2010

The sugar glider (Petaurus breviceps) shows considerable variation in external morphology and mitochondrial DNA (mtDNA) diversity across its distribution in New Guinea and Australia. Here we investigate the phylogeography of P. breviceps in Australia using data from two mitochondrial genes (ND2 and ND4) and a nuclear gene (ω-globin). Phylogenetic analyses revealed the existence of two divergent mtDNA clades that are distributed over distinct geographical regions, one from coastal New South Wales and south-eastern Queensland and a second over the remaining distributional range of the species in Australia. The two groups generally had distinct ω-globin haplotypes that differed by one or two mutational steps. Analyses of Molecular Variation further supported the presence of at least two populations, accounting for 84.8% of the total mtDNA variation and 44% of the ω-globin variation. The general concordance of phylogeographic and population analyses suggests that population subdivision, possibly resulting from the combined influences of aridification after the Pliocene and uplift of the Great Dividing Range has impacted the evolution of P. breviceps. Our results also show that the geographical distribution of the two evolutionary lineages does not correspond with the distribution of the current morphological subspecies and we further propose that they be considered as separate Evolutionarily Significant Units for the purposes of conservation management.
Induction of regulatory T cells by macrophages is dependent on production of reactive oxygen species
Authors: Kraaij Marina D. , Savage Nigel D. L. , van der Kooij Sandra W. , Koekkoek Karin , Wang Jun , van den Berg J. Merlijn , Ottenhoff Tom H. M. , Kuijpers Taco W. , Holmdahl Rikard , van Kooten Cees , Gelderman Kyra A.
Published: September 2010

The phagocyte NAPDH–oxidase complex consists of several phagocyte oxidase (
phox)
proteins, generating reactive oxygen species (ROS) upon activation. ROS are involved in the defense against microorganisms and also in immune regulation. Defective ROS formation leads to chronic granulomatous disease (CGD) with increased incidence of autoimmunity and disturbed resolution of inflammation. Because regulatory T cells (Tregs) suppress autoimmune T-cell responses and are crucial in down-regulating immune responses, we hypothesized that ROS deficiency may lead to decreased Treg induction. Previously, we showed that in p47

phox

-mutated mice, reconstitution of macrophages (Mph) with ROS-producing capacity was sufficient to protect the mice from arthritis. Now, we present evidence that Mph-derived ROS induce Tregs. In vitro, we showed that Mph ROS-dependently induce Treg, using an NADPH-oxidase inhibitor. This finding was confirmed genetically: rat or human CGD Mph with mutated p47

phox

or gp91

phox

displayed hampered Treg induction and T-cell suppression. However, basal Treg numbers in these subjects were comparable to those in controls, indicating a role for ROS in induction of peripheral Tregs. Induction of allogeneic delayed-type hypersensitivity with p47

phox

-mutated Mph confirmed the importance of Mph-derived ROS in Treg induction in vivo. We conclude that NAPDH oxidase activity in Mph is important for the induction of Tregs to regulate T cell-mediated inflammation.
Abl Tyrosine Kinase Phosphorylates Nonmuscle Myosin Light Chain Kinase to Regulate Endothelial Barrier Function
Authors: Dudek Steven M. , Chiang Eddie T. , Camp Sara M. , Guo Yurong , Zhao Jing , Brown Mary E. , Singleton Patrick A. , Wang Lichun , Desai Anjali , Arce Fernando T. , Lal Ratnesh , Van Eyk Jennifer E. , Imam Syed Z. , Garcia Joe G. N.
Published: September 2010

Nonmuscle myosin light chain kinase (nmMLCK), a multi-functional cytoskeletal protein critical to vascular homeostasis, is highly regulated by tyrosine phosphorylation. We identified multiple novel c-Abl–mediated nmMLCK phosphorylation sites by mass spectroscopy analysis (including Y231, Y464, Y556, Y846) and examined their influence on nmMLCK function and human lung endothelial cell (EC) barrier regulation. Tyrosine phosphorylation of nmMLCK increased kinase activity, reversed nmMLCK-mediated inhibition of Arp2/3-mediated actin polymerization, and enhanced binding to the critical actin-binding phosphotyrosine protein, cortactin. EC challenge with sphingosine 1-phosphate (S1P), a potent barrier-enhancing agonist, resulted in c-Abl and phosphorylated nmMLCK recruitment into caveolin-enriched microdomains, rapid increases in Abl kinase activity, and spatial targeting of c-Abl to barrier-promoting cortical actin structures. Conversely, reduced c-Abl expression in EC (siRNA) markedly attenuated S1P-mediated cortical actin formation, reduced the EC modulus of elasticity (assessed by atomic force microscopy), reduced nmMLCK and cortactin tyrosine phosphorylation, and attenuated S1P-mediated barrier enhancement. These studies indicate an essential role for Abl kinase in vascular barrier regulation via posttranslational modification of nmMLCK and strongly support c-Abl-cortactin-nmMLCK interaction as a novel determinant of cortical actin-based cytoskeletal rearrangement critical to S1P-mediated EC barrier enhancement.
Daughter Centriole Elongation Is Controlled by Proteolysis
Authors: Korzeniewski Nina , Cuevas Rolando , Duensing Anette , Duensing Stefan
Published: September 2010

The centrosome is the major microtubule-organizing center of most mammalian cells and consists of a pair of centrioles embedded in pericentriolar material. Before mitosis, the two centrioles duplicate and two new daughter centrioles form adjacent to each preexisting maternal centriole. After initiation of daughter centriole synthesis, the procentrioles elongate in a process that is poorly understood. Here, we show that inhibition of cellular proteolysis by Z-L3VS or MG132 induces abnormal elongation of daughter centrioles to approximately 4 times their normal length. This activity of Z-L3VS or MG132 was found to correlate with inhibition of intracellular protease-mediated substrate cleavage. Using a small interfering RNA screen, we identified a total of nine gene products that either attenuated (seven) or promoted (two) abnormal Z-L3VS–induced daughter centriole elongation. Our hits included known regulators of centriole length, including CPAP and CP110, but, interestingly, several proteins involved in microtubule stability and anchoring as well as centrosome cohesion. This suggests that nonproteasomal functions, specifically inhibition of cellular proteases, may play an important and underappreciated role in the regulation of centriole elongation. They also highlight the complexity of daughter centriole length control and provide a framework for future studies to dissect the molecular details of this process.
STAT1 Is Required for Redifferentiation during Madin-Darby Canine Kidney Tubulogenesis
Authors: Kim Minji , O'Brien Lucy Erin , Kwon Sang-Ho , Mostov Keith E.
Published: September 2010

Tubule formation in vitro using Madin-Darby canine kidney (MDCK) epithelial cells consists mainly of two processes. First, the cells undergo a partial epithelial–mesenchymal transition (pEMT), losing polarity and migrating. Second, the cells redifferentiate, forming cords and then tubules with continuous lumens. We have shown previously that extracellular signal-regulated kinase activation is required for pEMT. However, the mechanism of how the pEMT phase is turned off and the redifferentiation phase is initiated is largely unknown. To address the central question of the sequential control of these two phases, we used MDCK cells grown as cysts and treated with hepatocyte growth factor to model tubulogenesis. We show that signal transducer and activator of transcription (STAT)1 controls the sequential progression from the pEMT phase to the redifferentiation phase. Loss of STAT1 prevents redifferentiation. Constitutively active STAT1 allows redifferentiation to occur even when cells are otherwise prevented from progressing beyond the pEMT phase by exogenous activation of Raf. Moreover, tyrosine phosphorylation defective STAT1 partially restored cord formation in such cells, suggesting that STAT1 functions in part as nonnuclear protein mediating signal transduction in this process. Constitutively active or inactive forms of STAT1 did not promote lumen maturation, suggesting this requires a distinct signal.
Calponin 3 Regulates Actin Cytoskeleton Rearrangement in Trophoblastic Cell Fusion
Authors: Shibukawa Yukinao , Yamazaki Natsuko , Kumasawa Keiichi , Daimon Etsuko , Tajiri Michiko , Okada Yuka , Ikawa Masahito , Wada Yoshinao
Published: September 2010

Cell–cell fusion is an intriguing differentiation process, essential for placental development and maturation. A proteomic approach identified a cytoplasmic protein, calponin 3 (CNN3), related to the fusion of BeWo choriocarcinoma cells. CNN3 was expressed in cytotrophoblasts in human placenta. CNN3 gene knockdown promoted actin cytoskeletal rearrangement and syncytium formation in BeWo cells, suggesting CNN3 to be a negative regulator of trophoblast fusion. Indeed, CNN3 depletion promoted BeWo cell fusion. CNN3 at the cytoplasmic face of cytoskeleton was dislocated from F-actin with forskolin treatment and diffused into the cytoplasm in a phosphorylation-dependent manner. Phosphorylation sites were located at Ser293/296 in the C-terminal region, and deletion of this region or site-specific disruption of Ser293/296 suppressed syncytium formation. These CNN3 mutants were colocalized with F-actin and remained there after forskolin treatment, suggesting that dissociation of CNN3 from F-actin is modulated by the phosphorylation status of the C-terminal region unique to CNN3 in the CNN family proteins. The mutant missing these phosphorylation sites displayed a dominant negative effect on cell fusion, while replacement of Ser293/296 with aspartic acid enhanced syncytium formation. These results indicated that CNN3 regulates actin cytoskeleton rearrangement which is required for the plasma membranes of trophoblasts to become fusion competent.
Ablation of Nonmuscle Myosin II-B and II-C Reveals a Role for Nonmuscle Myosin II in Cardiac Myocyte Karyokinesis
Authors: Ma Xuefei , Jana Siddhartha S. , Anne Conti Mary , Kawamoto Sachiyo , Claycomb William C. , Adelstein Robert S.
Published: September 2010

Ablation of nonmuscle myosin (NM) II-A or NM II-B results in mouse embryonic lethality. Here, we report the results of ablating NM II-C as well as NM II-C/II-B together in mice. NM II-C ablated mice survive to adulthood and show no obvious defects compared with wild-type littermates. However, ablation of NM II-C in mice expressing only 12% of wild-type amounts of NM II-B results in a marked increase in cardiac myocyte hypertrophy compared with the NM II-B hypomorphic mice alone. In addition, these hearts develop interstitial fibrosis associated with diffuse N-cadherin and β-catenin localization at the intercalated discs, where both NM II-B and II-C are normally concentrated. When both NM II-C and II-B are ablated the B−C−/B−C− cardiac myocytes show major defects in karyokinesis. More than 90% of B−C−/B−C− myocytes demonstrate defects in chromatid segregation and mitotic spindle formation accompanied by increased stability of microtubules and abnormal formation of multiple centrosomes. This requirement for NM II in karyokinesis is further demonstrated in the HL-1 cell line derived from mouse atrial myocytes, by using small interfering RNA knockdown of NM II or treatment with the myosin inhibitor blebbistatin. Our study shows that NM II is involved in regulating cardiac myocyte karyokinesis by affecting microtubule dynamics.
The SARS Coronavirus E Protein Interacts with PALS1 and Alters Tight Junction Formation and Epithelial Morphogenesis
Authors: Teoh Kim-Tat , Siu Yu-Lam , Chan Wing-Lim , Schlüter Marc A. , Liu Chia-Jen , Peiris J. S. Malik , Bruzzone Roberto , Margolis Benjamin , Nal Béatrice
Published: September 2010

Intercellular tight junctions define epithelial apicobasal polarity and form a physical fence which protects underlying tissues from pathogen invasions. PALS1, a tight junction-associated protein, is a member of the CRUMBS3-PALS1-PATJ polarity complex, which is crucial for the establishment and maintenance of epithelial polarity in mammals. Here we report that the carboxy-terminal domain of the SARS-CoV E small envelope protein (E) binds to human PALS1. Using coimmunoprecipitation and pull-down assays, we show that E interacts with PALS1 in mammalian cells and further demonstrate that the last four carboxy-terminal amino acids of E form a novel PDZ-binding motif that binds to PALS1 PDZ domain. PALS1 redistributes to the ERGIC/Golgi region, where E accumulates, in SARS-CoV–infected Vero E6 cells. Ectopic expression of E in MDCKII epithelial cells significantly alters cyst morphogenesis and, furthermore, delays formation of tight junctions, affects polarity, and modifies the subcellular distribution of PALS1, in a PDZ-binding motif-dependent manner. We speculate that hijacking of PALS1 by SARS-CoV E plays a determinant role in the disruption of the lung epithelium in SARS patients.
Hypoxia Suppression of Bim and Bmf Blocks Anoikis and Luminal Clearing during Mammary Morphogenesis
Authors: Whelan Kelly A. , Caldwell Sarah A. , Shahriari Kristina S. , Jackson S. RaElle , Franchetti Lisa D. , Johannes Gregg J. , Reginato Mauricio J.
Published: September 2010

Proper adhesion to extracellular matrix is critical for epithelial cell survival. Detachment from matrix signals results in apoptosis, referred to as anoikis. Selective apoptosis of cells that become detached from matrix is associated with the formation of a lumen in three-dimensional mammary epithelial acinar structures in vitro. Because early breast cancer lesions such as carcinoma in situ, characterized by ducts exhibiting lumens filled with cells, are often associated with hypoxic markers, we sought to examine the role of hypoxia in anoikis and lumen formation in mammary epithelial cells. Here, we show that hypoxic conditions inhibit anoikis and block expression of proapoptotic BH3-only family members Bim and Bmf in epithelial cells. Hypoxia-mediated anoikis protection is associated with increased activation of the epidermal growth factor receptor–mitogen-activated protein kinase kinase–extracellular signal-regulated kinase (Erk) kinase pathway and requires the hypoxia-activated transcription factor. Consistent with these data, hypoxic conditions inhibit luminal clearing during morphogenesis in human mammary epithelial acini when grown in three-dimensional cultures and are associated with decreased expression of Bim and Bmf as well as Erk activation. We show that hypoxia regulates specific cell survival pathways that disrupt tissue architecture related to clearing of luminal space during mammary morphogenesis and suggest that hypoxia-mediated anoikis resistance may contribute to cancer progression.
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
Authors: Mariotti M. , Guigó R.
Published: September 2010

Motivation: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases.

Results: We present an homology-based in silico method to scan genomes for members of the known eukaryotic selenoprotein families: selenoprofiles. The core of the method is a set of manually curated highly reliable multiple sequence alignments of selenoprotein families, which are used as queries to scan genomic sequences. Results of the scan are processed through a number of steps, to produce highly accurate predictions of selenoprotein genes with little or no human intervention. Selenoprofiles is a valuable tool for bioinformatic characterization of eukaryotic selenoproteomes, and can complement genome annotation pipelines.

Availability and Implementation: Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise, SECISearch and a number of custom-made scripts and programs. The program is available at http://big.crg.cat/services/selenoprofiles. The predictions presented in this article are available through DAS at http://genome.crg.cat:9000/das/Selenoprofiles_ensembl.

Contact:  marco.mariotti@crg.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
Authors: Toedling Joern , Ciaudo Constance , Voinnet Olivier , Heard Edith , Barillot Emmanuel
Published: September 2010

Summary: The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals. Moreover, the package operates within and extends the ever-growing Bioconductor framework and thus enables users to leverage a multitude of methods for their data in order to answer specific research questions.

Availability and Implementation: The R package girafe is available from the Bioconductor web site: http://www.bioconductor.org/packages/release/bioc/html/girafe.html

An extensive vignette and the Bioconductor mailing lists provide additional documentation and help for using the package.

Contact:  joern.toedling@curie.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
Authors: Larget Bret R. , Kotha Satish K. , Dewey Colin N. , Ané Cécile
Published: September 2010

Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors.

Availability: BUCKy is open source and distributed under the GNU general public license at www.stat.wisc.edu/∼ane/bucky/.

Contact:  ane@stat.wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The binding site distance test score: a robust method for the assessment of predicted protein binding sites
Authors: Roche Daniel B. , Tetchner Stuart J. , McGuffin Liam J.
Published: September 2010

Motivation: We propose a novel method for scoring the accuracy of protein binding site predictions—the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community-wide prediction experiment—CASP8. While being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of non-binding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores while also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein–ligand binding site predictions.

Availability:  http://www.reading.ac.uk/bioinf/downloads/

Contact:  l.j.mcguffin@reading.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.