bluuebunny/crossref_metadata_2025 huggingface dataset:
Near-forward Raman study of a phonon-polariton reinforcement regime in the Zn(Se,S) alloy
Authors: Hajj Hussein R. , Pagès O. , Firszt F. , Marasek A. , Paszkowicz W. , Maillard A. , Broch L.
Published: August 2014

We investigate by near-forward Raman scattering a presumed reinforcement of the (A-C,B-C)-mixed phonon-polariton of a A1-xBxC zincblende alloy when entering its longitudinal optical-like (LO-like) regime near the Brillouin zone centre Γ, as predicted within the formalism of the linear dielectric response. A choice system to address such issue is ZnSe0.68S0.32 due to the moderate dispersion of its refractive index in the visible range, a sine qua non condition to bring the phonon-polariton insight near Γ. The LO-like reinforcement regime is actually accessed by using the 633.0 nm laser excitation, testified by the strong emergence of the (Zn-Se,Zn-S)-mixed phonon-polariton at ultimately small scattering angles.
Path dependent high strain, strain-rate deformation of polymer toroidal elements
Authors: Lee Chien-Wei , Nesterenko Vitali F.
Published: August 2014

The dynamic behavior of toroidal elements (o-rings) is investigated at the range of global engineering strains up to 0.7 and strain rates about 100 s−1. It was observed that the corresponding average dynamic stiffness of rubber toroidal elements increases up to 3 times in comparison with their quasistatic compression. The viscoelastic dynamic model using linear strain-rate dependence and Hertz damped model did not satisfactory agree with experimental data in investigated range of strains and strain-rates. In order to reflect experimental results, a modified viscoelastic model with power-law strain-rate dependence was proposed. Path dependent deformation of o-rings with different levels of pre-compression was investigated under dynamic loading conditions. It was found that dynamic response of pre-compressed o-rings at the initial strain range of 0.04–0.25 is similar to the behavior of uncompressed o-rings, but further increasing pre-compression to 0.4 and 0.5 results in different force-strain curves demonstrating memory effect. This phenomenon is explained using a model incorporating dependence of dynamic force on initial pre-compression introducing critical level of dynamic strain, after which memory of initial pre-compression fades. This model predicts that force history of weakly compressed o-rings (initial strain 4%) on the stage of loading represents an envelope for all other data in agreement with experiments. In all cases, the dynamic behavior was characterized by stiffer force-displacement curves in comparison with quasistatic compression of o-rings.
Ag and Au atoms intercalated in bilayer heterostructures of transition metal dichalcogenides and graphene
Authors: Iyikanat F. , Sahin H. , Senger R. T. , Peeters F. M.
Published: August 2014

The diffusive motion of metal nanoparticles Au and Ag on monolayer and between bilayer heterostructures of transition metal dichalcogenides and graphene are investigated in the framework of density functional theory. We found that the minimum energy barriers for diffusion and the possibility of cluster formation depend strongly on both the type of nanoparticle and the type of monolayers and bilayers. Moreover, the tendency to form clusters of Ag and Au can be tuned by creating various bilayers. Tunability of the diffusion characteristics of adatoms in van der Waals heterostructures holds promise for controllable growth of nanostructures.
Dual echelon femtosecond single-shot spectroscopy
Authors: Shin Taeho , Wolfson Johanna W. , Teitelbaum Samuel W. , Kandyla Maria , Nelson Keith A.
Published: August 2014

We have developed a femtosecond single-shot spectroscopic technique to measure irreversible changes in condensed phase materials in real time. Crossed echelons generate a two-dimensional array of time-delayed pulses with one femtosecond probe pulse. This yields 9 ps of time-resolved data from a single laser shot, filling a gap in currently employed measurement methods. We can now monitor ultrafast irreversible dynamics in solid-state materials or other samples that cannot be flowed or replenished between laser shots, circumventing limitations of conventional pump-probe methods due to sample damage or product buildup. Despite the absence of signal-averaging in the single-shot measurement, an acceptable signal-to-noise level has been achieved via background and reference calibration procedures. Pump-induced changes in relative reflectivity as small as 0.2%−0.5% are demonstrated in semimetals, with both electronic and coherent phonon dynamics revealed by the data. The optical arrangement and the space-to-time conversion and calibration procedures necessary to achieve this level of operation are described. Sources of noise and approaches for dealing with them are discussed.
High resolution electronic spectroscopy of the A 2Σ− − X 2Π1/2 transition of PtN
Authors: Womack Kaitlin , O’Brien Leah C. , Whittemore Sean , O’Brien James J. , Le Anh , Steimle Timothy C.
Published: August 2014

The (2,0) vibrational band of the A 2Σ− − X 2Π1/2 transition of platinum nitride, PtN, was recorded at Doppler-limited resolution using intracavity laser absorption spectroscopy (ILS) and at sub-Doppler resolution using molecular beam laser induced fluorescence (LIF) spectroscopy. Isotopologue structure for 194PtN, 195PtN, and 196PtN, magnetic hyperfine splitting due to 195Pt (I = ½), and nuclear quadrupole splitting due to 14N (I = 1) were observed in the spectrum. Molecular constants for the ground and excited states are derived. The hyperfine interactions are used to illuminate the nature of the A 2Σ− excited electronic state.
Probing the transition from an uncoupled to a strong near-field coupled regime between bright and dark mode resonators in metasurfaces
Authors: Singh Ranjan , Al-Naib Ibraheem , Chowdhury Dibakar Roy , Cong Longqing , Rockstuhl Carsten , Zhang Weili
Published: August 2014

The coupling of multiple plasmonic resonators that sustain bright or dark modes provide intriguing spectral signatures. However, probing the onset of coupling effects while engaging the resonators with an increasing proximity has not yet been studied experimentally in detail. Nevertheless, this is of utmost importance to bridge the phenomenological understanding with the peculiarities of real-world-samples. Here, we take advantage of the ability to control spatial dimensions of THz metasurfaces deep in the sub-wavelength domain to study different regimes that occur while coupling split-ring-resonators that sustain a bright and a dark mode with increasing strength. We identify the length scales at which the resonators are uncoupled and then enter the regimes of weak, moderate, and strong coupling. It is shown that a strong coupling takes place only at distances smaller than one hundredth of the resonance wavelength. Understanding the features that emerge from such hybridization is important to take advantage of fundamental effects in metamaterials such as classical analogs of electromagnetically induced transparency, lasing spaser, near-field manipulation, and sensing with dark mode resonances.
Automated single cell sorting and deposition in submicroliter drops
Authors: Salánki Rita , Gerecsei Tamás , Orgovan Norbert , Sándor Noémi , Péter Beatrix , Bajtay Zsuzsa , Erdei Anna , Horvath Robert , Szabó Bálint
Published: August 2014

Automated manipulation and sorting of single cells are challenging, when intact cells are needed for further investigations, e.g., RNA or DNA sequencing. We applied a computer controlled micropipette on a microscope admitting 80 PCR (Polymerase Chain Reaction) tubes to be filled with single cells in a cycle. Due to the Laplace pressure, fluid starts to flow out from the micropipette only above a critical pressure preventing the precise control of drop volume in the submicroliter range. We found an anomalous pressure additive to the Laplace pressure that we attribute to the evaporation of the drop. We have overcome the problem of the critical dropping pressure with sequentially operated fast fluidic valves timed with a millisecond precision. Minimum drop volume was 0.4–0.7 μl with a sorting speed of 15–20 s per cell. After picking NE-4C neuroectodermal mouse stem cells and human primary monocytes from a standard plastic Petri dish we could gently deposit single cells inside tiny drops. 94 ± 3% and 54 ± 7% of the deposited drops contained single cells for NE-4C and monocytes, respectively. 7.5 ± 4% of the drops contained multiple cells in case of monocytes. Remaining drops were empty. Number of cells deposited in a drop could be documented by imaging the Petri dish before and after sorting. We tuned the adhesion force of cells to make the manipulation successful without the application of microstructures for trapping cells on the surface. We propose that our straightforward and flexible setup opens an avenue for single cell isolation, critically needed for the rapidly growing field of single cell biology.
Band gap engineering for graphene by using Na+ ions
Authors: Sung S. J. , Lee P. R. , Kim J. G. , Ryu M. T. , Park H. M. , Chung J. W.
Published: August 2014

Despite the noble electronic properties of graphene, its industrial application has been hindered mainly by the absence of a stable means of producing a band gap at the Dirac point (DP). We report a new route to open a band gap (Eg) at DP in a controlled way by depositing positively charged Na+ ions on single layer graphene formed on 6H-SiC(0001) surface. The doping of low energy Na+ ions is found to deplete the π* band of graphene above the DP, and simultaneously shift the DP downward away from Fermi energy indicating the opening of Eg. The band gap increases with increasing Na+ coverage with a maximum Eg≥0.70 eV. Our core-level data, C 1s, Na 2p, and Si 2p, consistently suggest that Na+ ions do not intercalate through graphene, but produce a significant charge asymmetry among the carbon atoms of graphene to cause the opening of a band gap. We thus provide a reliable way of producing and tuning the band gap of graphene by using Na+ ions, which may play a vital role in utilizing graphene in future nano-electronic devices.
Impurity precipitation in atomized particles evidenced by nano x-ray diffraction computed tomography
Authors: Bonnin Anne , Wright Jonathan P. , Tucoulou Rémi , Palancher Hervé
Published: August 2014

Performances and physical properties of high technology materials are influenced or even determined by their initial microstructure and by the behavior of impurity phases. Characterizing these impurities and their relations with the surrounding matrix is therefore of primary importance but it unfortunately often requires a destructive approach, with the risk of misinterpreting the observations. The improvement we have done in high resolution X-ray diffraction computed tomography combined with the use of an X-ray nanoprobe allows non-destructive crystallographic description of materials with microscopic heterogeneous microstructure (with a grain size between 10 nm and 10 μm). In this study, the grain localization in a 2D slice of a 20 μm solidified atomized γU-Mo particle is shown and a minority U(C,O) phase (1 wt. %) with sub-micrometer sized grains was characterized inside. Evidence is presented showing that the onset of U(C,O) grain crystallization can be described by a precipitation mechanism since one single U-Mo grain has direct orientation relationship with more than one surrounding U(C,O) grains.
Valence and conduction band alignment at ScN interfaces with 3C-SiC (111) and 2H-GaN (0001)
Authors: King Sean W. , Nemanich Robert J. , Davis Robert F.
Published: August 2014

In order to understand and predict the behavior of future scandium nitride (ScN) semiconductor heterostructure devices, we have utilized in situ x-ray and ultra-violet photoelectron spectroscopy to determine the valence band offset (VBO) present at ScN/3C-SiC (111) and 2H-GaN (0001)/ScN (111) interfaces formed by ammonia gas source molecular beam epitaxy. The ScN/3C-SiC (111) VBO was dependent on the ScN growth temperature and resistivity. VBOs of 0.4 ± 0.1 and 0.1 ± 0.1 eV were, respectively, determined for ScN grown at 925 °C (low resistivity) and 800 °C (high resistivity). Using the band-gaps of 1.6 ± 0.2 and 1.4 ± 0.2 eV previously determined by reflection electron energy loss spectroscopy for the 925 and 800 °C ScN films, the respective conduction band offsets (CBO) for these interfaces were 0.4 ± 0.2 and 0.9 ± 0.2 eV. For a GaN (0001) interface with 925 °C ScN (111), the VBO and CBO were similarly determined to be 0.9 ± 0.1 and 0.9 ± 0.2 eV, respectively.
Enhanced and adjustable adsorption of organo-functional groups on Li decorated carbon nanotubes: A first principle study
Authors: Li Yutao , Wang Xiaojie , Shi Wenhao , Yan Zeyu , Zhao Chengbo , Chen Chi , Miao Ling , Jiang Jianjun
Published: August 2014

The adsorption of several organo-functional groups (−NH2, −CH3, −COOH, −CHO, and −OH) and alanine on Li decorated carbon nanotubes (CNTs) are studied, based on the first-principle calculations. The calculated binding energies on Li−CNTs show obvious enhancement relative to the cases on pure CNTs, from about 0.3 eV to about 1.4 eV except −CH3, which is attributed to strong electrostatic dipole attraction between positive Li ion and polarized organo-functional groups by charge population analysis. It is interesting that the adsorption could be effectively adjusted under external electric field for the interaction with Li−group dipole. For the combinational contribution of charge redistribution and interaction of inherent electric dipole with external electric field, the adsorption of these organo-functional groups shows two discriminative variety trends. Finally, the adsorption of alanine including −NH2, −CH3, and −COOH groups is studied as an illustration to generalize above conclusions to organic macromolecule on Li decorated CNTs.
Selenization of Sb2Se3 absorber layer: An efficient step to improve device performance of CdS/Sb2Se3 solar cells
Authors: Leng Meiying , Luo Miao , Chen Chao , Qin Sikai , Chen Jie , Zhong Jie , Tang Jiang
Published: August 2014

Sb2Se3 appeared as a very promising solar absorber because of their attractive material, optical and electrical properties. Previously, we reported thermal evaporated superstrate CdS/Sb2Se3 solar cell achieving 1.9% efficiency. In this letter, we improved device performance to 3.7% (Voc = 0.335 V, Jsc = 24.4 mA/cm2, and FF = 46.8%) by an additional selenization step. Careful external quantum efficiency, capacitance-voltage profiling, and photoresponse study indicated selenization probably compensated selenium loss during thermal evaporation, reducing VSe associated recombination loss and improving device performance.
Reduction of low frequency magnetic noise by voltage-induced magnetic anisotropy modulation in tunneling magnetoresistance sensors
Authors: Wisniowski P. , Dąbek M. , Skowronski W. , Stobiecki T. , Cardoso S. , Freitas P. P.
Published: August 2014

We demonstrate the reduction and control of magnetic noise by voltage-induced perpendicular anisotropy modulation in CoFeB/MgO/CoFeB sensors. The noise decreases with the increase of the perpendicular anisotropy energy induced by the bias voltage polarity reversal. The bias reversal between −1 and +1 V results in a reduction of the normalized 1/f magnetic noise parameters by a factor of 7.3 and the thermal magnetic noise by a factor of 6.8. In the state of the highest field sensitivity, the lowest normalized 1/f magnetic noise parameter reaches 6.45 × 10−14 μm3T. The results indicate that voltage-induced anisotropy modulation can be used to control and suppress magnetization fluctuations in the sensing layer and thus, significantly reduce the magnetic noise.
The impact of oxygen incorporation during intrinsic ZnO sputtering on the performance of Cu(In,Ga)Se2 thin film solar cells
Authors: Lee Kkotnim , Ok Eun-A , Park Jong-Keuk , Kim Won Mok , Baik Young-Joon , Kim Donghwan , Jeong Jeung-hyun
Published: August 2014

We investigated the impact of incorporating 2% oxygen during intrinsic ZnO sputtering on the efficiency of Cu(In,Ga)Se2 solar cells. The added oxygen not only reduced the optical absorption loss of the Al-doped ZnO overlaying layer but also improved the electronic properties of the underlying CdS/Cu(In,Ga)Se2 by increasing carrier density, lowering defect level, and increasing diffusion length, eventually enhancing JSC, VOC, and fill factor. It was found that the Na doping concentration was significantly increased around the CdS/Cu(In,Ga)Se2 junction due to the plasma-activated oxygen. The improved electronic properties are better explained by the increased Na concentration than simply the oxygen-related defect passivation.
Controlling the magnetization reversal in planar nanostructures with wire-ring morphology
Authors: Corona R. M. , Aranda A. , Palma J. L. , Lopez C. E. , Escrig J.
Published: August 2014

Magnetization reversal in planar nanowires has been controlled using structures with a larger area pad connected to a nanowire or by means of patterned variations in the planar nanowire such as notches. In this letter, we have introduced a magnetic nanostructure defined as a planar nanostructure with wire-ring morphology. In particular, we have performed micromagnetic simulations to investigate how the magnetic properties (coercivity and remanence) change as a function of the geometric parameters of the nanostructure. Additionally, we observe that when the ring is very thin, the system reverses its magnetization by nucleation and propagation of domain walls along the nanowire. Conversely, when the ring has very thick walls, or directly turns into a solid cylinder, the system nucleates a vortex in the ring/cylinder, and then propagates the domain walls toward the nanowire sections. This reversal process is characterized by a step or plateau in the hysteresis curve, that is, a region in which differential magnetic susceptibility presents a local minimum or, ideally, vanishes. Finally, this nanostructure can be used in many potential applications related to the control of domain walls in planar nanowires.
Boron-doped superlattices and Bragg mirrors in diamond
Authors: Fiori A. , Bousquet J. , Eon D. , Omnès F. , Bellet-Amalric E. , Bustarret E.
Published: August 2014

A periodic modulation of the boron doping level of single crystal diamond multilayers over more than three orders of magnitude during epitaxial growth by microwave plasma-enhanced chemical vapor deposition is shown to yield Bragg mirrors in the visible. The thicknesses and doping level of the individual layers were controlled by in situ spectroscopic ellipsometry, enabling to tune the reflectance peak to the wavelength range of diamond color centers, such as NV0 or NV−. The crystalline quality, periodicity, and sharpness of the doping transitions in these doping superlattices over tens of periods were confirmed by high resolution X-ray diffraction.
Spaces of Benevolent Abandonment: The German Air Security Decision of 2006
Authors: Hannah Matthew G
Published: August 2014

This paper presents the 2006 Air Security decision rendered by the German Constitutional Court as an occasion to question typical assumptions in critical scholarship about the relations between sovereign power and biopolitics and about the kinds of political spaces these logics can generate. After a brief overview of the argument the first part of the paper summarizes the 2006 Air Security decision and the legislation it addressed. Public debates in Germany around the issue are then surveyed, with an emphasis on the contrast drawn by a number of commentators between utilitarian and ‘Kantian’ ethical positions. As a result of the apparently Kantian line it took, the Court conjured a specific but ambivalent space of ‘benevolent abandonment’. The latter half of the paper explores the theoretical implications of the decision, arguing that understanding it as Kantian is too simple, and relating it to Michel Foucault's and Georgio Agamben's theorizations of the nexus of biopower and sovereignty. While the 2006 decision does not easily fit within Agamben's discussion of the ‘sovereign ban’ in Homo Sacer (Stanford University Press, 1998), it can be grasped by means of another strand of his reasoning, most fully developed in his discussion of “inoperativity” in The Kingdom and the Glory (Stanford University Press, 2011).
Transcriptional regulation of phosphate transporters from Lolium perenne and its mycorrhizal symbionts in response to phosphorus supply
Authors: Liu Qianhe , Parsons Anthony J. , Xue Hong , Jones Chris S. , Rasmussen Susanne
Published: August 2014

Phosphate (P) uptake is critical for plant growth, but to date little is known about P uptake and transport in the pasture grass Lolium perenne L. We have identified a putative P transporter (PT) from L. perenne mycorrhizal roots (LpPT1) and assessed its transcriptional regulation by soil P availability and mycorrhizal colonisation. We also investigated transcript levels of fungal PTs from the two arbuscular mycorrhizal species Rhizophagus intraradices and Funneliformis mosseae. Our analyses indicated that LpPT1 codes for a high affinity PT most likely responsible for direct P uptake from the soil. LpPT1 is highly expressed in roots of plants grown at low P, whereas high P repressed its expression. LpPT1 was not expressed in above-ground plant tissues. Colonisation with R. intraradices did not affect expression of LpPT1 significantly. Transcript levels of the R. intraradices PT were not affected by P availability but the F. mosseae PT was repressed by high P supply, particularly in intraradical hyphae. Our study could assist in deciphering the molecular mechanisms of P uptake in the pasture grass L. perenne.
Radial oxygen loss and physical barriers in relation to root tissue age in species with different types of aerenchyma
Authors: Manzur Milena E. , Grimoldi Agustín A. , Insausti Pedro , Striker Gustavo G.
Published: August 2014

Plant root aeration relies on aerenchyma and barrier formation in outer cortex influencing the radial oxygen loss (ROL) from roots towards the rhizosphere. Plant species display large variation in strategies for both responses. We investigated the impacts of root-zone hypoxia on aerenchyma formation and development of ROL apoplastic barriers in the outer cortex as a function of root tissue age using three lowland grassland species, each with alternative aerenchyma structure. All species increased root aerenchyma and continued with root elongation after imposing hypoxia. However, ROL barrier development differed: (i) Rumex crispus L. displayed only ‘partial’ barrier to ROL evidenced at older tissue ages, (ii) Cyperus eragrostis Lam. initiated a ‘tighter’ barrier to ROL following exposure to hypoxia in tissues older than 3 days, and (iii) Paspalidium geminatum (Forssk.) Stapf demonstrated highly effective inhibition of ROL under aerated and hypoxic conditions at all tissue ages related to constitutive ‘tight’ apoplastic barriers in outer cortex. Thus, hypoxic conditions affected root elongation and ‘tightness’ of apoplastic barriers depending on species. The physiological implications of the different ROL responses among species in relation to the differential formation of barriers are discussed.
Early age at first sex: associations with sexual health and sociodemographic factors among a sample of young music festival attendees in Melbourne
Authors: Vella Alyce M. , Agius Paul A. , Bowring Anna L. , Hellard Margaret E. , Lim Megan S. C.
Published: August 2014

Background
Age at first sex (AFS) is associated with adverse outcomes. We explore associated factors and correlates of ‘early’ AFS (<16 years). Methods: In 2009–11, participants (16–29 years) were recruited. Multivariate Cox regression explored correlates of AFS. Logistic regression analysis explored associations between early AFS and risk behaviours. Results: Of 3563 participants, 79% were sexually active. Median AFS was 17 years. Compared with those aged 25–29 years, younger participants reported younger AFS [16–17 years: adjusted hazard ratio (AHR) = 1.87, P < 0.01; 18–19 years: AHR = 1.47, P < 0.01, 20–24 years: AHR = 1.19, P < 0.01]. Of those sexually active, 29% reported early AFS. Early AFS was associated with being male [adjusted odds ratio (AOR) = 1.25, P < 0.05], being younger (16–17 years: AOR = 11.10, P < 0.01; 18–19 years: AOR = 3.60, P < 0.01; 20–24 years: AOR = 1.83, P < 0.01; compared with 25–29 years), having no education after high school (AOR = 1.52, P < 0.01), living alone (AOR = 1.84, P < 0.01) or with a partner (AOR = 1.57, P = 0.01), having more than five lifetime sex partners (AOR = 3.22, P = 0.01), inconsistent condom use in the past 12 months (AOR = 1.43, P < 0.01), ever using illicit drugs (AOR = 1.69, P < 0.01) and ever injecting drugs (AOR = 3.45, P < 0.01). Conclusions: The results highlight the importance of comprehensive sex education.
Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein
Authors: Kellner Ruth , Hofmann Hagen , Barducci Alessandro , Wunderlich Bengt , Nettels Daniel , Schuler Benjamin
Published: August 2014

Significance

Molecular chaperones are a group of proteins that are essential for avoiding the aggregation of other proteins in the crowded cellular environment. Chaperones function by interacting with these substrate proteins in different ways. However, it has remained a challenge to measure the changes that occur in the substrate proteins and understand how these changes prevent misfolding or aggregation. Here we investigate a chaperone system that keeps the substrate protein denatured by clamping the polypeptide chain. We observe an expansion of the substrate protein chain up to 30-fold in volume owing to steric repulsion between multiple copies of the chaperone bound to a single substrate protein. In this way, unwanted interactions within or between substrate proteins can be prevented.
The invisible war on nature: the Abyssinian war (1935–1936) in newsreels and documentaries in Fascist Italy
Authors: Caprotti Federico
Published: August 2014

This contribution to the special issue focuses on newsreels and documentaries that were produced concerning the Second Italo–Ethiopian War (1935–1936), commonly known as the Abyssinian War. It aims to contextualise LUCE's filmic production on the war, so as to create a framework in which the institute can be understood not only as being part of a wider politics of propaganda in Fascist Italy, but as an example of a modern socio-technical organisation that enabled the discursive construction of East African nature as ‘Other’ and therefore helped to justify colonial war as a process of sanitised creative destruction aimed at replacing a previous, negative ‘first nature’ with a positive, Fascist and Italian ‘second nature’. The article draws on archival documents from Mussolini's government cabinet, and on LUCE documentaries and newsreels; these sources are used to create a background against which LUCE's concern with the Second Italo–Ethiopian War can be understood.
Cdc1 removes the ethanolamine phosphate of the first mannose of GPI anchors and thereby facilitates the integration of GPI proteins into the yeast cell wall
Authors: Vazquez Hector M. , Vionnet Christine , Roubaty Carole , Conzelmann Andreas
Published: August 2014

Temperature-sensitive cdc1tsmutants are reported to stop the cell cycle upon a shift to 30°C in early G2, that is, as small budded cells having completed DNA replication but unable to duplicate the spindle pole body. A recent report showed that PGAP5, a human homologue of CDC1, acts as a phosphodiesterase removing an ethanolamine phosphate (EtN-P) from mannose 2 of the glycosylphosphatidylinositol (GPI) anchor, thus permitting efficient endoplasmic reticulum (ER)-to-Golgi transport of GPI proteins. We find that the essential CDC1 gene can be deleted in mcd4∆ cells, which do not attach EtN-P to mannose 1 of the GPI anchor, suggesting that Cdc1 removes the EtN-P added by Mcd4. Cdc1-314tsmutants do not accumulate GPI proteins in the ER but have a partial secretion block later in the secretory pathway. Growth tests and the genetic interaction profile of cdc1-314tspinpoint a distinct cell wall defect. Osmotic support restores GPI protein secretion and actin polarization but not growth. Cell walls of cdc1-314tsmutants contain large amounts of GPI proteins that are easily released by β-glucanases and not attached to cell wall β1,6-glucans and that retain their original GPI anchor lipid. This suggests that the presumed transglycosidases Dfg5 and Dcw1 of cdc1-314tstransfer GPI proteins to cell wall β1,6-glucans inefficiently.
More closely related plants have more distinct mycorrhizal communities
Authors: Reinhart Kurt O , Anacker Brian L
Published: August 2014

Neighbouring plants are known to vary from having similar to dissimilar arbuscular mycorrhizal fungal (AMF) communities. One possibility is that closely related plants have more similar AMF communities than more distantly related plants, an indication of phylogenetic host specificity. Here, we investigated the structure of AMF communities among dominant grassland plants at three sites in the Northern Great Plains to test whether the pairwise phylogenetic distance among plant species was correlated with pairwise AMF community dissimilarity. For eight dominant and co-occurring grassland plant species, we reconstructed a phylogeny based on DNA data and characterized the AMF communities of their roots at each site. Community analyses revealed that AMF communities varied among sites and among plant species. Contrary to expectations for phylogenetic host specificity, we found that within a site more closely related plants had more distinct AMF communities despite their having similar phenologies. Associations with unique AMF communities may enhance the functional complementarity of related species and promote their coexistence.
Estimating biomass, fishing mortality, and “total allowable discards” for surveyed non-target fish
Authors: Shephard Samuel , Reid David G. , Gerritsen Hans D. , Farnsworth Keith D.
Published: August 2014

Demersal fisheries targeting a few high-value species often catch and discard other “non-target” species. It is difficult to quantify the impact of this incidental mortality when population biomass of a non-target species is unknown. We calculate biomass for 14 demersal fish species in ICES Area VIIg (Celtic Sea) by applying species- and length-based catchability corrections to catch records from the Irish Groundfish Survey (IGFS). We then combine these biomass estimates with records of commercial discards (and landings for marketable non-target species) to calculate annual harvesting rates (HR) for each study species. Uncertainty is incorporated into estimates of both biomass and HR. Our survey-based HR estimates for cod and whiting compared well with HR-converted fishing mortality (F) estimates from analytical assessments for these two stocks. Of the non-target species tested, red gurnard (Chelidonichthys cuculus) recorded some annual HRs greater than those for cod or whiting; challenging “Pope’s postulate” that F on non-target stocks in an assemblage will not exceed that on target stocks. We relate HR for each species to two corresponding maximum sustainable yield (MSY) reference levels; six non-target species (including three ray species) show annual HRs ≥ HRMSY. This result suggests that it may not be possible to conserve vulnerable non-target species when F is coupled to that of target species. Based on biomass, HR, and HRMSY, we estimate “total allowable catch” for each non-target species.
Attraction of Walnut Twig Beetle Pityophthorus juglandis (Coleoptera: Curculionidae) to the Fungus Geosmithia morbida
Authors: Luna Emily , Cranshaw Whitney , Tisserat Ned
Published: August 2014

Geosmithia morbida causes thousand cankers disease of Juglans nigra and it is transmitted by the walnut twig beetle (WTB, Pityophthorus juglandis). Along with WTB, an ambrosia beetle, Xyleborinus saxeseni, is commonly associated with thousand cankers disease in the later stages of J. nigra decline, although X. saxeseni is not a known vector of G. morbida. We initiated studies to determine whether WTBs or X. saxeseni were attracted to volatiles produced by G. morbida and other bark fungi in a laboratory choice-test setting. There was no difference between the numbers of emerged WTB adults that were collected in tubes containing potato dextrose agar colonized by G. morbida and those in tubes containing agar only. More adult X. saxeseni were collected in tubes containing agar only compared with G. morbida. Walnut twig beetle larvae migrated more frequently toward an agar plug colonized by G. morbida and Fusarium solani compared with an un-colonized agar plug. No larval preference was observed when agar plugs colonized by F. solani and G. morbida, or G. morbida and Penicillium solitum, were placed in the same petri dish. These results suggest that WTB larvae are attracted to bark fungi in general, but not specifically to G. morbida.

Accepted 27 June 2014. Published 13 August 2014.
Survey of Plant-Parasitic Nematodes in Kansas and Eastern Colorado Wheat Fields
Authors: Todd T. C. , Appel J. A. , Vogel J. , Tisserat N. A.
Published: August 2014

Observations on the prevalence and abundance of plant-parasitic nematodes were made from soil and root samples collected from 2,640 wheat fields in Kansas and Colorado during 2007-2010. Stunt nematodes (predominately Merlinius brevidens and Quinisulcius acutus), root-lesion nematodes (predominately Pratylenchus neglectus), and pin nematodes (Paratylenchus projectus) were the most commonly encountered taxa. Maximum soil population densities of 6,520 and 1,880 nematodes/100 cm3 soil were observed for pin and stunt nematodes, respectively, while a maximum root population density of 90,309 nematodes/g dry root was observed for root-lesion nematodes. Lower nematode densities were associated with wheat following corn, grain sorghum, or soybean for pin and stunt nematodes, and with wheat following fallow for root-lesion nematodes. Based on the results of this survey, 6% and 8% of wheat acreage in the central Great Plains are estimated to be at risk for significant (>5%) yield loss due to stunt nematodes and root-lesion nematodes, respectively. The number of fields with high population densities of both stunt and root-lesion nematodes was negligible (1%); therefore, the total wheat acreage with nematode populations above provisional economic thresholds is estimated to be ∼13%. Damage relationships with greater accuracy, precision, and relevance are necessary to establish reliable yield loss estimates for this region.

3 June 2014. 11 August 2014.
A Microfluidic Assay for Identifying Differential Responses of Plant and Human Fungal Pathogens to Tobacco Phylloplanins
Authors: Mattupalli Chakradhar , Spraker Joseph E. , Berthier Erwin , Charkowski Amy O. , Keller Nancy P. , Shepherd Ryan W.
Published: August 2014

Phylloplanins are defensive glycoproteins secreted onto leaf surfaces by trichome-bearing plants such as tobacco (Nicotiana tabacum). They are of interest because of their antimicrobial properties, but like other natural product bioactives, the assessment and screening of phylloplanins biological activity is impeded by limited availabilities of active compounds. Here we report an inexpensive microfluidic approach that requires ≤ 20 microliters of tobacco phylloplanins to assess spore germination inhibition of plant and human fungal pathogens. Spores of Colletotrichum coccodes and Aspergillus fumigatus suspended in solutions containing tobacco phylloplanins did not germinate at 48 and 30 h post-treatment, respectively. Tobacco phylloplanins transiently inhibited spore germination of Fusarium sambucinum, but had no detectable activity against Alternaria solani or Verticillium albo-atrum at the concentrations tested, demonstrating differential sensitivity of fungi to tobacco phylloplanins.

4 August 2014. 14 August 2014.
Effect of Foliar Fungicides on Late-season Anthracnose Stem Blight on Soybean
Authors: Bestor Nathan R. C. , Robertson Alison E. , Mueller Daren S.
Published: August 2014

Anthracnose stem blight, caused by Colletotrichum truncatum, is responsible for soybean (Glycine max) yield losses in subtropical and tropical growing regions. There are inadequate data regarding the effect of anthracnose stem blight on yield in Iowa, and it is unknown if fungicide application can manage this disease. Field studies were conducted from 2008 to 2010 to determine the effect of fungicide application timing on late-season development of this disease. We also investigated the effect of anthracnose stem blight on yield and specific yield components. Fungicides reduced late-season symptom development when compared to the untreated control; however, there were no differences in yield and yield components. While foliar fungicides can reduce late-season disease development, anthracnose stem blight typically should not affect crop management decisions involving use of foliar fungicides on soybean in Iowa.

Accepted 7 July 2014. Publication 14 August 2014.
Effect of Fusarium tricinctum on Growth of Soybean and a Molecular-based Method of Identification
Authors: Chitrampalam Periasamy , Nelson Berlin D.
Published: August 2014

Infection of soybean seedlings by Fusarium tricinctum and effects of isolates on growth and yield were evaluated in laboratory and field experiments in Fargo, North Dakota. Twenty one isolates from soybean roots collected in the field-infected cortical root tissue of soybean seedlings within 40 h at 23°C. In two field experiments conducted in 2012 and 2013, selected isolates significantly reduced emergence by 38 to 59% at three weeks after planting compared with noninoculated control. In 2013, isolates 91-1-8 and 91-319-3 significantly reduced plant height, number of plants with trifoliate leaves, and root biomass, but the reduction was significantly greater with isolate 91-1-8. Percent yield reduction with isolate 91-1-8 was significantly higher (90%) than with isolate 91-319-3 (31%) compared with noninoculated control. Primers specific for F. tricinctum were developed, and the presence of the pathogen in roots was verified in PCR. The problems associated with identification of F. tricinctum are discussed and a method for verifying identification of this species is suggested to aid identification of this pathogen from field samples. Results indicate F. tricinctum may have an important role in soybean root health in the northern soybean production area.

4 August 2014. 15 August 2014.
Dysgenesis of Enteroendocrine Cells in Aristaless‐Related Homeobox Polyalanine Expansion Mutations
Authors: Terry Natalie A. , Lee Randall A. , Walp Erik R. , Kaestner Klaus H. , Lee May Catherine
Published: August 2014

Objectives:

Severe congenital diarrhea occurs in approximately half of patients with Aristaless‐Related Homeobox (ARX) null mutations. The cause of this diarrhea is unknown. In a mouse model of intestinal Arx deficiency, the prevalence of a subset of enteroendocrine cells is altered, leading to diarrhea. Because polyalanine expansions within the ARX protein are the most common mutations found in ARX‐related disorders, we sought to characterize the enteroendocrine population in human tissue of an ARX(GGC)7 mutation and in a mouse model of the corresponding polyalanine expansion (Arx(GCG)7).

Methods:

Immunohistochemistry and quantitative real‐time polymerase chain reaction were the primary modalities used to characterize the enteroendocrine populations. Daily weights were determined for the growth curves, and Oil‐Red‐O staining on stool and tissue identified neutral fats.

Results:

An expansion of 7 alanines in the first polyalanine tract of both human ARX and mouse Arx altered enteroendocrine differentiation. In human tissue, cholecystokinin, glucagon‐like peptide 1, and somatostatin populations were reduced, whereas the chromogranin A population was unchanged. In the mouse model, cholecystokinin and glucagon‐like peptide 1 populations were also lost, although the somatostatin‐expressing population was increased. The ARX(GGC)7 protein was present in human tissue, whereas the Arx(GCG)7 protein was degraded in the mouse intestine.

Conclusions:

ARX/Arx is required for the specification of a subset of enteroendocrine cells in both humans and mice. Owing to protein degradation, the Arx(GCG)7 mouse recapitulates findings of the intestinal Arx null model, but is not able to further the study of the differential effects of the ARX(GCG)7 protein on its transcriptional targets in the intestine.
Influence of turbulence on the wake of a marine current turbine simulator
Authors: Blackmore T. , Batten W. M. J. , Bahaj A. S.
Published: August 2014

Marine current turbine commercial prototypes have now been deployed and arrays of multiple turbines under design. The tidal flows in which they operate are highly turbulent, but the characteristics of the inflow turbulence have not being considered in present design methods. This work considers the effects of inflow turbulence on the wake behind an actuator disc representation of a marine current turbine. Different turbulence intensities and integral length scales were generated in a large eddy simulation using a gridInlet, which produces turbulence from a grid pattern on the inlet boundary. The results highlight the significance of turbulence on the wake profile, with a different flow regime occurring for the zero turbulence case. Increasing the turbulence intensity reduced the velocity deficit and shifted the maximum deficit closer to the turbine. Increasing the integral length scale increased the velocity deficit close to the turbine due to an increased production of turbulent energy. However, the wake recovery was increased due to the higher rate of turbulent mixing causing the wake to expand. The implication of this work is that marine current turbine arrays could be further optimized, increasing the energy yield of the array when the site-specific turbulence characteristics are considered.
Negative regulation of germination-arrest factor production in Pseudomonas fluorescens WH6 by a putative extracytoplasmic function sigma factor
Authors: Okrent Rachel A. , Halgren Anne B. , Azevedo Mark D. , Chang Jeff H. , Mills Dallice I. , Maselko Maciej , Armstrong Donald J. , Banowetz Gary M. , Trippe Kristin M.
Published: August 2014

Pseudomonas fluorescensWH6 secretes a germination-arrest factor (GAF) that we have identified previously as 4-formylaminooxyvinylglycine. GAF irreversibly inhibits germination of the seeds of numerous grassy weeds and selectively inhibits growth of the bacterial plant pathogenErwinia amylovora. WH6-3, a mutant that has lost the ability to produce GAF, contains a Tn5insertion inprtR,a gene that has been described previously in some strains ofP. fluorescensas encoding a transmembrane regulator. As in these other pseudomonads, in WH6,prtRoccurs immediately downstream ofprtI, which encodes a protein homologous to extracytoplasmic function (ECF) sigma factors. These two genes have been proposed to function as a dicistronic operon. In this study, we demonstrated that deletion ofprtIin WT WH6 had no effect on GAF production. However, deletion ofprtIin the WH6-3 mutant overcame the effects of the Tn5insertion inprtRand restored GAF production in the resulting double mutant. Complementation of the doubleprtIRmutant withprtIsuppressed GAF production. This overall pattern ofprtIRregulation was also observed for the activity of an AprX protease. Furthermore, reverse transcription quantitative real-time PCR analysis demonstrated that alterations in GAF production were mirrored by changes in the transcription of two putative GAF biosynthetic genes. Thus, we concluded that PrtI exerted a negative regulatory effect on GAF production, although the mechanism has not yet been determined. In addition, evidence was obtained that the transcription ofprtIandprtRin WH6 may be more complex than predicted by existing models.
Crystallization, preliminary X-ray crystallographic and cryo-electron microscopy analysis of a bifunctional enzyme fucokinase/L-fucose-1-P-guanylyltransferase fromBacteroides fragilis
Authors: Cheng Chongyun , Gu Jianhua , Su Jing , Ding Wei , Yin Jie , Liang Wenguang , Yu Xiaoxia , Ma Jun , Wang Peng George , Xiao Zhicheng , Liu Zhi-Jie
Published: August 2014

Fucokinase/L-fucose-1-P-guanylyltransferase (FKP) is a bifunctional enzyme which converts L-fucose to Fuc-1-P and thence to GDP-L-fucose through a salvage pathway. The molecular weights of full-length FKP (F-FKP) and C-terminally truncated FKP (C-FKP, residues 300–949) are 105.7 and 71.7 kDa, respectively. In this study, both recombinant F-FKP and C-FKP were expressed and purified. Size-exclusion chromatography experiments and analytical ultracentrifugation results showed that both F-FKP and C-FKP are trimers. Native F-FKP protein was crystallized by the vapour-diffusion method and the crystals belonged to space groupP212121and diffracted synchrotron X-rays to 3.7 Å resolution. The crystal unit-cell parameters area= 91.36,b= 172.03,c= 358.86 Å, α = β = γ = 90.00°. The three-dimensional features of the F-FKP molecule were observed by cryo-EM (cryo-electron microscopy). The preliminary cryo-EM experiments showed the F-FKP molecules as two parallel disc-shaped objects stacking together. Combining all results together, it is assumed that there are six FKP molecules in one asymmetric unit, which corresponds to a calculated Matthews coefficient of 2.19 Å3 Da−1with 43.83% solvent content. These preliminary crystallographic and cryo-EM microscopy analyses provide basic structural information on FKP.
Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus
Authors: Fukumura Takuma , Furukawa Yukio , Kawaguchi Tatsuya , Saijo-Hamano Yumiko , Namba Keiichi , Imada Katsumi , Minamino Tohru
Published: August 2014

The bacterial flagellar proteins are transportedviaa specific export apparatus to the distal end of the growing structure for their self-assembly. FliP is an essential membrane component of the export apparatus. FliP has an N-terminal signal peptide and is predicted to have four transmembrane (TM) helices and a periplasmic domain (FliPP) between TM-2 and TM-3. In this study, FliPPfromThermotoga maritima(TmFliPP) and its selenomethionine derivative (SeMet-TmFliPP) were purified and crystallized. TmFliPPformed a homotetramer in solution. Crystals of TmFliPPand SeMet-TmFliPPwere obtained by the hanging-drop vapour-diffusion technique with 2-methyl-2,4-pentanediol as a precipitant. These two crystals grew in the hexagonal space groupP6222 orP6422, with unit-cell parametersa=b= 114.9,c= 193.8 Å. X-ray diffraction data were collected from crystals of TmFliPPand SeMet-TmFliPPto 2.4 and 2.8 Å resolution, respectively.
Cloning, purification, crystallization and preliminary X-ray studies of a carbohydrate-binding module (CBM_E1) derived from sugarcane soil metagenome
Authors: Campos Bruna Medeia , Alvarez Thabata Maria , Liberato Marcelo Vizona , Polikarpov Igor , Gilbert Harry J. , Zeri Ana Carolina de Mattos , Squina Fabio Marcio
Published: August 2014

In recent years, owing to the growing global demand for energy, dependence on fossil fuels, limited natural resources and environmental pollution, biofuels have attracted great interest as a source of renewable energy. However, the production of biofuels from plant biomass is still considered to be an expensive technology. In this context, the study of carbohydrate-binding modules (CBMs), which are involved in guiding the catalytic domains of glycoside hydrolases for polysaccharide degradation, is attracting growing attention. Aiming at the identification of new CBMs, a sugarcane soil metagenomic library was analyzed and an uncharacterized CBM (CBM_E1) was identified. In this study, CBM_E1 was expressed, purified and crystallized. X-ray diffraction data were collected to 1.95 Å resolution. The crystals, which were obtained by the sitting-drop vapour-diffusion method, belonged to space groupI23, with unit-cell parametersa=b=c= 88.07 Å.