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  • 1
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    Molecular characterization of acidic peptide:N-glycanase from the dimorphic yeast Yarrowia lipolytica (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-07
    Description: Peptide: N -glycanase (PNGase) A is used preferentially to cleave the glycans from plant and insect glycopeptides. Although many putative PNGase A homologous genes have been found in the plant and fungus kingdoms through sequence similarity analyses, only several PNGases from plants and one from a filamentous fungus have been characterized. In this study, we identified and characterized a PNGase A-like enzyme, PNGase Yl, in the dimorphic yeast Yarrowia lipolytica . The corresponding gene was cloned and recombinantly expressed in Pichia pastoris . The purified enzyme cleaved glycans from glycopeptides with the maximum activity at pH 5. No metal ions were required for full activity, and rather it was repressed by three metal ions (Fe 3+ , Cu 2+ and Zn 2+ ). Using glycopeptide substrates, PNGase Yl was shown to release various types of N -glycans including high-mannose and complex-type glycans as well as glycans containing core-linked α(1,3)-fucose that are frequently found in plants and insects. Moreover, in comparison with PNGase A, PNGase Yl was able to cleave with higher efficiency the glycans from some denatured glycoproteins. Taken together, our results suggest that PNGase Yl, the first biochemically characterized yeast PNGase A homologue, can be developed through protein engineering as a useful deglycosylation tool for N -glycosylation study.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 2
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    Highly efficient full-wave electromagnetic analysis of 3D arbitrarily-shaped waveguide microwave devices using an integral equation technique (2015)
    Wiley
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    Publication Date: 2015-06-04
    Description: A novel technique for the full-wave analysis of 3D complex waveguide devices is presented. This new formulation, based on the Boundary Integral-Resonant Mode Expansion (BI-RME) method, allows the rigorous full-wave electromagnetic characterization of 3D arbitrarily-shaped metallic structures making use of extremely low CPU resources (both time and memory). The unknown electric current density on the surface of the metallic elements is represented by means of Rao-Wilton-Glisson basis functions, and an algebraic procedure based on a singular value decomposition is applied to transform such functions into the classical solenoidal and non-solenoidal basis functions needed by the original BI-RME technique. The developed tool also provides an accurate computation of the electromagnetic fields at an arbitrary observation point of the considered device, so it can be used for predicting high-power breakdown phenomena. In order to validate the accuracy and efficiency of this novel approach, several new designs of band-pass waveguides filters are presented. The obtained results (S-parameters and electromagnetic fields) are successfully compared both to experimental data, and to numerical simulations provided by a commercial software based on the finite-element technique. The results obtained show that the new technique is specially suitable for the efficient full-wave analysis of complex waveguide devices considering an integrated coaxial excitation, where the coaxial probes may be in contact with the metallic insets of the component.
    Print ISSN: 0048-6604
    Electronic ISSN: 1944-799X
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: mock galaxy catalogues for the low-redshift sample (2014)
    Oxford University Press
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    Publication Date: 2014-12-18
    Description: We present 1000 mock galaxy catalogues (mocks) for the analysis of the low-redshift sample (LOWZ; effective redshift z  ~ 0.32) of the Baryon Oscillation Spectroscopic Survey (BOSS) Data Releases 10 and 11. These mocks have been created following the PTHalos method revised to include new developments. The main improvement is the introduction of a redshift dependence in the halo occupation distribution in order to account for the change of the galaxy number density with redshift. These mock galaxy catalogues are used in the analyses of the LOWZ galaxy clustering by the BOSS collaboration.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: baryon acoustic oscillations in the correlation function of LOWZ and CMASS galaxies in Data Release 12 (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-06
    Description: We present distance scale measurements from the baryon acoustic oscillation signal in the constant stellar mass and low-redshift sample samples from the Data Release 12 of the Baryon Oscillation Spectroscopic Survey. The total volume probed is 14.5 Gpc 3 , a 10 per cent increment from Data Release 11. From an analysis of the spherically averaged correlation function, we infer a distance to z = 0.57 of $D_V(z)r^{\rm fid}_{\rm d}/r_{\rm d} = 2028\pm 21$  Mpc and a distance to z = 0.32 of $D_V(z)r^{\rm fid}_{\rm d}/r_{\rm d} = 1264\pm 22$  Mpc assuming a cosmology in which $r^{\rm fid}_{\rm d} = 147.10$  Mpc. From the anisotropic analysis, we find an angular diameter distance to z = 0.57 of $D_{\rm A}(z)r^{\rm fid}_{\rm d}/r_{\rm d} = 1401\pm 21$  Mpc and a distance to z = 0.32 of 981 ± 20 Mpc, a 1.5 and 2.0 per cent measurement, respectively. The Hubble parameter at z = 0.57 is $H(z)r_{\rm d}/r^{\rm fid}_{\rm d} = 100.3\pm 3.7$  km s –1  Mpc –1 and its value at z = 0.32 is 79.2 ± 5.6 km s –1  Mpc –1 , a 3.7 and 7.1 per cent measurement, respectively. These cosmic distance scale constraints are in excellent agreement with a cold dark matter model with cosmological parameters released by the recent Planck 2015 results.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Can N2O stable isotopes and isotopomers be useful tools to characterize sources and microbial pathways of N2O production and consumption in tropical soils? (2011)
    Wiley
    Details
    Publication Date: 2011-01-05
    Description: Nitrous oxide (N2O) is an important greenhouse gas in which the main sources are tropical rainforest and agricultural soils. N2O is produced in soils by microbial processes, which are enhanced by the application of nitrogenous fertilizers. The soil N2O bulk isotopic composition (δ15Nbulk and δ18O) and the “site-specific,” or intramolecular, 15N isotopic composition, i.e., the 15N/14N ratio at the cenral (α) or terminal (β) nitrogen position, expressed in this study as δ15Nα and δ15Nβ could help identify both the sources (natural and anthropogenic) and microbial pathways of N2O production and consumption prior to emission.We report new isotope measurements of soil N2O emissions and from soil air collected during the rainy season in a mature tropical forest (Tapajos National Forest, Para, Brazil) and in a tropical agricultural corn field (“Fundo Tierra Nueva,” Guárico State, Venezuela). The statistically different δ15Nbulk emission weighted average between the mature forest (−18.0‰ ± 4.0‰, n = 6) and agricultural corn field (−34.3‰ ± 12.4‰, n = 17) suggest that the δ15Nbulk data are useful for distinguishing N2O fluxes from fertilized agricultural and natural “background” soils. They also demonstrate that the site-specific δ15N measurements have the potential to provide a new tool to differentiate between the production and consumption N2O microbiological processes in soils. This study further demonstrates that the observed correlations (or lack thereof) between δ15Nα, δ15Nβ, and δ18O can be used to estimate the relative proportion of N2O that would have been emitted to the air but was consumed via reduction of N2O to N2 within the soil.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Interpretation of the coherency matrix for three-dimensional polarization states (2014)
    American Physical Society (APS)
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    Publication Date: 2014-10-30
    Description: Author(s): José J. Gil From an appropriate parameterization of the three-dimensional (3D) coherency matrix R that characterizes the second-order, classical states of polarization, the coherency matrices are classified and interpreted in terms of incoherent decompositions. The relevant physical quantities derived from R, s... [Phys. Rev. A 90, 043858] Published Wed Oct 29, 2014
    Keywords: Quantum optics, physics of lasers, nonlinear optics, classical optics
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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  • 7
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    Analysis of the multipactor effect in circular waveguides excited by two orthogonal polarization waves (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-08-07
    Description: Circular waveguides, either employed as resonant cavities or as irises connecting adjacent guides, are widely present in many passive components used in different applications (i.e., particle accelerators and satellite subsystems). In this paper, we present the study of the multipactor effect in circular waveguides considering the coexistence of the two polarizations of the fundamental TE 11 circular waveguide mode. For a better understanding of the problem, only low multipactor orders have been explored as a function of the polarization ellipse eccentricity. Special attention has been paid to the linear and circular polarizations, but other more general configurations have also been explored.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 8
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    Ground penetrating radar evaluation of the internal structure of fluvial tufa deposits (Devanos-Anavieja system, NE Spain): an approach to different scales of heterogeneity (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-26
    Description: The Quaternary Añavieja-Dévanos tufa system is located in the northern sector of the Iberian Chain. It has been previously tackled by means sedimentological studies focused on the available outcrops and some boreholes. They have permitted the proposal of a sedimentary scenario that fits with a pool-barrage fluvial tufa model. However a better knowledge of the characteristics and internal distribution of the usually non-outcropping pool deposits as well as of its relationship with barrage deposits has not been evaluated in detail yet. Palaeoenvironmental studies on tufas are usually biased because tufas are commonly delicate facies exposed to intense erosion during water level fall stages; for this reason outcrops are usually scarce and very often coincide with the most cemented barrage deposits. In order to analyse the internal characteristics of the tufa deposits under study, but also the lateral correlation among different facies, ground penetrating radar (GPR) has been employed both for the evaluation of its applicability in such kind of environments and to improve, if possible, the sedimentary model using geophysical data in sectors without outcrops. A GPR survey including different antennas ranging from 50 to 500 MHz along different sectors and its comparison with natural outcrops has been carried out. GPR results have permitted to deduce clear differences between pool and barrage deposits and to recognise its internal structure and geometrical relationships. The survey also permitted an approach to different scales of heterogeneities in the radarfacies evaluation by using distinct antennas and therefore, reaching different resolutions and penetrations. The resulting integration from different antennas allows three different attenuant and eight reflective radarfacies to be defined permitting a better approach to the real extension of the pool areas. These results have permitted to decipher the horizontal and vertical facies changes and the identification of a scarcer development of pool deposits than expected in the studied system.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
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    Leaf morphological and physiological adaptations of a deciduous oak (Quercus faginea Lam.) to the Mediterranean climate: a comparison with a closely related temperate species (Quercus robur L.) (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-19
    Description: ‘White oaks’—one of the main groups of the genus Quercus L.—are represented in western Eurasia by the ‘roburoid oaks’, a deciduous and closely related genetic group that should have an Arcto-Tertiary origin under temperate-nemoral climates. Nowadays, roburoid oak species such as Quercus robur L. are still present in these temperate climates in Europe, but others are also present in southern Europe under Mediterranean-type climates, such as Quercus faginea Lam. We hypothesize the existence of a coordinated functional response at the whole-shoot scale in Q. faginea under Mediterranean conditions to adapt to more xeric habitats. The results reveal a clear morphological and physiological segregation between Q. robur and Q. faginea , which constitute two very contrasting functional types in response to climate dryness. The most outstanding divergence between the two species is the reduction in transpiring area in Q. faginea , which is the main trait imposed by the water deficit in Mediterranean-type climates. The reduction in leaf area ratio in Q. faginea should have a negative effect on carbon gain that is partially counteracted by a higher inherent photosynthetic ability of Q. faginea when compared with Q. robur , as a consequence of higher mesophyll conductance, higher maximum velocity of carboxylation and much higher stomatal conductance ( g s ). The extremely high g s of Q. faginea counteracts the expected reduction in g s imposed by the stomatal sensitivity to vapor pressure deficit, allowing this species to diminish water losses maintaining high net CO 2 assimilation values along the vegetative period under nonlimiting soil water potential values. In conclusion, the present study demonstrates that Q. faginea can be regarded as an example of adaptation of a deciduous oak to Mediterranean-type climates.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 10
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    Short Communications: Respiratory costs of woody tissues in a Quercus pyrenaica coppice (2018)
    Italian Society of Silviculture and Forest Ecology
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    Publication Date: 2018-12-17
    Description: Salomón RL, Rodríguez-Calcerrada J, Gil L, Valbuena-Carabaña M RESPIRATORY COSTS OF WOODY TISSUES IN A QUERCUS PYRENAICA COPPICE Abstract : Long-term coppicing leads to the development of massive root systems. A disproportionate carbon investment in root maintenance has been pointed as a cause of the widespread decline of abandoned coppices. We aimed at assessing how coppicing has influenced root and shoot development and related carbon loss ascribed to maintenance of woody tissues in Quercus pyrenaica. For this goal, results from published studies on root dynamics, woody biomass and respired CO2 fluxes in an abandoned Q. pyrenaica coppice were integrated and extended to quantify overall respiratory expenditures of above- and below-ground woody organs. Internal and external CO2 fluxes together with soil CO2 efflux were monitored in eight stems from one clone across a growing season. Stems and roots were later harvested to quantify the functional biomass and scale up root and stem respiration (RR and RS, respectively) to the clone and stand levels. Below- and above-ground biomass was roughly equal. However, the root-to-shoot ratio of respiration (RR/RS) was generally below one. Relatively higher RS suggests enhanced metabolic activity aboveground during the growing season, and highlights an unexpected but substantial contribution of RS to respiratory carbon losses. Moreover, soil and stem CO2 efflux to the atmosphere in Q. pyrenaica fell in the upper range of reported rates for various forest stands distributed worldwide. We conclude that both RS and RR represent an important carbon sink in this Q. pyrenaica abandoned coppice. Comparatively high energetic costs in maintaining multiple stems per tree and centennial root systems might constrain aboveground performance and contribute to coppice stagnation. Keywords : Carbon Loss, CO2 Fluxes, Coppice Stagnation, Oak, Resprouting Species, Root Respiration, Stem Respiration iForest 11 (3): 437-441 (2018) - doi: 10.3832/ifor2599-011 http://iforest.sisef.org/contents/?id=ifor2599-011
    Electronic ISSN: 1971-7458
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Italian Society of Silviculture and Forest Ecology
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