Detection of gfp expression from gfp-labelled bacteria spot inoculated onto sugarcane tissues

Green fluorescent protein (GFP) as a marker gene has facilitated biological research in plant-microbe interactions. However, there is one major limiting factor in the detection of GFP in living organisms whose cells emit background autofluorescence. In this study, Herbaspirillum sp. B501gfp1 bacterial cells were spot inoculated onto 5 month-old sterile micro-propagated sugarcane tissues to detect if the GFP fluorescence expression could be distinguished from the tissue’s background fluorescence. Stem tissues and leaf sections mounted on glass slides were directly inoculated with a single touch using the tip of a syringe previously dipped into the inoculum containing 108 bacterial cells/ml. We observed that GFP fluorescence could be easily distinguished in the stem than in the leaf tissues. However, the brightness level of the fluorescence varied with time as a result of fluctuations in the bacterial celldensity. The presence of chloroplasts in the leaf tissues of sugarcane requires the use of bright GFP variants when monitoring bacteria-plant interactions using GFP labelled bacteria

Colonization ability of Herbaspirillum spp. B501gfp1 in sugarcane, a non-host plant in the presence of indigenous diazotrophic endophytes

Inoculating sugarcane with a mixture of diazotrophic endophytic bacteria has shown that they can provide substantial amount of biologically fixed nitrogen to the plant. The genera of diazotrophic endophytes previously isolated from sugarcane have been reported associating with other nonleguminousplants showing a broad host range. This study examined the colonization ability of a wild rice isolate, Herbaspirillum spp., in sugarcane plants in the presence of indigenous endophytes using two inoculum concentrations (102 and 108 bacterial cells ml-1). Internal tissue colonization was observed in plants inoculated with both the 102 and 108 B501gfp1 bacterial cells ml-1 inoculum concentrations. However, extensive colonization and higher bacterial numbers were determined only in the basal stem tissues of plants inoculated with the 108 bacterial cells ml-1

Mass-conserving tracer transport modelling on a reduced latitude-longitude grid with NIES-TM

The need to perform long-term simulations with reasonable accuracy has led to the development of mass-conservative and efficient numerical methods for solving the transport equation in forward and inverse models. We designed and implemented a flux-form (Eulerian) tracer transport algorithm in the National Institute for Environmental Studies Transport Model (NIES TM), which is used for simulating diurnal and synoptic-scale variations of tropospheric long-lived constituents, as well as their seasonal and inter-annual variability. Implementation of the flux-form method requires the mass conservative wind fields. However, the model is off-line and is driven by datasets from a global atmospheric model or data assimilation system, in which vertically integrated mass changes are not in balance with the surface pressure tendency and mass conservation is not achieved. To rectify the mass-imbalance, a flux-correction method is employed. To avoid a singularity near the poles, caused by the small grid size arising from the meridional convergence problem, the proposed model uses a reduced latitude–longitude grid scheme, in which the grid size is doubled several times approaching the poles. This approach overcomes the Courant condition in the Polar Regions, maintains a reasonably high integration time-step, and ensures adequate model performance during simulations. To assess the model performance, we performed global transport simulations for SF<sub>6</sub>, <sup>222</sup>Rn, and CO<sub>2</sub>. The results were compared with observations available from the World Data Centre for Greenhouse Gases, GLOBALVIEW, and the Hateruma monitoring station, Japan. Overall, the results show that the proposed flux-form version of NIES TM can produce tropospheric tracer transport more realistically than previously possible. The reasons for this improvement are discussed

A Conditional Yeast E1 Mutant Blocks the Ubiquitin–Proteasome Pathway and Reveals a Role for Ubiquitin Conjugates in Targeting Rad23 to the Proteasome

E1 ubiquitin activating enzyme catalyzes the initial step in all ubiquitin-dependent processes. We report the isolation of uba1-204, a temperature-sensitive allele of the essential Saccharomyces cerevisiae E1 gene, UBA1. Uba1-204 cells exhibit dramatic inhibition of the ubiquitin–proteasome system, resulting in rapid depletion of cellular ubiquitin conjugates and stabilization of multiple substrates. We have employed the tight phenotype of this mutant to investigate the role ubiquitin conjugates play in the dynamic interaction of the UbL/UBA adaptor proteins Rad23 and Dsk2 with the proteasome. Although proteasomes purified from mutant cells are intact and proteolytically active, they are depleted of ubiquitin conjugates, Rad23, and Dsk2. Binding of Rad23 to these proteasomes in vitro is enhanced by addition of either free or substrate-linked ubiquitin chains. Moreover, association of Rad23 with proteasomes in mutant and wild-type cells is improved upon stabilizing ubiquitin conjugates with proteasome inhibitor. We propose that recognition of polyubiquitin chains by Rad23 promotes its shuttling to the proteasome in vivo

The {\L}ojasiewicz exponent of a set of weighted homogeneous ideals

We give an expression for the {\L}ojasiewicz exponent of a set of ideals which are pieces of a weighted homogeneous filtration. We also study the application of this formula to the computation of the {\L}ojasiewicz exponent of the gradient of a semi-weighted homogeneous function (\C^n,0)\to (\C,0) with an isolated singularity at the origin.Comment: 15 page

Spectroscopic evidence of the formation of (V,Ti)O₂ solid solution in VO₂ thinner films grown on TiO₂(001) substrates

We have prepared VO2 thin films epitaxially grown on TiO2(001) substrates with thickness systematically varied from 2.5 to 13 nm using a pulsed laser deposition method, and studied the transport property and electronic states of the films by means of resistivity and in situ synchrotron photoemission spectroscopy (SRPES). In resistivity measurements, the 13-nm-thick film exhibits a metal-insulator transition at around 290 K on cooling with change of three orders of magnitudes in resistivity. As the film thickness decreases, the metal-insulator transition broadens and the transition temperature increases. Below 4 nm, the films do not show the transition and become insulators. In situ SRPES measurements of near the Fermi level valence band find that the electronic state of the 2.5-nm-thick film is different than that of the temperature-induced insulator phase of VO2 itself although these two states are insulating. Ti 2p core-level photoemission measurements reveal that Ti ions exist near the interface between the films and TiO2 substrates, with a chemical state similar to that in (V,Ti)O-2 solid solution. These results indicate that insulating (V,Ti)O-2 solid solution is formed in the thinner films. We propose a simple growth model of a VO2 thin film on a TiO2(001) substrate. Near the interface, insulating (V,Ti) O-2 solid solution is formed due to the diffusion of Ti ions from the TiO2 substrate into the VO2 film. The concentration of Ti in (V,Ti) O-2 is relatively high near the interface and decreases toward the surface of the film. Beyond a certain film thickness (about 7 nm in the case of the present 13-nm-thick film), the VO2 thin film without any Ti ions starts to grow. Our work suggests that developing a technique for preparing the sharp interface between the VO2 thin films and TiO2 substrates is a key issue to study the physical property of an ultrathin film of "pure" VO2, especially to examine the presence of the novel electronic state called a semi-Dirac point phase predicted by calculations

Interactive Visualization for Singular Fibers of Functions f : R3 → R2

Scalar topology in the form of Morse theory has provided computational tools that analyze and visualize data from scientific and engineering tasks. Contracting isocontours to single points encapsulates variations in isocontour connectivity in the Reeb graph. For multivariate data, isocontours generalize to fibers—inverse images of points in the range, and this area is therefore known as fiber topology. However, fiber topology is less fully developed than Morse theory, and current efforts rely on manual visualizations. This paper presents how to accelerate and semi-automate this task through an interface for visualizing fiber singularities of multivariate functions R3 → R2. This interface exploits existing conventions of fiber topology, but also introduces a 3D view based on the extension of Reeb graphs to Reeb spaces. Using the Joint Contour Net, a quantized approximation of the Reeb space, this accelerates topological visualization and permits online perturbation to reduce or remove degeneracies in functions under study. Validation of the interface is performed by assessing whether the interface supports the mathematical workflow both of experts and of less experienced mathematicians