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

Towards Pure Spinor Type Covariant Description of Supermembrane -- An Approach from the Double Spinor Formalism --

In a previous work, we have constructed a reparametrization invariant worldsheet action from which one can derive the super-Poincare covariant pure spinor formalism for the superstring at the fully quantum level. The main idea was the doubling of the spinor degrees of freedom in the Green-Schwarz formulation together with the introduction of a new compensating local fermionic symmetry. In this paper, we extend this "double spinor" formalism to the case of the supermembrane in 11 dimensions at the classical level. The basic scheme works in parallel with the string case and we are able to construct the closed algebra of first class constraints which governs the entire dynamics of the system. A notable difference from the string case is that this algebra is first order reducible and the associated BRST operator must be constructed accordingly. The remaining problems which need to be solved for the quantization will also be discussed.Comment: 40 pages, no figure, uses wick.sty; v2: a reference added, published versio

Origin of Pure Spinor Superstring

The pure spinor formalism for the superstring, initiated by N. Berkovits, is derived at the fully quantum level starting from a fundamental reparametrization invariant and super-Poincare invariant worldsheet action. It is a simple extension of the Green-Schwarz action with doubled spinor degrees of freedom with a compensating local supersymmetry on top of the conventional kappa-symmetry. Equivalence to the Green-Schwarz formalism is manifest from the outset. The use of free fields in the pure spinor formalism is justified from the first principle. The basic idea works also for the superparticle in 11 dimensions.Comment: 21 pages, no figure; v2: refs. adde

M-theory and Seven-Dimensional Inhomogeneous Sasaki-Einstein Manifolds

Seven-dimensional inhomogeneous Sasaki-Einstein manifolds $Y^{p,k}(KE_4)$ present a challenging example of AdS/CFT correspondence. At present, their field theory duals for $KE_4=\mathbb{CP}^2$ base are proposed only within a restricted range $3p/2\le k \le 2p$ as ${\cal N}=2$ quiver Chern-Simons-matter theories with $SU(N)\times SU(N)\times SU(N)$ gauge group, nine bifundamental chiral multiplets interacting through a cubic superpotential. To further elucidate this correspondence, we use particle approximation both at classical and quantum level. We setup a concrete AdS/CFT mapping of conserved quantities using geodesic motions, and turn to solutions of scalar Laplace equation in $Y^{p,k}$. The eigenmodes also provide an interesting subset of Kaluza-Klein spectrum for $D=11$ supergravity in ${\rm AdS}_4\times Y^{p,k}$, and are dual to protected operators written in terms of matter multiplets in the dual conformal field theory.Comment: v2 refs added. 19 pages 1 figur

On "Dotsenko-Fateev" representation of the toric conformal blocks

We demonstrate that the recent ansatz of arXiv:1009.5553, inspired by the original remark due to R.Dijkgraaf and C.Vafa, reproduces the toric conformal blocks in the same sense that the spherical blocks are given by the integral representation of arXiv:1001.0563 with a peculiar choice of open integration contours for screening insertions. In other words, we provide some evidence that the toric conformal blocks are reproduced by appropriate beta-ensembles not only in the large-N limit, but also at finite N. The check is explicitly performed at the first two levels for the 1-point toric functions. Generalizations to higher genera are briefly discussed.Comment: 10 page

Outcome of Patients with Localized Prostate Cancer Treated by Radiotherapy After Confirming the Absence of Lymph Node Invasion

doi:10.1093/jjco/hyq03

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized. Thus, as a sub-database of H-InvDB, an integrated database of annotated human genes (http://h-invitational.jp/), we constructed a fully curated database of evolutionary features of human genes, called ‘Evola’. In the process of the ortholog detection, computational analysis based on conserved genome synteny and transcript sequence similarity was followed by manual curation by researchers examining phylogenetic trees. In total, 18 968 human genes have orthologs among 11 vertebrates (chimpanzee, mouse, cow, chicken, zebrafish, etc.), either computationally detected or manually curated orthologs. Evola provides amino acid sequence alignments and phylogenetic trees of orthologs and homologs. In ‘dN/dS view’, natural selection on genes can be analyzed between human and other species. In ‘Locus maps’, all transcript variants and their exon/intron structures can be compared among orthologous gene loci. We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/evola/

Brane geometry and dimer models

The field content and interactions of almost all known gauge theories in AdS5/CFT4 can be expressed in terms of dimer models or bipartite graphs drawn on a torus. Associated with the fundamental cell is a complex structure parameter τ R . Based on the brane realization of these theories, we can specify a special Lagrangian (SLag) torus fibration that is the natural candidate to be identified as the torus on which the dimer lives. Using the metrics known in the literature, we compute the complex structure τ G of this torus. For the theories on ℂ3 and the conifold and for orbifolds thereof τ R = τ G . However, for more complicated examples, we show that the two complex structures cannot be equal and yet, remarkably, differ only by a few percent. We leave the explanation for this extraordinary proximity as an open challenge