A possible role for endogenous glucocorticoids in orchiectomy-induced atrophy of the rat levator ani muscle: Studies with RU38486, a potent and selective antiglucocorticoid

RU38486, a potent and selective antiglucocorticoid, was employed to study a possible role for endogenous glucocorticoids in atrophy of the levator ani muscle secondary to castration of male rats. RU38486 was shown to block (3H) triamcinolone acetonide binding to cytosol from levator ani muscle. Daily oral administration of RU38486 to castrated rats partially prevented atrophy of the levator ani muscle, as well as a decrease in RNA concentration. In a control group receiving RU38486 alone, the levator ani underwent significant (20%) hypertrophy. Administration of exogenous dexamethasone also caused pronounced atrophy of the levator ani muscle. This atrophy was prevented, to a significant degree, by simultaneous oral administration of RU38486. It is concluded that endogenous glucocorticoids, the actions of which are blocked by RU38486, may be involved in regulation of the mass of the levator ani muscle in intact rats

Trends in life science grid: from computing grid to knowledge grid

BACKGROUND: Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity of a single institution. RESULTS: This survey reviews the latest grid technologies from the viewpoints of computing grid, data grid and knowledge grid. Computing grid technologies have been matured enough to solve high-throughput real-world life scientific problems. Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics. Knowledge grids should be designed not only from sharing explicit knowledge on computers but also from community formulation for sharing tacit knowledge among a community. CONCLUSION: Extending the concept of grid from computing grid to knowledge grid, it is possible to make use of a grid as not only sharable computing resources, but also as time and place in which people work together, create knowledge, and share knowledge and experiences in a community

A non-perturbative study of 4d U(1) non-commutative gauge theory -- the fate of one-loop instability

Recent perturbative studies show that in 4d non-commutative spaces, the trivial (classically stable) vacuum of gauge theories becomes unstable at the quantum level, unless one introduces sufficiently many fermionic degrees of freedom. This is due to a negative IR-singular term in the one-loop effective potential, which appears as a result of the UV/IR mixing. We study such a system non-perturbatively in the case of pure U(1) gauge theory in four dimensions, where two directions are non-commutative. Monte Carlo simulations are performed after mapping the regularized theory onto a U(N) lattice gauge theory in d=2. At intermediate coupling strength, we find a phase in which open Wilson lines acquire non-zero vacuum expectation values, which implies the spontaneous breakdown of translational invariance. In this phase, various physical quantities obey clear scaling behaviors in the continuum limit with a fixed non-commutativity parameter $\theta$, which provides evidence for a possible continuum theory. The extent of the dynamically generated space in the non-commutative directions becomes finite in the above limit, and its dependence on $\theta$ is evaluated explicitly. We also study the dispersion relation. In the weak coupling symmetric phase, it involves a negative IR-singular term, which is responsible for the observed phase transition. In the broken phase, it reveals the existence of the Nambu-Goldstone mode associated with the spontaneous symmetry breaking.Comment: 29 pages, 23 figures, references adde

Difluoromethylborates and muonium for the study of isonitrile insertion affording phenanthridines via imidoyl radicals

The 6-(difluoromethyl)phenanthridine unit is a highly attractive fluoroalkyl-substituted planar nitrogen heterocycle in pharmaceutical and agrochemical research. In this paper, we report that difluoromethylborates can be used as a source of difluoromethyl radicals for isonitrile insertion, leading to 6-(difluoromethyl)phenanthridines. Tuning the aryl substituents in the difluoromethylborates and oxidizing reagents enabled the synthesis of 6-(difluoromethyl)phenanthridines through the generation of difluoromethyl radical and spontaneous intramolecular cyclization of the CF2H-imidoyl radical intermediates. The presence of difluoromethyl radicals was experimentally confirmed, and the reaction mechanisms including imidoyl radical and prompt cyclization reactions could be supported theoretically. Furthermore, we obtained valuable information about the imidoyl radical intermediate by performing transverse-field muon spin rotation (TF-μSR) measurements of 2-isocyano-4′-methoxy-1,1′-biphenyl and using density functional theory (DFT) calculations to interpret the spectra. Muonium, a simple free radical, preferentially adds to the carbon atom of the isonitrile unit, yielding the corresponding imidoyl radical. The temperature dependence of the muon hyperfine coupling constant and the spin relaxation of the muoniated radical signal are compatible with the intramolecular cyclization of biaryl-substituted imidoyl radicals on the μs time scale

Establishing bioinformatics research in the Asia Pacific

In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5(th )annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand) and Busan (South Korea). This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community

Particle simulation approach for subcellular dynamics and interactions of biological molecules

BACKGROUND: Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video imaging (SFVI) are now being applied to observation of molecular-level dynamics. However, little is known concerning how molecular-level dynamics affect properties at the cellular level. RESULTS: We propose an algorithm designed for three-dimensional simulation of the reaction-diffusion dynamics of molecules, based on a particle model. Chemical reactions proceed through the interactions of particles in space, with activation energies determining the rates of these chemical reactions at each interaction. This energy-based model can include the cellular membrane, membranes of other organelles, and cytoskeleton. The simulation algorithm was tested for a reversible enzyme reaction model and its validity was confirmed. Snapshot images taken from simulated molecular interactions on the cell-surface revealed clustering domains (size ~0.2 μm) associated with rafts. Sample trajectories of raft constructs exhibited "hop diffusion". These domains corralled the diffusive motion of membrane proteins. CONCLUSION: These findings demonstrate that our approach is promising for modelling the localization properties of biological phenomena

Agrobacterium-mediated transformation of kabocha squash (Cucurbita moschata Duch) induced by wounding with aluminum borate whiskers

An efficient genetic transformation method for kabocha squash (Cucurbita moschata Duch cv. Heiankogiku) was established by wounding cotyledonary node explants with aluminum borate whiskers prior to inoculation with Agrobacterium. Adventitious shoots were induced from only the proximal regions of the cotyledonary nodes and were most efficiently induced on Murashige–Skoog agar medium with 1 mg/L benzyladenine. Vortexing with 1% (w/v) aluminum borate whiskers significantly increased Agrobacterium infection efficiency in the proximal region of the explants. Transgenic plants were screened at the T0 generation by sGFP fluorescence, genomic PCR, and Southern blot analyses. These transgenic plants grew normally and T1 seeds were obtained. We confirmed stable integration of the transgene and its inheritance in T1 generation plants by sGFP fluorescence and genomic PCR analyses. The average transgenic efficiency for producing kabocha squashes with our method was about 2.7%, a value sufficient for practical use

Tomato TFT1 Is Required for PAMP-Triggered Immunity and Mutations that Prevent T3S Effector XopN from Binding to TFT1 Attenuate Xanthomonas Virulence

XopN is a type III effector protein from Xanthomonas campestris pathovar vesicatoria that suppresses PAMP-triggered immunity (PTI) in tomato. Previous work reported that XopN interacts with the tomato 14-3-3 isoform TFT1; however, TFT1's role in PTI and/or XopN virulence was not determined. Here we show that TFT1 functions in PTI and is a XopN virulence target. Virus-induced gene silencing of TFT1 mRNA in tomato leaves resulted in increased growth of Xcv ΔxopN and Xcv ΔhrpF demonstrating that TFT1 is required to inhibit Xcv multiplication. TFT1 expression was required for Xcv-induced accumulation of PTI5, GRAS4, WRKY28, and LRR22 mRNAs, four PTI marker genes in tomato. Deletion analysis revealed that the XopN C-terminal domain (amino acids 344–733) is sufficient to bind TFT1. Removal of amino acids 605–733 disrupts XopN binding to TFT1 in plant extracts and inhibits XopN-dependent virulence in tomato, demonstrating that these residues are necessary for the XopN/TFT1 interaction. Phos-tag gel analysis and mass spectrometry showed that XopN is phosphorylated in plant extracts at serine 688 in a putative 14-3-3 recognition motif. Mutation of S688 reduced XopN's phosphorylation state but was not sufficient to inhibit binding to TFT1 or reduce XopN virulence. Mutation of S688 and two leucines (L64,L65) in XopN, however, eliminated XopN binding to TFT1 in plant extracts and XopN virulence. L64 and L65 are required for XopN to bind TARK1, a tomato atypical receptor kinase required for PTI. This suggested that TFT1 binding to XopN's C-terminal domain might be stabilized via TARK1/XopN interaction. Pull-down and BiFC analyses show that XopN promotes TARK1/TFT1 complex formation in vitro and in planta by functioning as a molecular scaffold. This is the first report showing that a type III effector targets a host 14-3-3 involved in PTI to promote bacterial pathogenesis