Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model

<p>Abstract</p> <p>Background</p> <p>Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to evaluate dynamical changes in data are therefore important to filter experimental noise and to enable extraction of unexpected, biologically important information.</p> <p>Results</p> <p>Here we demonstrate the effectiveness of a Markov model, named the Linear Dynamical System, to simulate the dynamics of a transcript or metabolite time series, and propose a probabilistic index that enables detection of time-sensitive changes. This method was applied to time series datasets from <it>Bacillus subtilis </it>and <it>Arabidopsis thaliana </it>grown under stress conditions; in the former, only gene expression was studied, whereas in the latter, both gene expression and metabolite accumulation. Our method not only identified well-known changes in gene expression and metabolite accumulation, but also detected novel changes that are likely to be responsible for each stress response condition.</p> <p>Conclusion</p> <p>This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism.</p

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method

Treatment for Churg-Strauss Syndrome: Induction of Remission and Efficacy of Intravenous Immunoglobulin Therapy

ABSTRACTChurg-Strauss syndrome (CSS) is characterized by the presence of asthma, eosinophilia, and small-vessel vasculitis with granuloma. It is a distinct entity, as determined from all classifications of systemic vasculitis. The poor prognostic factors in CSS are renal insufficiency, cardiomyopathy, severe gastrointestinal (GI) tract, and central nervous systems (CNS) involvement. The initial management of CSS should include a high dose of a corticosteroid: prednisone at 1 mg/kg/day or its equivalent for methylprednisolone with tapering over 6 months. In patients with severe or rapidly progressing CSS, the administration of methylprednisolone pulse at 1 g/body/day for 3 days is recommended. When corticosteroid therapy does not induce remission, or when patients have poor prognostic factors, immunosuppressive cytotoxic therapy is indicated. However, some patients with severe CSS often show resistance to conventional treatment. We think that IVIG therapy is a hopeful candidate for second-line treatment for CSS patients, particularly in the case of neuropathy and/or cardiomyopathy, which are resistant to conventional therapy. However, there is not much evidence supporting the effectiveness of IVIG in CSS, and the mechanisms underlying the action of IVIG remain unclear. Now we are performing clinical trials of IVIG therapy for CSS patients who are resistant to conventional treatment, through a nationwide double-blinded placebo-controlled study in Japan

Definitive Identification of the Transition between Small- to Large-Scale Clustering for Lyman Break Galaxies

We report angular correlation function (ACF) of Lyman Break Galaxies (LBGs) with unprecedented statistical quality on the basis of 16,920 LBGs at z=4 detected in the 1 deg^2 sky of the Subaru/XMM-Newton Deep Field. The ACF significantly departs from a power law, and shows an excess on small scale. Particularly, the ACF of LBGs with i'<27.5 have a clear break between the small and large-scale regimes at the angular separation of ~7'' whose projected length corresponds to the virial radius of dark halos with a mass of 10^11-12 Mo, indicating multiple LBGs residing in a single dark halo. Both on small (2''<theta<3'') and large (40''<theta<400'') scales, clustering amplitudes monotonically increase with luminosity for the magnitude range of i'=24.5-27.5, and the small-scale clustering shows a stronger luminosity dependence than the large-scale clustering. The small-scale bias reaches b~10-50, and the outskirts of small-scale excess extend to a larger angular separation for brighter LBGs. The ACF and number density of LBGs can be explained by the cold dark matter model.Comment: Accepted for publication in ApJL. 5 pages, 4 figures. The text and Figures 2-4 have been revised. There is no major change which affects to the main discussion shown in the original preprint. This paper with high resolution figures is available at http://www-int.stsci.edu/~ouchi/work/astroph/sxds_z4LBG/ouchi_highres.pdf (PDF

Spontaneous Basal Cell Carcinoma of the Submandibular Gland in a Rat

At necropsy, a white nodule (about 5 × 3 mm in size) was observed in the right submandibular gland of a 10-week-old female GALAS rat. Histopathologically, oval to spindle-shaped and pale basophilic tumor cells proliferated closely, and formed variably sized foci. The nodule partially spread into or invaded the surrounding normal tissue, and necrotic foci were recognized in the tumor. Immunohistochemically, the nuclei of the tumor cells showed a diffusely positive reaction for p63, and the cytoplasm showed a diffusely positive reaction for cytokeratin and negative reaction for αSMA, vimentin, desmin and S-100. Many tumor cells were positive for PCNA. Ultrastructurally, the tumor cells contained many tonofilaments in the cytoplasm and a few desmosomes at the intercellular portion. Based on these findings, the tumor was diagnosed as a basal cell carcinoma originating from the duct in the rat submandibular gland

The Rapeseed Project for Restoring Tsunami-Salt-Damaged Farmland after the GEJE

Oral Presentatio