Joint stage recognition and anatomical annotation of drosophila gene expression patterns

Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms

Oribatid mites show how climate and latitudinal gradients in organic matter can drive large-scale biodiversity patterns of soil communities

Aim: The factors determining spatial distributions and diversity of terrestrial invertebrates are typically investigated at small scales. Large‐scale studies are lacking for soil animals, which control microbial communities and represent one of the most diverse yet poorly known animal assemblages. Here, we analyzed a major group (Oribatida) to test whether belowground macroecological patterns can be predicted by climatic variables, vegetation and large‐scale variation in key soil properties. Location: We modelled the multivariate distribution of more than 100 species using biodiversity data collected across Great Britain in the framework of the Countryside Survey (http://www.countrysidesurvey.org.uk). Methods: We analyzed species‐level data from 582 samples collected across 162 hectads (10 × 10 km) covering the largest possible range of vegetation types, soil properties and climatic conditions within GB. We created the first large‐scale maps of soil animal diversity metrics at the GB scale, including novel estimates of metrics of phylogenetic diversity (PD). Using structural equation modelling, we quantified the direct and indirect effects of location (latitude, longitude), plant community structure and abiotic factors such as precipitation on species composition, richness and PD. Results: We found that variation in species composition follows a latitudinal gradient with diversity generally increasing northward. The latitudinal variation in species composition drives PD via changes in both species richness and phylogenetic distance between species. This gradient is mostly determined by latitudinal variation in precipitation and organic matter, which were very good predictors of species composition. Precipitation and organic matter were, however, relatively weak while statistically significant predictors of diversity metrics. Conclusions: Past studies have emphasized the unpredictability of species distributions and variation in species composition in hyper diverse soil animal communities. However, past studies were conducted at small scales, where stochastic factors may weaken the signal of deterministic factors. Oribatid mites in our study show for the first time that the large scale latitudinal gradients in climate and organic matter predict not only variation in species composition but also taxonomic and PD of soil animal communities

Smooth Paths on Three Dimensional Lattice

A particular class of random walks with a spin factor on a three dimensional cubic lattice is studied. This three dimensional random walk model is a simple generalization of random walk for the two dimensional Ising model. All critical diffusion constants and associated critical exponents are calculated. Continuum field theories such as Klein-Gordon, Dirac and massive Chern-Simons theories are constructed near several critical points.Comment: 7 pages,NUP-A-94-

Quantum phase transitions and collapse of the Mott gap in the d=1+ϵd=1+\epsilon dimensional half-filled Hubbard model

We study the low-energy asymptotics of the half-filled Hubbard model with a circular Fermi surface in $d=1+\epsilon$ continuous dimensions, based on the one-loop renormalization-group (RG) method. Peculiarity of the $d=1+\epsilon$ dimensions is incorporated through the mathematica structure of the elementary particle-partcile (PP) and particle-hole (PH) loops: infrared logarithmic singularity of the PH loop is smeared for $\epsilon>0$. The RG flows indicate that a quantum phase transition (QPT) from a metallic phase to the Mott insulator phase occurs at a finite on-site Coulomb repulsion $U$ for $\epsilon>0$. We also discuss effects of randomness.Comment: 12 pages, 10 eps figure

Differential effects of fluvoxamine and other antidepressants on the biotransformation of melatonin

Melatonin, the predominant product of the pineal gland, is involved in the maintenance of diurnal rhythms. Nocturnal blood concentrations of melatonin have been shown to be enhanced by fluvoxamine, but not by other serotonin reuptake inhibitors. Because fluvoxamine is an inhibitor of several cytochrome P450 (CYP) enzymes, the authors studied the biotransformation of melatonin and the effects of fluvoxamine on the metabolism of melatonin in vitro using human liver microsomes and recombinant human CYP isoenzymes. Melatonin was found to be almost exclusively metabolized by CYP1A2 to 6-hydroxymelatonin and N-acetylserotonin with a minimal contribution of CYP2C19. Both reactions were potently inhibited by fluvoxamine, with a Ki of 0.02 microM for the formation of 6-hydroxymelatonin and 0.05 microM for the formation of N-acetylserotonin. Other than fluvoxamine, fluoxetine, paroxetine, citalopram, imipramine, and desipramine were also tested at 2 and 20 microM. Among the other antidepressants, only paroxetine was able to affect the metabolism of melatonin at supratherapeutic concentrations of 20 microM, which did not reach by far the magnitude of the inhibitory potency of fluvoxamine. The authors concluded that fluvoxamine is a potent inhibitor of melatonin degradation. Because this inhibitory action is also found in vivo, fluvoxamine might be used as an enhancer of melatonin, which might offer new therapeutic possibilities of fluvoxamine

The Transcription Factor T-bet Regulates Mucosal T Cell Activation in Experimental Colitis and Crohn's Disease

The balance between pro and antiinflammatory cytokines secreted by T cells regulates both the initiation and perpetuation of inflammatory bowel diseases (IBD). In particular, the balance between interferon (IFN)-γ/interleukin (IL)-4 and transforming growth factor (TGF)-β activity controls chronic intestinal inflammation. However, the molecular pathways that evoke these responses are not well understood. Here, we describe a critical role for the transcription factor T-bet in controlling the mucosal cytokine balance and clinical disease. We studied the expression and function of T-bet in patients with IBD and in mucosal T cells in various T helper (Th)1- and Th2-mediated animal models of chronic intestinal inflammation by taking advantage of mice that lack T-bet and retroviral transduction techniques, respectively. Whereas retroviral transduction of T-bet in CD62L+ CD4+ T cells exacerbated colitis in reconstituted SCID mice, T-bet–deficient T cells failed to induce colitis in adoptive transfer experiments suggesting that overexpression of T-bet is essential and sufficient to promote Th1-mediated colitis in vivo. Furthermore, T-bet–deficient CD62L− CD4+ T cells showed enhanced protective functions in Th1-mediated colitis and exhibited increased TGF-β signaling suggesting that a T-bet driven pathway of T cell activation controls the intestinal balance between IFN-γ/IL-4 and TGF-β responses and the development of chronic intestinal inflammation in T cell–mediated colitis. Furthermore, TGF-β was found to suppress T-bet expression suggesting a reciprocal relationship between TGF-β and T-bet in mucosal T cells. In summary, our data suggest a key regulatory role of T-bet in the pathogenesis of T cell–mediated colitis. Specific targeting of this pathway may be a promising novel approach for the treatment of patients with Crohn's disease and other autoimmune diseases mediated by Th1 T lymphocytes

Composite quasiparticle formation and the low-energy effective Hamiltonians of the one- and two-dimensional Hubbard Model

We investigate the effect of hole doping on the strong-coupling Hubbard model at half-filling in spatial dimensions $D\ge 1$. We start with an antiferromagnetic mean-field description of the insulating state, and show that doping creates solitons in the antiferromagnetic background. In one dimension, the soliton is topological, spinless, and decoupled from the background antiferromagnetic fluctuations at low energies. In two dimensions and above, the soliton is non-topological, has spin quantum number 1/2, and is strongly coupled to the antiferromagnetic fluctuations. We derive the effective action governing the quasiparticle motion, study the properties of a single carrier, and comment on a possible description at finite concentration.Comment: REVTEX 3.0, 22 pages with 14 figures in the PostScript format compressed using uufile. Submitted to Phys. Rev. B. The complete PostScript file including figures can be obtained via ftp at ftp://serval.berkeley.edu/hubbard.ps . It is also available via www at http://roemer.fys.ku.dk/recent.ht

Quiescence: early evolutionary origins and universality do not imply uniformity

Cell cycle investigations have focused on relentless exponential proliferation of cells, an unsustainable situation in nature. Proliferation of cells, whether microbial or metazoan, is interrupted by periods of quiescence. The vast majority of cells in an adult metazoan lie quiescent. As disruptions in this quiescence are at the foundation of cancer, it will be important for the field to turn its attention to the mechanisms regulating quiescence. While often presented as a single topic, there are multiple forms of quiescence each with complex inputs, some of which are tied to conceptually challenging aspects of metazoan regulation such as size control. In an effort to expose the enormity of the challenge, I describe the differing biological purposes of quiescence, and the coupling of quiescence in metazoans to growth and to the structuring of tissues during development. I emphasize studies in the organism rather than in tissue culture, because these expose the diversity of regulation. While quiescence is likely to be a primitive biological process, it appears that in adapting quiescence to its many distinct biological settings, evolution has diversified it. Consideration of quiescence in different models gives us an overview of this diversity