Mining topological relations from the web

Topological relations between geographic regions are of interest in many applications. When the exact boundaries of regions are not available, such relations can be established by analysing natural language information from web documents. In particular we demonstrate how redundancy-based techniques can be used to acquire containment and adjacency relations, and how fuzzy spatial reasoning can be employed to maintain the consistency of the resulting knowledge base

The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs

Pacman/Xrn1 is a highly conserved exoribonuclease known to play a critical role in gene regulatory events such as control of mRNA stability, RNA interference and regulation via miRNAs. Although Pacman has been well studied in Drosophila tissue culture cells, the biologically relevant cellular pathways controlled by Pacman in natural tissues are unknown. This study shows that a hypomorphic mutation in pacman (pcm5) results in smaller wing imaginal discs. These tissues, found in the larva, are known to grow and differentiate to form wing and thorax structures in the adult fly. Using microarray analysis, followed by quantitative RT-PCR, we show that eight mRNAs were increased in level by >2 fold in the pcm5 mutant wing discs compared to the control. The levels of pre mRNAs were tested for five of these mRNAs; four did not increase in the pcm5 mutant, showing that they are regulated at the post-transcriptional level and therefore could be directly affected by Pacman. These transcripts include one that encodes the heat-shock protein Hsp67Bc, which is upregulated 11.9-fold at the post-transcriptional level and 2.3-fold at the protein level. One miRNA, miR-277-3p, is 5.6-fold downregulated at the post-transcriptional level in mutant discs, suggesting that Pacman affects its processing in this tissue. Together, these data show that a relatively small number of mRNAs and miRNAs substantially change in abundance in pacman mutant wing imaginal discs. Since Hsp67Bc is known to regulate autophagy and protein synthesis, it is possible that Pacman may control the growth of wing imaginal discs by regulating these processes

RNA-seq reveals post-transcriptional regulation of Drosophila insulin-like peptide dilp8 and the neuropeptide-like precursor Nplp2 by the exoribonuclease Pacman/XRN1

Ribonucleases are critically important in many cellular and developmental processes and defects in their expression are associated with human disease. Pacman/XRN1 is a highly conserved cytoplasmic exoribonuclease which degrades RNAs in a 5' - 3' direction. In Drosophila, null mutations in pacman result in small imaginal discs, a delay in onset of pupariation and lethality during the early pupal stage. In this paper, we have used RNA-seq in a genome-wide search for mRNAs misregulated in pacman null wing imaginal discs. Only 4.2% of genes are misregulated ±>2-fold in pacman null mutants compared to controls, in line with previous work showing that Pacman has specificity for particular mRNAs. Further analysis of the most upregulated mRNAs showed that Pacman post-transcriptionally regulates the expression of the secreted insulin-like peptide Dilp8. Dilp8 is related to human IGF-1, and has been shown to co-ordinate tissue growth with developmental timing in Drosophila. The increased expression of Dilp8 is consistent with the developmental delay seen in pacman null mutants. Our analysis, together with our previous results, show that the normal role of this exoribonuclease in imaginal discs is to suppress the expression of transcripts that are crucial in apoptosis and growth control during normal development

Carbonate Control of H(2) and Ch(4) Production in Serpentinization Systems at Elevated P-Ts

Serpentinization of forsteritic olivine results in the inorganic synthesis of molecular hydrogen (H(2)) in ultramafic hydrothermal systems (e. g., mid-ocean ridge and forearc environments). Inorganic carbon in those hydrothermal systems may react with H(2) to produce methane (CH(4)) and other hydrocarbons or react with dissolved metal ions to form carbonate minerals. Here, we report serpentinization experiments at 200 degrees C and 300 bar demonstrating Fe(2+) being incorporated into carbonates more rapidly than Fe(2+) oxidation (and concomitant H(2) formation) leading to diminished yields of H(2) and H(2)-dependent CH(4). In addition, carbonate formation is temporally fast in carbonate oversaturated fluids. Our results demonstrate that carbonate chemistry ultimately modulates the abiotic synthesis of both H(2) and CH(4) in hydrothermal ultramafic systems and that ultramafic systems present great potential for CO(2)-mineral sequestration

The roles of the exoribonucleases DIS3L2 and XRN1 in disease

RNA degradation is a vital post-transcriptional process which ensures that transcripts are maintained at the correct level within the cell. DIS3L2 and XRN1 are conserved exoribonucleases which are critical for the degradation of cytoplasmic RNAs. Although the molecular mechanisms of RNA degradation by DIS3L2 and XRN1 have been well studied, less is known about their specific roles in development of multicellular organisms or human disease. This review focusses on the roles of DIS3L2 and XRN1 in the pathogenesis of human disease, particularly in relation to phenotypes seen in model organisms. The known diseases associated with loss of activity of DIS3L2 and XRN1 are discussed, together with possible mechanisms and cellular pathways leading to these disease conditions

Correlation of the Quasi-Periodic Oscillation Frequencies of White Dwarf, Neutron Star, and Black Hole Binaries

Using data obtained in 1994 June/July with the Extreme Ultraviolet Explorer deep survey photometer and in 2001 January with the Chandra X-ray Observatory Low Energy Transmission Grating Spectrograph, we investigate the extreme-ultraviolet (EUV) and soft X-ray oscillations of the dwarf nova SS Cyg in outburst. We find quasi-periodic oscillations (QPOs) at nu_0 ~ 0.012 Hz and nu_1 ~ 0.13 Hz in the EUV flux and at nu_0 ~ 0.0090 Hz, nu_1 ~ 0.11 Hz, and possibly nu_2 ~ nu_0 + nu_1 ~ 0.12 Hz in the soft X-ray flux. These data, combined with the optical data of Woudt & Warner for VW Hyi, extend the Psaltis, Belloni, & van der Klis nu_high-nu_low correlation for neutron star and black hole low-mass X-ray binaries (LMXBs) nearly two orders of magnitude in frequency, with nu_low ~ 0.08 nu_high. This correlation identifies the high-frequency quasi-coherent oscillations (so-called ``dwarf nova oscillations'') of cataclysmic variables (CVs) with the kilohertz QPOs of LMXBs, and the low-frequency QPOs of CVs with the horizontal branch oscillations (or the broad noise component identified as such) of LMXBs. Assuming that the same mechanisms produce the QPOs in white dwarf, neutron star, and black hole binaries, we find that the data exclude the relativistic precession model and the magnetospheric and sonic-point beat-frequency models (as well as any model requiring the presence or absence of a stellar surface or magnetic field); more promising are models that interpret QPOs as manifestations of disk accretion onto any low-magnetic field compact object.Comment: 15 pages including 4 encapsulated postscript figures; LaTeX format, uses aastex.cls; accepted on 2002 July 23 for publication in The Astrophysical Journa

First Simultaneous Optical and EUV Observations of the Quasi-Coherent Oscillations of SS Cygni

Using EUV photometry obtained with the Extreme Ultraviolet Explorer (EUVE) satellite and UBVR optical photometry obtained with the 2.7-m telescope at McDonald Observatory, we have detected quasi-coherent oscillations (so-called ``dwarf nova oscillations'') in the EUV and optical flux of the dwarf nova SS Cygni during its 1996 October outburst. There are two new results from these observations. First, we have for the first time observed ``frequency doubling:'' during the rising branch of the outburst, the period of the EUV oscillation was observed to jump from 6.59 s to 2.91 s. Second, we have for the first time observed quasi-coherent oscillations simultaneously in the optical and EUV. We find that the period and phase of the oscillations are the same in the two wavebands, finally confirming the long-held assumption that the periods of the optical and EUV/soft X-ray oscillations of dwarf novae are equal. The UBV oscillations can be simply the Rayleigh-Jeans tail of the EUV oscillations if the boundary layer temperature kT_bb <~ 15 eV and hence the luminosity L_bb >~ 1.2e34 (d/75 pc)^2 erg/s (comparable to that of the accretion disk). Otherwise, the lack of a phase delay between the EUV and optical oscillations requires that the optical reprocessing site lies within the inner third of the accretion disk. This is strikingly different from other cataclysmic variables, where much or all of the disk contributes to the optical oscillations.Comment: 16 pages including 3 tables and 4 encapsulated postscript figures; LaTeX format, uses aastex.cls; accepted on 2001 August 2 for publication in The Astrophysical Journa

Xrn1/Pacman affects apoptosis and regulates expression of hid and reaper

Programmed cell death, or apoptosis, is a highly conserved cellular process that is crucial for tissue homeostasis under normal development as well as environmental stress. Misregulation of apoptosis is linked to many developmental defects and diseases such as tumour formation, autoimmune diseases and neurological disorders. In this paper, we show a novel role for the exoribonuclease Pacman/Xrn1 in regulating apoptosis. Using Drosophila wing imaginal discs as a model system, we demonstrate that a null mutation in pacman results in small imaginal discs as well as lethality during pupation. Mutant wing discs show an increase in the number of cells undergoing apoptosis, especially in the wing pouch area. Compensatory proliferation also occurs in these mutant discs, but this is insufficient to compensate for the concurrent increase in apoptosis. The phenotypic effects of the pacman null mutation are rescued by a deletion that removes one copy of each of the pro-apoptotic genes reaper, hid and grim, demonstrating that pacman acts through this pathway. The null pacman mutation also results in a significant increase in the expression of the pro-apoptotic mRNAs, hid and reaper, with this increase mostly occurring at the post-transcriptional level, suggesting that Pacman normally targets these mRNAs for degradation. Our results uncover a novel function for the conserved exoribonuclease Pacman and suggest that this exoribonuclease is important in the regulation of apoptosis in other organisms