海洋性プランクトン群の進化と生態についての研究

平成30年度 京都大学化学研究所 スーパーコンピュータシステム 利用報告

Existence of the thermodynamic limit for disordered quantum Coulomb systems

Following a recent method introduced by C. Hainzl, J.P. Solovej and the second author of this article, we prove the existence of the thermodynamic limit for a system made of quantum electrons, and classical nuclei whose positions and charges are randomly perturbed in an ergodic fashion. All the particles interact through Coulomb forces.Comment: To appear in J. Math. Phys. (special issue in honor of E.H. Lieb

Sterol biosynthesis pathway is part of the interferon host defence response

Recently, cholesterol metabolism has been shown to modulate the infection of several viruses and there is growing evidence that inflammatory response to infection also modulates lipid metabolism. However little is known about the role of inflammatory processes in modulating lipid metabolism and their consequences for the viral infection. This study investigates host-lipid viral interaction pathways using mouse cytomegalovirus, a large double-stranded DNA genome, which represents one of the few models for a natural infection of its natural host. In this study, transcriptomic and lipidomic profiling of macrophages shows that there is a specific coordinated regulation of the sterol pathways upon viral infection or treatment with IFNγ or β (but not TNFα, IL1β or IL6) resulting in the decrease of free cellular cholesterol. Furthermore, we show that pharmacological and RNAi inhibition of the sterol pathway augments protection against infection in vitro and in vivo and we identified that the prenylation branch of the sterol metabolic network was involved in the protective response. Finally, we show that genetic knock out of IFNβ results in a partial reduction while genetic knock out of Ifnar1 completely abolishes the reduction of the sterol biosynthetic activity upon infection. Overall these results support a role for part of the sterol metabolic network in protective immunity and show that type 1 IFN signalling is both necessary and sufficient for reducing the sterol metabolic network upon infection; thereby linking the sterol pathway with IFN defence responses

THE USE OF GLOBAL SENSITIVITY ANALYSIS FOR ASSESSING CAPABILITY OF THE MTG/FCI INSTRUMENT TO DETECT AEROSOLS

International audienceThe Flexible Combined Imager (FCI) is an instrument to be borne by the future geostationary meteorological satellite Meteosat Third Generation (MTG). A numerical simulator was set up to provide simulated outputs of the instrument. It includes top-of-atmosphere scene of upwelling spectral radiance obtained by a radiative transfer model in the clear atmosphere, and the transfer function of the FCI. The sensitivity of the sensor outputs to aerosol properties is studied by varying the inputs defining the scenes and their illumination. The Global Sensitivity Analysis (GSA) with the Sobol' decomposition is applied to the outputs of the simulator, yielding a ranking of the inputs with respect to their influence on the FCI numerical outputs. The results are presented for all visible and near infrared channels of the FCI for desert type of aerosols according to the OPAC database. The study highlights the most relevant channels for aerosol detection and characterization and gives assessment of the different sources of uncertainties in aerosol retrieval with such channels

Asp Viper (Vipera aspis) Envenomation: Experience of the Marseille Poison Centre from 1996 to 2008

A retrospective case review study of viper envenomations collected by the Marseille’s Poison Centre between 1996 and 2008 was performed. Results: 174 cases were studied (52 grade 1 = G1, 90 G2 and 32 G3). G1 patients received symptomatic treatments (average hospital stay 0.96 day). One hundred and six (106) of the G2/G3 patients were treated with the antivenom Viperfav* (2.1+/-0.9 days in hospital), while 15 of them received symptomatic treatments only (plus one immediate death) (8.1+/-4 days in hospital, 2 of them died). The hospital stay was significantly reduced in the antivenom treated group (p < 0.001), and none of the 106 antivenom treated patients had immediate (anaphylaxis) or delayed (serum sickness) allergic reactions. Conclusion: Viperfav* antivenom was safe and effective for treating asp viper venom-induced toxicity

High efficiency image restoration using mirror images and adaptive Kalman filtering

The purpose of this paper is image restoration by means of fast parallel Kalman filtering . This algorithm was introduced by Biemond et al. in 1983 [13] for image restoration . The problem is the appearance of ringing in the restored image. It results front the implicit assumption of rows periodicity, when FFT is applied on the image rows. Since left and right boundaries values are différent, discontinuity points appear . In order to achieve boundary condition suitable for the ID horizontal FFT processing, we use in the algorithm a mirror image . We first give the description of this mirror image, and then we exploit in the algorithm its horizontal properties of boundaries continuity and symmetry. Then, an adaptive Kalman filtering is introduced to avoid non consistency of the Kalman gains factors on some frequencies, and to reduce the remaining ringing. Finally results are shown for some images and PSF .Notre propos est la restauration d'image dégradée par un flou ou un bougé, additionné d'un bruit . La méthode proposée est dérivée de l'algorithme de filtrage récursif introduit par Biemond en 1983 [13] qui offre l'avantage d'être plus rapide que d'autres méthodes de restauration d'image, et de réaliser une déconvolution significative . L'écriture vectorielle du modèle AR 2D de l'image et de la dégradation fait apparaître des matrices de Toeplitz . Celles-ci approchées par des matrices circulantes, sont facilement diagonalisées par FFT. Cette diagonalisation permet de transformer le système 2D de taille N x N, en N systèmes 1D disjoints de taille N : l'application de N FFT sur les lignes permet d'obtenir N filtres de Kalman disjoints sur les colonnes . L'utilisation de la FFT, qui suppose la périodicité du signal traité, fait apparaître une discontinuité entre les bords droit et gauche de l'image . Cette discontinuité du signal crée des fréquences parasites qui se traduisent sur l'image restaurée, par des bandes verticales blanches et noires . Afin d'éliminer ces rayures, nous proposons d'utiliser dans cet algorithme une image miroir construite à partir de l'image originale : l'image à traiter possède alors des propriétés de continuité et de symétrie que nous exploitons . Enfin, nous développons un filtre adaptatif de Kalman appliqué au signal 1D à restaurer, afin de réduire la dynamique des gains du filtre de certains de ces signaux . Des résultats sont présentés sur des images artificiellement rendues floues ou bougées

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

Summary: KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. Availability and implementation: KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/). Supplementary information: Supplementary data are available at Bioinformatics online

Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses

Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments

Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water

ヒストン遺伝子を全セット持つ巨大ウイルスの発見 --DNA関連遺伝子のウイルス起源に新たな証拠--. 京都大学プレスリリース. 2019-02-08.Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae