Progression of the canonical reference malaria parasite genome from 2002–2019

Here we describe the ways in which the sequence and annotation of the Plasmodium falciparum reference genome has changed since its publication in 2002. As the malaria species responsible for the most deaths worldwide, the richness of annotation and accuracy of the sequence are important resources for the P. falciparum research community as well as the basis for interpreting the genomes of subsequently sequenced species. At the time of publication in 2002 over 60% of predicted genes had unknown functions. As of March 2019, this number has been significantly decreased to 33%. The reduction is due to the inclusion of genes that were subsequently characterised experimentally and genes with significant similarity to others with known functions. In addition, the structural annotation of genes has been significantly refined; 27% of gene structures have been changed since 2002, comprising changes in exon-intron boundaries, addition or deletion of exons and the addition or deletion of genes. The sequence has also undergone significant improvements. In addition to the correction of a large number of single-base and insertion or deletion errors, a major miss-assembly between the subtelomeres of chromosome 7 and 8 has been corrected. As the number of sequenced isolates continues to grow rapidly, a single reference genome will not be an adequate basis for interpretating intra-species sequence diversity. We therefore describe in this publication a population reference genome of P. falciparum, called Pfref1. This reference will enable the community to map to regions that are not present in the current assembly. P. falciparum 3D7 will be continued to be maintained with ongoing curation ensuring continual improvements in annotation quality

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality

Fragmentation transitions in multi-state voter models

Adaptive models of opinion formation among humans can display a fragmentation transition, where a social network breaks into disconnected components. Here, we investigate this transition in a class of models with arbitrary number of opinions. In contrast to previous work we do not assume that opinions are equidistant or arranged on a one-dimensional conceptual axis. Our investigation reveals detailed analytical results on fragmentations in a three-opinion model, which are confirmed by agent-based simulations. Furthermore, we show that in certain models the number of opinions can be reduced without affecting the fragmentation points.Comment: 11 pages, 8 figure

Exhaustive generation of kk-critical H\mathcal H-free graphs

We describe an algorithm for generating all $k$-critical $\mathcal H$-free graphs, based on a method of Ho\`{a}ng et al. Using this algorithm, we prove that there are only finitely many $4$-critical $(P_7,C_k)$-free graphs, for both $k=4$ and $k=5$. We also show that there are only finitely many $4$-critical graphs $(P_8,C_4)$-free graphs. For each case of these cases we also give the complete lists of critical graphs and vertex-critical graphs. These results generalize previous work by Hell and Huang, and yield certifying algorithms for the $3$-colorability problem in the respective classes. Moreover, we prove that for every $t$, the class of 4-critical planar $P_t$-free graphs is finite. We also determine all 27 4-critical planar $(P_7,C_6)$-free graphs. We also prove that every $P_{10}$-free graph of girth at least five is 3-colorable, and determine the smallest 4-chromatic $P_{12}$-free graph of girth five. Moreover, we show that every $P_{13}$-free graph of girth at least six and every $P_{16}$-free graph of girth at least seven is 3-colorable. This strengthens results of Golovach et al.Comment: 17 pages, improved girth results. arXiv admin note: text overlap with arXiv:1504.0697

Digoxin net secretory transport in bronchial epithelial cell layers is not exclusively mediated by P-glycoprotein/MDR1

Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original author and source are creditedThe impact of P-glycoprotein (MDR1, ABCB1) on drug disposition in the lungs as well as its presence and activity in in vitro respiratory drug absorption models remain controversial to date. Hence, we characterised MDR1 expression and the bidirectional transport of the common MDR1 probe 3H-digoxin in air-liquid interfaced (ALI) layers of normal human bronchial epithelial (NHBE) cells and of the Calu-3 bronchial epithelial cell line at different passage numbers. Madin-Darby Canine Kidney (MDCKII) cells transfected with the human MDR1 were used as positive controls. 3H-digoxin efflux ratio (ER) was low and highly variable in NHBE layers. In contrast, ER=11.4 or 3.0 was measured in Calu-3 layers at a low or high passage number, respectively. These were, however, in contradiction with increased MDR1 protein levels observed upon passaging. Furthermore, ATP depletion and the two MDR1 inhibitory antibodies MRK16 and UIC2 had no or only a marginal impact on 3H-digoxin net secretory transport in the cell line. Our data do not support an exclusive role of MDR1 in 3H-digoxin apparent efflux in ALI Calu-3 layers and suggest the participation of an ATP-independent carrier. Identification of this transporter might provide a better understanding of drug distribution in the lungs.Peer reviewe

Optimierung des Wasserstandes zur Verbesserung der Klimabilanz in landwirtschaftlich genutzten Hochmooren

Entwässerte Moore sind Hotspots für Treibhausgasemissionen (THG), insbesondere für Kohlenstoffdioxid (CO2). Die Menge an freigesetztem CO2 in die Atmosphäre wird dabei maßgeblich über den Wasserstand im Moorkörper gesteuert. So sind vor allem intensiv genutzte Moorstandorte mit tiefen Wasserständen durch sehr hohe THG-Emissionen gekennzeichnet. Eine adäquate Entwässerung ist für die landwirtschaftliche Moornutzung essentiell, um die Bewirtschaftung (z.B. Düngung, Ernte) sowie eine optimale Pflanzenentwicklung zu gewährleisten. Die hohe flächenmäßige Bedeutung der landwirtschaftlichen Moornutzung in Niedersachsen (ca. 256.000 ha auf Nieder- und Hochmoor, davon ca. 81% Grünland) in Kombination mit hohen THG-Emissionen führen dazu, dass Moore in der Treibhausgasbilanz des Bundeslandes eine wichtige Größe darstellen (ca. 10 % der Gesamtemissionen). Aufgrund dieser landesweiten Bedeutung von landwirtschaftlich genutzten Moorflächen könnte eine Reduktion von THG-Emissionen durch angepasstes Wassermanagement zu einem großen THG-Einsparpotenzial in Niedersachsen führen. Dem Anheben des Wasserstandes durch geeignete Wassermaßnahmen zur Reduktion der THG steht die Notwendigkeit von tragfähigen Grasnarben und guter Befahrbarkeit für die Bewirtschaftung der Flächen gegenüber, welche derzeit noch vorwiegend über sehr tief abgesenkte Wasserstände erreicht wird. Ein Ziel des Modellprojektes im Gnarrenburger Moor ist es daher, die Wasserstände im Jahresverlauf so zu optimieren, dass eine Reduktion der THG-Emissionen unter Beibehaltung der landwirtschaftlichen Nutzung möglich wird. Darüber hinaus soll durch aktive Einbindung der kooperierenden Landwirte in das Projekt die grundsätzliche Akzeptanz für Wassermanagementmaßnahmen auf landwirtschaftlichen Grünlandflächen geschaffen werden. Grundbaustein des Modellprojektes ist das Anlegen von Demonstrationsversuchen. Basierend auf der Nutzungsintensität (Intensivgrünland, Extensivgrünland) werden in den Versuchen verschiedene Wassermanagementoptionen (z.B. Grabenanstau, Unterflurbewässerung) auf ihre Umsetzbarkeit sowie hinsichtlich der Auswirkungen auf die Bewirtschaftung, die Pflanzenerträge und die Wasserstandsdynamik untersucht. Das Poster stellt den grundlegenden Aufbau sowie die Ziele des Projektes dar und liefert darüber hinaus Informationen zu den Demoversuchen sowie den wissenschaftlichen Begleituntersuchungen

A Survey of Satisfiability Modulo Theory

Satisfiability modulo theory (SMT) consists in testing the satisfiability of first-order formulas over linear integer or real arithmetic, or other theories. In this survey, we explain the combination of propositional satisfiability and decision procedures for conjunctions known as DPLL(T), and the alternative "natural domain" approaches. We also cover quantifiers, Craig interpolants, polynomial arithmetic, and how SMT solvers are used in automated software analysis.Comment: Computer Algebra in Scientific Computing, Sep 2016, Bucharest, Romania. 201

Photoinduced 3D orientational order in side chain liquid crystalline azopolymers

We apply experimental technique based on the combination of methods dealing with principal refractive indices and absorption coefficients to study the photoinduced 3D orientational order in the films of liquid crystalline (LC) azopolymers. The technique is used to identify 3D orientational configurations of trans azobenzene chromophores and to characterize the degree of ordering in terms of order parameters. We study two types of LC azopolymers which form structures with preferred in-plane and out-of-plane alignment of azochromophores, correspondingly. Using irradiation with the polarized light of two different wavelengths we find that the kinetics of photoinduced anisotropy can be dominated by either photo-reorientation or photoselection mechanisms depending on the wavelength. We formulate the phenomenological model describing the kinetics of photoinduced anisotropy in terms of the isomer concentrations and the order parameter tensor. We present the numerical results for absorption coefficients that are found to be in good agreement with the experimental data. The model is also used to interpret the effect of changing the mechanism with the wavelength of the pumping light.Comment: uses revtex4 28 pages, 10 figure

Measurement of triple gauge boson couplings from W⁺W⁻ production at LEP energies up to 189 GeV

A measurement of triple gauge boson couplings is presented, based on W-pair data recorded by the OPAL detector at LEP during 1998 at a centre-of-mass energy of 189 GeV with an integrated luminosity of 183 pb⁻¹. After combining with our previous measurements at centre-of-mass energies of 161–183 GeV we obtain κ = 0.97_{-0.16}^{+0.20}, g_{1}^{z} = 0.991_{-0.057}^{+0.060} and λ = -0.110_{-0.055}^{+0.058}, where the errors include both statistical and systematic uncertainties and each coupling is determined by setting the other two couplings to their Standard Model values. These results are consistent with the Standard Model expectations