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      Molecular evolution of mitochondrial introns in the liverwort Marchantia polymorpha

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          Abstract

          We here describe in detail the characterization and molecular evolution of group II introns in the mitochondrial genome of the liverwort Marchantia polymorpha. We find that 18 introns of the 25 group II introns can be assigned by their similarities to six clusters, indicating an intra-genomic propagation of one ancestral intron each into the respective clusters in the liverwort mitochondrial genome. Interestingly, the intra-genomic propagation of some of these introns occurred only after the evolutionary separation of the bryophytes from the other clades of plants. Finally we report that the maturase-like sequences in the liverwort group II introns have further evolved by horizontal and independent transposition and substitution by analogous sequences from other fungal introns.

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          Rapid planetesimal formation in turbulent circumstellar discs

          Anders Johansen, Jeffrey S. Oishi, Mordecai-Mark Mac Low … (2007)
          The initial stages of planet formation in circumstellar gas discs proceed via dust grains that collide and build up larger and larger bodies (Safronov 1969). How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem (Dominik et al. 2007): boulders stick together poorly (Benz 2000), and spiral into the protostar in a few hundred orbits due to a head wind from the slower rotating gas (Weidenschilling 1977). Gravitational collapse of the solid component has been suggested to overcome this barrier (Safronov 1969, Goldreich & Ward 1973, Youdin & Shu 2002). Even low levels of turbulence, however, inhibit sedimentation of solids to a sufficiently dense midplane layer (Weidenschilling & Cuzzi 1993, Dominik et al. 2007), but turbulence must be present to explain observed gas accretion in protostellar discs (Hartmann 1998). Here we report the discovery of efficient gravitational collapse of boulders in locally overdense regions in the midplane. The boulders concentrate initially in transient high pressures in the turbulent gas (Johansen, Klahr, & Henning 2006), and these concentrations are augmented a further order of magnitude by a streaming instability (Youdin & Goodman 2005, Johansen, Henning, & Klahr 2006, Johansen & Youdin 2007) driven by the relative flow of gas and solids. We find that gravitationally bound clusters form with masses comparable to dwarf planets and containing a distribution of boulder sizes. Gravitational collapse happens much faster than radial drift, offering a possible path to planetesimal formation in accreting circumstellar discs.
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            The Dicke Quantum Phase Transition with a Superfluid Gas in an Optical Cavity

            Ferdinand Brennecke, Tilman Esslinger, Christine Guerlin … (2009)
            A phase transition describes the sudden change of state in a physical system, such as the transition between a fluid and a solid. Quantum gases provide the opportunity to establish a direct link between experiment and generic models which capture the underlying physics. A fundamental concept to describe the collective matter-light interaction is the Dicke model which has been predicted to show an intriguing quantum phase transition. Here we realize the Dicke quantum phase transition in an open system formed by a Bose-Einstein condensate coupled to an optical cavity, and observe the emergence of a self-organized supersolid phase. The phase transition is driven by infinitely long-ranged interactions between the condensed atoms. These are induced by two-photon processes involving the cavity mode and a pump field. We show that the phase transition is described by the Dicke Hamiltonian, including counter-rotating coupling terms, and that the supersolid phase is associated with a spontaneously broken spatial symmetry. The boundary of the phase transition is mapped out in quantitative agreement with the Dicke model. The work opens the field of quantum gases with long-ranged interactions, and provides access to novel quantum phases.
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              Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome.

              K. Akashi, E Ohta, K Oda … (1992)
              Analysis of the mitochondrial DNA of a liverwort Marchantia polymorpha by electron microscopy and restriction endonuclease mapping indicated that the liverwort mitochondrial genome was a single circular molecule of about 184,400 base-pairs. We have determined the complete sequence of the liverwort mitochondrial DNA and detected 94 possible genes in the sequence of 186,608 base-pairs. These included genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins (16 ribosomal proteins, 3 subunits of H(+)-ATPase, 3 subunits of cytochrome c oxidase, apocytochrome b protein and 7 subunits of NADH ubiquinone oxidoreductase). Three ORFs showed similarity to ORFs of unknown function in the mitochondrial genomes of other organisms. Furthermore, 29 ORFs were predicted as possible genes by using the index of G + C content in first, second and third letters of codons (42.0 +/- 10.9%, 37.0 +/- 13.2% and 26.4 +/- 9.4%, respectively) obtained from the codon usages of identified liverwort genes. To date, 32 introns belonging to either group I or group II intron have been found in the coding regions of 17 genes including ribosomal RNA genes (rrn18 and rrn26), a transfer RNA gene (trnS) and a pseudogene (psi nad7). RNA editing was apparently lacking in liverwort mitochondria since the nucleotide sequences of the liverwort mitochondrial DNA were well-conserved at the DNA level.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Proc Jpn Acad Ser B Phys Biol Sci
                Journal ID (publisher-id): PJAB
                Title: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
                Publisher: The Japan Academy (Tokyo, Japan )
                ISSN (Print): 0386-2208
                ISSN (Electronic): 1349-2896
                Publication date (Print): January 2008
                Publication date (Electronic): 9 January 2008
                Volume: 84
                Issue: 1
                Pages: 17-23
                Affiliations
                [*1 ]Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan.
                Author notes
                [† ]Correspondence should be addressed: K. Ohyama,Ishikawa Prefectural University, 1-308 Suematsu, Nonoichimachi, Ishikawa 921-8836 Japan (e-mail: kohyama@ 123456ishikawa-pu.ac.jp ).

                (Communicated by Yasuyuki YAMADA, M.J.A.)

                Article
                Publisher ID: pjab-84-017
                DOI: 10.2183/pjab.84.17
                PMC ID: 2805501
                PubMed ID: 18941284
                SO-VID: fc7aa6d8-6b2d-40dc-89b9-d6471772d228
                Copyright © © 2008 The Japan Academy
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 12 November 2007
                Date accepted : 27 November 2007
                Categories
                Subject: Original Paper

                ScienceOpen disciplines: Life sciences
                Keywords: mitochondrial introns,intra-genomic propagation of introns,marchantia polymorpha,intron evolution,maturase-like orfs
                Data availability:
                ScienceOpen disciplines: Life sciences
                Keywords: mitochondrial introns, intra-genomic propagation of introns, marchantia polymorpha, intron evolution, maturase-like orfs

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