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  • 1
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    The Selaginella genome identifies genetic changes associated with the evolution of vascular plants (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-10
    Description: Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banks, Jo Ann -- Nishiyama, Tomoaki -- Hasebe, Mitsuyasu -- Bowman, John L -- Gribskov, Michael -- dePamphilis, Claude -- Albert, Victor A -- Aono, Naoki -- Aoyama, Tsuyoshi -- Ambrose, Barbara A -- Ashton, Neil W -- Axtell, Michael J -- Barker, Elizabeth -- Barker, Michael S -- Bennetzen, Jeffrey L -- Bonawitz, Nicholas D -- Chapple, Clint -- Cheng, Chaoyang -- Correa, Luiz Gustavo Guedes -- Dacre, Michael -- DeBarry, Jeremy -- Dreyer, Ingo -- Elias, Marek -- Engstrom, Eric M -- Estelle, Mark -- Feng, Liang -- Finet, Cedric -- Floyd, Sandra K -- Frommer, Wolf B -- Fujita, Tomomichi -- Gramzow, Lydia -- Gutensohn, Michael -- Harholt, Jesper -- Hattori, Mitsuru -- Heyl, Alexander -- Hirai, Tadayoshi -- Hiwatashi, Yuji -- Ishikawa, Masaki -- Iwata, Mineko -- Karol, Kenneth G -- Koehler, Barbara -- Kolukisaoglu, Uener -- Kubo, Minoru -- Kurata, Tetsuya -- Lalonde, Sylvie -- Li, Kejie -- Li, Ying -- Litt, Amy -- Lyons, Eric -- Manning, Gerard -- Maruyama, Takeshi -- Michael, Todd P -- Mikami, Koji -- Miyazaki, Saori -- Morinaga, Shin-ichi -- Murata, Takashi -- Mueller-Roeber, Bernd -- Nelson, David R -- Obara, Mari -- Oguri, Yasuko -- Olmstead, Richard G -- Onodera, Naoko -- Petersen, Bent Larsen -- Pils, Birgit -- Prigge, Michael -- Rensing, Stefan A -- Riano-Pachon, Diego Mauricio -- Roberts, Alison W -- Sato, Yoshikatsu -- Scheller, Henrik Vibe -- Schulz, Burkhard -- Schulz, Christian -- Shakirov, Eugene V -- Shibagaki, Nakako -- Shinohara, Naoki -- Shippen, Dorothy E -- Sorensen, Iben -- Sotooka, Ryo -- Sugimoto, Nagisa -- Sugita, Mamoru -- Sumikawa, Naomi -- Tanurdzic, Milos -- Theissen, Gunter -- Ulvskov, Peter -- Wakazuki, Sachiko -- Weng, Jing-Ke -- Willats, William W G T -- Wipf, Daniel -- Wolf, Paul G -- Yang, Lixing -- Zimmer, Andreas D -- Zhu, Qihui -- Mitros, Therese -- Hellsten, Uffe -- Loque, Dominique -- Otillar, Robert -- Salamov, Asaf -- Schmutz, Jeremy -- Shapiro, Harris -- Lindquist, Erika -- Lucas, Susan -- Rokhsar, Daniel -- Grigoriev, Igor V -- GM065383/GM/NIGMS NIH HHS/ -- GM84051/GM/NIGMS NIH HHS/ -- HG004164/HG/NHGRI NIH HHS/ -- R01 GM043644/GM/NIGMS NIH HHS/ -- R01 GM084051/GM/NIGMS NIH HHS/ -- R01 GM084051-01A1/GM/NIGMS NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-02/HG/NHGRI NIH HHS/ -- R01 HG004164-03/HG/NHGRI NIH HHS/ -- R01 HG004164-04/HG/NHGRI NIH HHS/ -- T32 GM007757/GM/NIGMS NIH HHS/ -- T32-HG00035/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA. banksj@purdue.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21551031" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/chemistry/genetics ; *Biological Evolution ; Bryopsida/genetics ; Chlamydomonas/chemistry/genetics ; DNA Transposable Elements ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant ; *Genome, Plant ; MicroRNAs/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/metabolism ; Proteome/analysis ; RNA Editing ; RNA, Plant/genetics ; Repetitive Sequences, Nucleic Acid ; Selaginellaceae/*genetics/growth & development/metabolism ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Polarized notum activation at wounds inhibits Wnt function to promote planarian head regeneration (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-14
    Description: Regeneration requires initiation of programs tailored to the identity of missing parts. Head-versus-tail regeneration in planarians presents a paradigm for study of this phenomenon. After injury, Wnt signaling promotes tail regeneration. We report that wounding elicits expression of the Wnt inhibitor notum preferentially at anterior-facing wounds. This expression asymmetry occurs at essentially any wound, even if the anterior pole is intact. Inhibition of notum with RNA interference (RNAi) causes regeneration of an anterior-facing tail instead of a head, and double-RNAi experiments indicate that notum inhibits Wnt signaling to promote head regeneration. notum expression is itself controlled by Wnt signaling, suggesting that regulation of feedback inhibition controls the binary head-tail regeneration outcome. We conclude that local detection of wound orientation with respect to tissue axes results in distinct signaling environments that initiate appropriate regeneration responses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320723/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320723/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petersen, Christian P -- Reddien, Peter W -- R01 GM080639/GM/NIGMS NIH HHS/ -- R01 GM080639-04/GM/NIGMS NIH HHS/ -- R01GM080639/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 May 13;332(6031):852-5. doi: 10.1126/science.1202143.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21566195" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Feedback, Physiological ; Gene Expression Regulation ; Genes, Helminth ; Head ; Helminth Proteins/genetics/*metabolism ; Hydrolases/genetics/*metabolism ; Molecular Sequence Data ; Planarians/cytology/genetics/*physiology ; RNA Interference ; *Regeneration ; *Signal Transduction ; Tail ; Wnt Proteins/genetics/*metabolism ; Wnt1 Protein/genetics/metabolism ; beta Catenin/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Hydrogen is an energy source for hydrothermal vent symbioses (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-08-13
    Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petersen, Jillian M -- Zielinski, Frank U -- Pape, Thomas -- Seifert, Richard -- Moraru, Cristina -- Amann, Rudolf -- Hourdez, Stephane -- Girguis, Peter R -- Wankel, Scott D -- Barbe, Valerie -- Pelletier, Eric -- Fink, Dennis -- Borowski, Christian -- Bach, Wolfgang -- Dubilier, Nicole -- England -- Nature. 2011 Aug 10;476(7359):176-80. doi: 10.1038/nature10325.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21833083" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atlantic Ocean ; Bivalvia/drug effects/metabolism/*microbiology ; Dose-Response Relationship, Drug ; *Ecosystem ; *Energy Metabolism ; Geologic Sediments/chemistry ; Gills/drug effects/metabolism/microbiology ; Hot Springs/*chemistry/microbiology ; Hydrogen/analysis/*metabolism/pharmacology ; Hydrogenase/genetics/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Partial Pressure ; Seawater/chemistry/microbiology ; Sulfides/metabolism ; Sulfur/metabolism ; Symbiosis/drug effects/genetics/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Predominant archaea in marine sediments degrade detrital proteins (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-03-29
    Description: Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells are members of the Archaea, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota and Aigarchaeota, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lloyd, Karen G -- Schreiber, Lars -- Petersen, Dorthe G -- Kjeldsen, Kasper U -- Lever, Mark A -- Steen, Andrew D -- Stepanauskas, Ramunas -- Richter, Michael -- Kleindienst, Sara -- Lenk, Sabine -- Schramm, Andreas -- Jorgensen, Bo Barker -- England -- Nature. 2013 Apr 11;496(7444):215-8. doi: 10.1038/nature12033. Epub 2013 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus 8000, Denmark. klloyd@utk.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23535597" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/metabolism ; Archaea/classification/enzymology/genetics/*metabolism ; Cysteine Endopeptidases/metabolism ; Geologic Sediments/chemistry/*microbiology ; Marine Biology ; Molecular Sequence Data ; Peptide Hydrolases/*metabolism ; Phylogeny ; Proteolysis ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-08-31
    Description: Locomotion in mammals relies on a central pattern-generating circuitry of spinal interneurons established during development that coordinates limb movement. These networks produce left-right alternation of limbs as well as coordinated activation of flexor and extensor muscles. Here we show that a premature stop codon in the DMRT3 gene has a major effect on the pattern of locomotion in horses. The mutation is permissive for the ability to perform alternate gaits and has a favourable effect on harness racing performance. Examination of wild-type and Dmrt3-null mice demonstrates that Dmrt3 is expressed in the dI6 subdivision of spinal cord neurons, takes part in neuronal specification within this subdivision, and is critical for the normal development of a coordinated locomotor network controlling limb movements. Our discovery positions Dmrt3 in a pivotal role for configuring the spinal circuits controlling stride in vertebrates. The DMRT3 mutation has had a major effect on the diversification of the domestic horse, as the altered gait characteristics of a number of breeds apparently require this mutation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523687/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523687/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersson, Lisa S -- Larhammar, Martin -- Memic, Fatima -- Wootz, Hanna -- Schwochow, Doreen -- Rubin, Carl-Johan -- Patra, Kalicharan -- Arnason, Thorvaldur -- Wellbring, Lisbeth -- Hjalm, Goran -- Imsland, Freyja -- Petersen, Jessica L -- McCue, Molly E -- Mickelson, James R -- Cothran, Gus -- Ahituv, Nadav -- Roepstorff, Lars -- Mikko, Sofia -- Vallstedt, Anna -- Lindgren, Gabriella -- Andersson, Leif -- Kullander, Klas -- R01 HD059862/HD/NICHD NIH HHS/ -- R01HD059862/HD/NICHD NIH HHS/ -- England -- Nature. 2012 Aug 30;488(7413):642-6. doi: 10.1038/nature11399.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75124 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22932389" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Codon, Nonsense/genetics ; Gait/*genetics/physiology ; Gene Expression Profiling ; Gene Frequency ; Horses/classification/*genetics/*physiology ; Iceland ; Mice ; Molecular Sequence Data ; Mutation/*genetics ; Neural Pathways/physiology ; Psychomotor Performance/physiology ; Spinal Cord/cytology/*physiology ; Transcription Factors/deficiency/*genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Filamentous bacteria transport electrons over centimetre distances (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-10-30
    Description: Oxygen consumption in marine sediments is often coupled to the oxidation of sulphide generated by degradation of organic matter in deeper, oxygen-free layers. Geochemical observations have shown that this coupling can be mediated by electric currents carried by unidentified electron transporters across centimetre-wide zones. Here we present evidence that the native conductors are long, filamentous bacteria. They abounded in sediment zones with electric currents and along their length they contained strings with distinct properties in accordance with a function as electron transporters. Living, electrical cables add a new dimension to the understanding of interactions in nature and may find use in technology development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeffer, Christian -- Larsen, Steffen -- Song, Jie -- Dong, Mingdong -- Besenbacher, Flemming -- Meyer, Rikke Louise -- Kjeldsen, Kasper Urup -- Schreiber, Lars -- Gorby, Yuri A -- El-Naggar, Mohamed Y -- Leung, Kar Man -- Schramm, Andreas -- Risgaard-Petersen, Nils -- Nielsen, Lars Peter -- England -- Nature. 2012 Nov 8;491(7423):218-21. doi: 10.1038/nature11586. Epub 2012 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23103872" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/cytology/metabolism/ultrastructure ; Deltaproteobacteria/cytology/*metabolism/ultrastructure ; Denmark ; *Electric Conductivity ; Electron Transport ; Geologic Sediments/microbiology ; Glass ; Microspheres ; Molecular Sequence Data ; Molecular Typing ; Oceans and Seas ; Oxygen/metabolism ; Porosity ; RNA, Ribosomal, 16S/analysis/genetics ; Sulfides/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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