Origins Life
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Proquest Dissertations
RICE UNIVERSITY Meteorite evidence for deep crustal magma chambers on Mars suggests crustal growth driven by underplating and intrusion by Heather Anne Dalton A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE Master of Science APPROVED, THESIS COMMITTEE: Cin-Ty Lee, A^ociate Professor Earth Science Raj deep Dasgupta, Assistant Professor Earth Science rian Lenardic/Professor Earth Science , Dale Sawyer, Professor Earth Science HOUSTON, TEXAS JANUARY 2010 UMI Number: 1485997 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI Dissertation Publishing UMI 1485997 Copyright 2010 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ABSTRACT Meteorite evidence for deep crustal magma chambers on Mars suggests crustal growth driven by underplating and intrusion by Heather Anne Dalton Meteorite RBT04262 is one of only two Martian meteorites made of composite lithologies. Lithology 1 is composed of coarse-grained olivines enclosed inpoikilitic pigeonites, resembling lherzolitic shergottites. Lithology 2 is finer-grained and composed of olivine phenocrysts set within a groundmass of augite, olivine, plagioclase (shocked to maskelynite) and accessory phases such as Ca-phosphates, representing an olivine-phyric shergottite. Lithology 1 may be an early-formed cumulate while Lithology 2 may represent a cooled liquid laden with accumulated olivine crystals. -
POSTER SESSION 5:30 P.M
Monday, July 27, 1998 POSTER SESSION 5:30 p.m. Edmund Burke Theatre Concourse MARTIAN AND SNC METEORITES Head J. W. III Smith D. Zuber M. MOLA Science Team Mars: Assessing Evidence for an Ancient Northern Ocean with MOLA Data Varela M. E. Clocchiatti R. Kurat G. Massare D. Glass-bearing Inclusions in Chassigny Olivine: Heating Experiments Suggest Nonigneous Origin Boctor N. Z. Fei Y. Bertka C. M. Alexander C. M. O’D. Hauri E. Shock Metamorphic Features in Lithologies A, B, and C of Martian Meteorite Elephant Moraine 79001 Flynn G. J. Keller L. P. Jacobsen C. Wirick S. Carbon in Allan Hills 84001 Carbonate and Rims Terho M. Magnetic Properties and Paleointensity Studies of Two SNC Meteorites Britt D. T. Geological Results of the Mars Pathfinder Mission Wright I. P. Grady M. M. Pillinger C. T. Further Carbon-Isotopic Measurements of Carbonates in Allan Hills 84001 Burckle L. H. Delaney J. S. Microfossils in Chondritic Meteorites from Antarctica? Stay Tuned CHONDRULES Srinivasan G. Bischoff A. Magnesium-Aluminum Study of Hibonites Within a Chondrulelike Object from Sharps (H3) Mikouchi T. Fujita K. Miyamoto M. Preferred-oriented Olivines in a Porphyritic Olivine Chondrule from the Semarkona (LL3.0) Chondrite Tachibana S. Tsuchiyama A. Measurements of Evaporation Rates of Sulfur from Iron-Iron Sulfide Melt Maruyama S. Yurimoto H. Sueno S. Spinel-bearing Chondrules in the Allende Meteorite Semenenko V. P. Perron C. Girich A. L. Carbon-rich Fine-grained Clasts in the Krymka (LL3) Chondrite Bukovanská M. Nemec I. Šolc M. Study of Some Achondrites and Chondrites by Fourier Transform Infrared Microspectroscopy and Diffuse Reflectance Spectroscopy Semenenko V. -
12.007 Geobiology Spring 2009
MIT OpenCourseWare http://ocw.mit.edu 12.007 Geobiology Spring 2009 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. Geobiology 2009 Lecture 10 The Antiquity of Life on Earth Homework #5 Topics (choose 1): Describe criteria for biogenicity in microscopic fossils. How do the oldest describes fossils compare? Use this to argue one side of the Brasier-Schopf debate OR What are stromatolites; where are they found and how are they formed? Articulate the two sides of the debate on antiquity and biogenicity. Up to 4 pages, including figures. Due 3/31/2009 Need to know • How C and S- isotopic data in rocks are informative about the advent and antiquity of biogeochemical cycles • Morphological remains and the antiquity of life; how do we weigh the evidence? • Indicators of changes in atmospheric pO2 • A general view of the course of oxygenation of the atm-ocean system Readings for this lecture Schopf J.W. et al., (2002) Laser Raman Imagery of Earth’s earliest fossils. Nature 416, 73. Brasier M.D. et al., (2002) Questioning the evidence for Earth’s oldest fossils. Nature 416, 76. Garcia-Ruiz J.M., Hyde S.T., Carnerup A. M. , Christy v, Van Kranendonk M. J. and Welham N. J. (2003) Self-Assembled Silica-Carbonate Structures and Detection of Ancient Microfossils Science 302, 1194-7. Hofmann, H.J., Grey, K., Hickman, A.H., and Thorpe, R. 1999. Origin of 3.45 Ga coniform stromatolites in Warrawoona Group, Western Australia. Geological Society of America, Bulletin, v. 111 (8), p. -
Insights Into the Dynamics Between Viruses and Their Hosts in a Hot Spring Microbial Mat
The ISME Journal (2020) 14:2527–2541 https://doi.org/10.1038/s41396-020-0705-4 ARTICLE Insights into the dynamics between viruses and their hosts in a hot spring microbial mat 1,2,11 1,2 1,2 1,2 1,2 Jessica K. Jarett ● Mária Džunková ● Frederik Schulz ● Simon Roux ● David Paez-Espino ● 1,2 1,2 1,2 3 4 Emiley Eloe-Fadrosh ● Sean P. Jungbluth ● Natalia Ivanova ● John R. Spear ● Stephanie A. Carr ● 5 6 7 8,9 1,2 Christopher B. Trivedi ● Frank A. Corsetti ● Hope A. Johnson ● Eric Becraft ● Nikos Kyrpides ● 9 1,2,10 Ramunas Stepanauskas ● Tanja Woyke Received: 13 January 2020 / Revised: 3 June 2020 / Accepted: 11 June 2020 / Published online: 13 July 2020 © The Author(s) 2020. This article is published with open access Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics – 1234567890();,: 1234567890();,: applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. -
GSC Workshop 10 Grant Finances Monthly Teleconference Calls
Standards in Genomic Sciences (2010) 3:225-231 DOI:10.4056/sigs.1423520 Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10 Elizabeth Glass1, Folker Meyer1,2, Jack A Gilbert1,3, Dawn Field4, Sarah Hunter5, Renzo Kottmann6, Nikos Kyrpides7, Susanna Sansone8, Lynn Schriml9, Peter Sterk10, Owen White9 and John Wooley11 1 Argonne National Laboratory, Argonne, IL USA 2 Computation Institute, University of Chicago, Chicago, IL USA 3 Department of Ecology and Evolution, University of Chicago, Chicago, IL USA, 4 Centre for Ecology & Hydrology, Oxfordshire, UK 5 European Molecular Biology Laboratory (EMBL) Outstation, European Bioinformatics Insti- tute (EBI), Hinxton, Cambridge UK 6 Microbial Genomics Group, Max Planck Institute for Marine Microbiology and Jacobs University Bremen, Bremen, Germany 7 DOE Joint Genome Institute, Walnut Creek, CA, USA 8 University of Oxford, Oxford e-Research Centre, Oxford, UK 9 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA 10 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK 11 University of California San Diego, La Jolla, CA USA *Corresponding Author: Dawn Field This report summarizes the proceedings of the 10th workshop of the Genomic Standards Consortium (GSC), held at Argonne National Laboratory, IL, USA. It was the second GSC workshop to have open registration and attracted over 60 participants who worked together to progress the full range of projects ongoing within the GSC. Overall, the primary focus of the workshop was on advancing the M5 platform for next-generation collaborative computa- tional infrastructures. Other key outcomes included the formation of a GSC working group focused on MIGS/MIMS/MIENS compliance using the ISA software suite and the formal launch of the GSC Developer Working Group. -
The Minimum Information About a Genome Sequence (MIGS) Specification
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2008 The minimum information about a genome sequence (MIGS) specification Dawn Field Natural Environmental Research Council Centre for Ecology and Hydrology, [email protected] George Garrity Michigan State University Tanya Gray Natural Environmental Research Council Centre for Ecology and Hydrology Norman Morrison FUnivollowersity this of and Manchester additional works at: https://digitalcommons.unl.edu/usdoepub Jer emyPart ofSelengut the Bior esource and Agricultural Engineering Commons J. Craig Venter Institute SeeField, next Dawn; page Garrity for additional, George; Grauthorsay, Tany a; Morrison, Norman; Selengut, Jeremy; Sterk, Peter; Tatusova, Tatiana; Thomson, Nicholas; Allen, Michael J.; Angiuoli, Samuel V.; Ashburner, Michael; Axelrod, Nelson; Baldauf, Sandra; Ballard, Stuart; Boore, Jeffrey; Cochrane, Guy; Cole, James; Dawyndt, Peter; De Vos, Paul; dePamphilis, Claude; Edwards, Robert; Faruque, Nadeem; Feldman, Robert; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Goldstein, Philip; Guralnick, Robert; Haft, Dan; Hancock, David; Hermjakob, Henning; Hertz-Fowler, Christiane; Hugenholtz, Phil; Joint, Ian; Kagan, Leonid; Kane, Matthew; Kennedy, Jessie; Kowalchuk, George; Kottmann, Renzo; Kolker, Eugene; Kravitz, Saul; Kyrpides, Nikos; Leebens-Mack, Jim; Lewis, Suzanna E.; Li, Kelvin; Lister, Allyson L.; Lord, Phillip; Maltsev, Natalia; Markowitz, Victor; Martiny, Jennifer; Methe, Barbara; Mizrachi, Ilene; Moxon, Richard; Nelson, Karen; Parkhill, Julian; Proctor, Lita; White, Owen; Sansone, Susanna-Assunta; Spiers, Andrew; Stevens, Robert; Swift, Paul; Taylor, Chris; Tateno, Yoshio; Tett, Adrian; Turner, Sarah; Ussery, David; Vaughan, Bob; Ward, Naomi; Whetzel, Trish; San Gil, Ingio; Wilson, Gareth; and Wipat, Anil, "The minimum information about a genome sequence (MIGS) specification" (2008). US Department of Energy Publications. -
Meeting Report: “Metagenomics, Metadata and Meta-Analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010
Standards in Genomic Sciences (2010) 2:357-360 DOI:10.4056/sigs.802738 Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010 Lynette Hirschman1, Peter Sterk2,3, Dawn Field2, John Wooley4, Guy Cochrane5, Jack Gilbert6, Eugene Kolker7, Nikos Kyrpides8, Folker Meyer9, Ilene Mizrachi10, Yasukazu Nakamura11, Susanna-Assunta Sansone5, Lynn Schriml12, Tatiana Tatusova10, Owen White12 and Pelin Yilmaz13 1 Information Technology Center, The MITRE Corporation, Bedford, MA, USA 2 NERC Center for Ecology and Hydrology, Oxford, OX1 3SR, UK 3 Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK 4 University of California San Diego, La Jolla, CA, USA 5 European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Hinxton, Cambridge, UK 6 Plymouth Marine Laboratory (PML), Plymouth, UK 7 Seattle Children’s Hospital, Seattle, WA, USA 8 Genome Biology Program, DOE Joint Genome Institute, Walnut Creek, California, USA 9 Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA 10 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA 11 DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Japan 12 University of Maryland School of Medicine, Baltimore, MD, USA 13 Microbial Genomics Group, Max Planck Institute for Marine Microbiology & Jacobs University Bremen, Bremen, Germany This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, in- cluded five contributed talks, a series of short presentations from stakeholders in the genom- ics standards community, a poster session, and, in the evening, an open discussion session to review current projects and examine future directions for the GSC and its stakeholders. -
Cause of Cambrian Explosion - Terrestrial Or Cosmic?
Progress in Biophysics and Molecular Biology xxx (2018) 1e21 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio Cause of Cambrian Explosion - Terrestrial or Cosmic? * Edward J. Steele a, j, , Shirwan Al-Mufti b, Kenneth A. Augustyn c, Rohana Chandrajith d, John P. Coghlan e, S.G. Coulson b, Sudipto Ghosh f, Mark Gillman g, Reginald M. Gorczynski h, Brig Klyce b, Godfrey Louis i, Kithsiri Mahanama j, Keith R. Oliver k, Julio Padron l, Jiangwen Qu m, John A. Schuster n, W.E. Smith o, Duane P. Snyder b, Julian A. Steele p, Brent J. Stewart a, Robert Temple q, Gensuke Tokoro o, Christopher A. Tout r, Alexander Unzicker s, Milton Wainwright b, j, Jamie Wallis b, Daryl H. Wallis b, Max K. Wallis b, John Wetherall t, D.T. Wickramasinghe u, J.T. Wickramasinghe b, N. Chandra Wickramasinghe b, j, o, Yongsheng Liu v, w a CY O'Connor ERADE Village Foundation, Piara Waters, WA, Australia b Buckingham Centre for Astrobiology, University of Buckingham, UK c Center for the Physics of Living Organisms, Department of Physics, Michigan Technological University, Michigan, United States d Department of Geology, University of Peradeniya, Peradeniya, Sri Lanka e University of Melbourne, Office of the Dean, Faculty Medicine, Dentistry and Health Sciences, 3rd Level, Alan Gilbert Building, Australia f Metallurgical & Materials Engineering IIT, Kanpur, India g South African Brain Research Institute, 6 Campbell Street, Waverly, Johannesburg, South Africa h University Toronto -
The Positive Role of the Ecological Community in the Genomic Revolution
The positive role of the ecological community in the genomic revolution Dawn Field, Barbara Methe, Karen Nelson, and Nikos Kyrpides, An increasing number of ecologists are turning to the use of genomic technologies to complement and extend traditional methods of characterizing microbial diversity and its biological consequences (Xu, 2006). The SCOPE meeting on Microbial Environmental Genomics (MicroEnGen-II, Shanghai, June 12-15, 2006) provided a rich set of examples of progress at this interface (van Veen, Kowalchuk, 2006), many of which are described in this special issue. The session of this meeting entitled ‘new frontiers’ included two presentations on informatics and data management. We (DF and NK) talked about projects we are involved in, namely, the Integrated Microbial Genomes Resource (IMG) (Markowitz et al., 2006), the Genomic Standards Consortium (GSC) (Field et al., et al, in review) and the NERC Environmental Bioinformatics Centre (NEBC) (Field et al., 2005). In this commentary we briefly describe these projects, provide updated information on their development and attempt to expand on the wider issue of the increasing need for ecologists to become involved in the development of these and similar genomic resources. These projects have all benefited from the direct and indirect contribution of ecologists. Further, each is working in its own way to help strengthen the position of researchers working in eco- and environmental genomics. The IMG system is an example of a new generation database project attempting to standardize access to the publicly available collection of genomes, through a comparative genomics approach (Markowitz et al., 2006). The GSC represents an international effort to produce consensus on the ways in which we collect, exchange and represent genomic metadata (Field et al., et al, in review). -
F. Nucleatum Sub Spp Vincentii and Its Comparison with the Genome of F
Letter Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586 Vinayak Kapatral,1 Natalia Ivanova, Iain Anderson, Gary Reznik, Anamitra Bhattacharyya, Warren L. Gardner, Natalia Mikhailova, Alla Lapidus, Niels Larsen, Mark D’Souza, Theresa Walunas, Robert Haselkorn, Ross Overbeek, and Nikos Kyrpides Integrated Genomics Inc., Chicago, Illinois 60612, USA We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FNhave been identified. Of these, 118 ORFs have no known fun ction and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H2S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been identified in FNV. ORFs for ethanolamine utilization, thermostable carboxypeptidase, ␥ glutamyl-transpeptidase, and deblocking aminopeptidases are absent from FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes for resistance to antibiotics such as acriflavin, bacitracin, bleomycin, daunorubicin, florfenicol, and other general multidrug resistance are present. -
Paleontology1
PALEONTOLOGY1 Thoreau’s firm grasp of paleontology laid the groundwork for the climax of WALDEN, which describes the emergence of complexity and beauty from the simple flow of muddy sand at the Deep Cut. It also was the taproot of his lifelong frustration with Christian supernaturalists, who insisted on a fairly brief history of life. Paraphrasing Lyell’s PRINCIPLES, he jested [in A WEEK ON THE C ONCORD AND M ERRIMACK R IVERS]: “It took 100 years to prove that fossils are organic, and 150 more, to prove that they are not to be referred to the Noachian deluge.” Not everyone believes this, even today. Modern “young Earth” creationists still insist that the Elizabethan-era Mosaic chronology of Archbishop Ussher is the correct one, and that we twenty-first century scientists are in error. — Professor Robert M. Thorson, WALDEN’S SHORE, pages 60-1 1. (“Paleology” would be the study of antiques, how much they might fetch at auction.) HDT WHAT? INDEX PALEONTOLOGY PALEONTOLOGY 23,000 BCE Full glacial world, cold and dry; Stage 2 (includes the latest “Glacial Maximum”). This period includes the two ‘coldest phases’ –Heinrich Events– at something like 21,000 BCE-19,000 BCE and at something like 15,000 BCE-12,500 BCE. Music was produced by humans in what is now France; archaeological evidence includes cave paintings, footprints in caves that seem to be those of dancers, and carved bones that seem to be wind and percussion instruments. People made artifacts with primitive geometrical designs. THE WISCONSONIAN GLACIATION “NARRATIVE HISTORY” AMOUNTS TO FABULATION, THE REAL STUFF BEING MERE CHRONOLOGY “Stack of the Artist of Kouroo” Project Paleontology HDT WHAT? INDEX PALEONTOLOGY PALEONTOLOGY 18,000 BCE On the basis of Carbon-14 measurements, this was the last Glacial Maximum, the coldest period of the most recent Ice Age. -
Geobiology 2007 Lecture 4 the Antiquity of Life on Earth Homework #2
Geobiology 2007 Lecture 4 The Antiquity of Life on Earth Homework #2 Topics (choose 1): Describe criteria for biogenicity in microscopic fossils. How do the oldest described fossils compare? How has the Brasier-Schopf debate shifted in five years? OR What are stromatolites; where are they found and how are they formed? Articulate the two sides of the debate on antiquity and biogenicity. Up to 4 pages, including figures. Due 3/01/2006 Required readings for this lecture Nisbet E. G. & Sleep N. H. (2001) The habitat and nature of early life, Nature 409, 1083. Schopf J.W. et al., (2002) Laser Raman Imagery of Earth’s earliest fossils. Nature 416, 73. Brasier M.D. et al., (2002) Questioning the evidence for Earth’s oldest fossils. Nature 416, 76. Garcia-Ruiz J.M., Hyde S.T., Carnerup A. M. , Christy v, Van Kranendonk M. J. and Welham N. J. (2003) Self-Assembled Silica-Carbonate Structures and Detection of Ancient Microfossils Science 302, 1194-7. Hofmann, H.J., Grey, K., Hickman, A.H., and Thorpe, R. 1999. Origin of 3.45 Ga coniform stromatolites in Warrawoona Group, Western Australia. Geological Society of America, Bulletin, v. 111 (8), p. 1256-1262. Allwood et al., (2006) Stromatolite reef from the Early Archaean era of Australia. Nature 441|, 714 J. William Schopf, Fossil evidence of Archaean life (2006) Phil. Trans. R. Soc. B 361, 869–885. Martin Brasier, Nicola McLoughlin, Owen Green and David Wacey (2006) A fresh look at the fossil evidence for early Archaean cellular life. Phil. Trans. R. Soc. B 361, 887–902 What is Life? “Life can be recognized by its deeds — life is disequilibrium, leaving behind the signatures of disequilibrium such as fractionated isotopes or complex molecules.