The Archaeal Concept and the World It Lives In: a Retrospective
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Direct Charging of Trnacua with Pyrrolysine in Vitro and in Vivo
letters to nature .............................................................. gene product (see Supplementary Fig. S1). The tRNA pool extracted from Methanosarcina acetivorans or tRNACUA transcribed in vitro Direct charging of tRNACUA with was used in charging experiments. Charged and uncharged tRNA species were separated by electrophoresis in a denaturing acid-urea pyrrolysine in vitro and in vivo 10,11 polyacrylamide gel and tRNACUA was specifically detected by northern blotting with an oligonucleotide probe. The oligonucleo- Sherry K. Blight1*, Ross C. Larue1*, Anirban Mahapatra1*, tide complementary to tRNA could hybridize to a tRNA in the David G. Longstaff1, Edward Chang1, Gang Zhao2†, Patrick T. Kang4, CUA Kari B. Green-Church5, Michael K. Chan2,3,4 & Joseph A. Krzycki1,4 pool of tRNAs isolated from wild-type M. acetivorans but not to the tRNA pool from a pylT deletion mutant of M. acetivorans (A.M., 1Department of Microbiology, 484 West 12th Avenue, 2Department of Chemistry, A. Patel, J. Soares, R.L. and J.A.K., unpublished observations). 3 100 West 18th Avenue, Department of Biochemistry, 484 West 12th Avenue, Both tRNACUA and aminoacyl-tRNACUA were detectable in the The Ohio State University, Columbus, Ohio 43210, USA isolated cellular tRNA pool (Fig. 1). Alkaline hydrolysis deacylated 4Ohio State University Biochemistry Program, 484 West 12th Avenue, The Ohio the cellular charged species, but subsequent incubation with pyrro- State University, Columbus, Ohio 43210, USA lysine, ATP and PylS-His6 resulted in maximal conversion of 50% of 5CCIC/Mass Spectrometry and Proteomics Facility, The Ohio State University, deacylated tRNACUA to a species that migrated with the same 116 W 19th Ave, Columbus, Ohio 43210, USA electrophoretic mobility as the aminoacyl-tRNACUA present in the * These authors contributed equally to this work. -
James A. Mccloskey, Jr
CHEMICAL HERITAGE FOUNDATION JAMES A. MCCLOSKEY, JR. Transcript of Interviews Conducted by Michael A. Grayson at the McCloskeys’ Home Helotes, Texas on 19 and 20 March 2012 (With Subsequent Corrections and Additions) James A. McCloskey, Jr. ACKNOWLEDGMENT This oral history is one in a series initiated by the Chemical Heritage Foundation on behalf of the American Society for Mass Spectrometry. The series documents the personal perspectives of individuals related to the advancement of mass spectrometric instrumentation, and records the human dimensions of the growth of mass spectrometry in academic, industrial, and governmental laboratories during the twentieth century. This project is made possible through the generous support of the American Society for Mass Spectrometry. This oral history is designated Free Access. Please note: Users citing this interview for purposes of publication are obliged under the terms of the Chemical Heritage Foundation (CHF) Center for Oral History to credit CHF using the format below: James A. McCloskey, Jr., interview by Michael A. Grayson at the McCloskeys’ home, Helotes, Texas, 19-20 March 2012 (Philadelphia: Chemical Heritage Foundation, Oral History Transcript # 0702). Chemical Heritage Foundation Center for Oral History 315 Chestnut Street Philadelphia, Pennsylvania 19106 The Chemical Heritage Foundation (CHF) serves the community of the chemical and molecular sciences, and the wider public, by treasuring the past, educating the present, and inspiring the future. CHF maintains a world-class collection of materials that document the history and heritage of the chemical and molecular sciences, technologies, and industries; encourages research in CHF collections; and carries out a program of outreach and interpretation in order to advance an understanding of the role of the chemical and molecular sciences, technologies, and industries in shaping society. -
The Great-Grandmother of LUCA (Last Universal Common Ancestor)
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 4 June 2018 doi:10.20944/preprints201806.0035.v1 Be introduced to the First Universal Common Ancestor (FUCA): the great-grandmother of LUCA (Last Universal Common Ancestor) Francisco Prosdocimi1*, Marco V José2 and Sávio Torres de Farias3* 1 Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil. 2 Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 CDMX, Mexico. 3 Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brasil. * Correspondence: [email protected]; [email protected] Abstract The existence of a common ancestor to all living organisms in Earth is a necessary corollary of Darwin idea of common ancestry. The Last Universal Common Ancestor (LUCA) has been normally considered as the ancestor of cellular organisms that originated the three domains of life: Bacteria, Archaea and Eukarya. Recent studies about the nature of LUCA indicate that this first organism should present hundreds of genes and a complex metabolism. Trying to bring another of Darwin ideas into the origins of life discussion, we went back into the prebiotic chemistry trying to understand how LUCA could be originated 1 © 2018 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 4 June 2018 doi:10.20944/preprints201806.0035.v1 under gradualist assumptions. Along this line of reasoning, it became clear to us that the definition of another ancestral should be of particular relevance to the understanding about the emergence of biological systems. -
Beyond the Big Bang • the Amazon's Lost Civilizations • the Truth
SFI Bulletin winter 2006, vol. 21 #1 Beyond the Big Bang • The Amazon’s Lost Civilizations • The Truth Behind Lying The Bulletin of the Santa Fe Institute is published by SFI to keep its friends and supporters informed about its work. The Santa Fe Institute is a private, independent, multidiscipli- nary research and education center founded in 1984. Since its founding, SFI has devoted itself to creating a new kind of sci- entific research community, pursuing emerging synthesis in science. Operating as a visiting institution, SFI seeks to cat- alyze new collaborative, multidisciplinary research; to break down the barriers between the traditional disciplines; to spread its ideas and methodologies to other institutions; and to encourage the practical application of its results. Published by the Santa Fe Institute 1399 Hyde Park Road Santa Fe, New Mexico 87501, USA phone (505) 984-8800 fax (505) 982-0565 home page: http://www.santafe.edu Note: The SFI Bulletin may be read at the website: www.santafe.edu/sfi/publications/Bulletin/. If you would prefer to read the Bulletin on your computer rather than receive a printed version, contact Patrisia Brunello at 505/984-8800, Ext. 2700 or [email protected]. EDITORIAL STAFF: Ginger Richardson Lesley S. King Andi Sutherland CONTRIBUTORS: Brooke Harrington Janet Yagoda Shagam Julian Smith Janet Stites James Trefil DESIGN & PRODUCTION: Paula Eastwood PHOTO: ROBERT BUELTEMAN ©2004 BUELTEMAN PHOTO: ROBERT SFI Bulletin Winter 2006 TOCtable of contents 3 A Deceptively Simple Formula 2 How Life Began 3 From -
2003 Archaea: Ecology, Metabolism and Molecular Biology
GORDON RESEARCH CONFERENCES frontiers of science P.O. Box 984, West Kingston, RI 02892-0984 Phone: 401 783-4011 Fax: 401 783-7644 E-Mail: [email protected] World Wide Web: http://www.grc.org founded in 1931 Nancy Ryan Gray, Ph.D. Director 2003 GORDON RESEARCH CONFERENCE on 2003 Archaea: Ecology, Metabolism and Molecular Biology FINAL PROGRESS REPORT DOE DE-FG02-03ER15432 The Gordon Research Conference (GRC) on 2003 Archaea: Ecology, Metabolism and Molecular Biology was held at Proctor Academy, Andover, NH from August 3-8, 2003. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, "free time" was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field. I want to personally thank you for your support of this Conference. As you know, in the interest of promoting the presentation of unpublished and frontier- breaking research, Gordon Research Conferences does not permit publication of meeting proceedings. -
A Korarchaeal Genome Reveals Insights Into the Evolution of the Archaea
A korarchaeal genome reveals insights into the evolution of the Archaea James G. Elkinsa,b, Mircea Podarc, David E. Grahamd, Kira S. Makarovae, Yuri Wolfe, Lennart Randauf, Brian P. Hedlundg, Ce´ line Brochier-Armaneth, Victor Kunini, Iain Andersoni, Alla Lapidusi, Eugene Goltsmani, Kerrie Barryi, Eugene V. Koonine, Phil Hugenholtzi, Nikos Kyrpidesi, Gerhard Wannerj, Paul Richardsoni, Martin Kellerc, and Karl O. Stettera,k,l aLehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, D-93053 Regensburg, Germany; cBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; dDepartment of Chemistry and Biochemistry, University of Texas, Austin, TX 78712; eNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; fDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; gSchool of Life Sciences, University of Nevada, Las Vegas, NV 89154; hLaboratoire de Chimie Bacte´rienne, Unite´ Propre de Recherche 9043, Centre National de la Recherche Scientifique, Universite´de Provence Aix-Marseille I, 13331 Marseille Cedex 3, France; iU.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; jInstitute of Botany, Ludwig Maximilians University of Munich, D-80638 Munich, Germany; and kInstitute of Geophysics and Planetary Physics, University of California, Los Angeles, CA 90095 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, April 2, 2008 (received for review January 7, 2008) The candidate division Korarchaeota comprises a group of uncul- and sediment samples from Obsidian Pool as an inoculum. The tivated microorganisms that, by their small subunit rRNA phylog- cultivation system supported the stable growth of a mixed commu- eny, may have diverged early from the major archaeal phyla nity of hyperthermophilic bacteria and archaea including an or- Crenarchaeota and Euryarchaeota. -
Hydrogenases of Methanogens
ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. -
Signature of Controversy
I n “In this volume Granville Sewell provides “As the debate over intelligent design grows T delightful and wide-ranging commentary on increasingly heated... it is refreshing to find a HE the origins debate and intelligent design... discussion of the topic that is calm, thoughtful, Sewell provides much needed clarity on topics and far-ranging, with no sense of having to B e ignature f that are too often misunderstood. His discussion advance an agenda or decimate the opposition. G I S o of the commonly confused problem of entropy In this regard, Granville Sewell’s In the NNI is a must read.” Beginning succeeds brilliantly.” Cornelius G. Hunter, Ph.D. William A. Dembski, Ph.D. N author of The Design Inference author of Science’s Blind Spot G ontroversy A N c In this wide-ranging collection of essays on origins, mathematician Granville Sewell looks at the D big bang, the fine-tuning of the laws of physics, and the evolution of life. He concludes that while O there is much in the history of life that seems to suggest natural causes, there is nothing to support THER Responses to critics of signature in the cEll Charles Darwin’s idea that natural selection of random variations can explain major evolutionary E S advances (“easily the dumbest idea ever taken seriously by science,” he calls it). Sewell explains S A Y why evolution is a fundamentally different and much more difficult problem than others solved s ON by science, and why increasing numbers of scientists are now recognizing what has long been I obvious to the layman, that there is no explanation possible without design. -
Characterization of Methanosarcina Barkeri MST and 227, Methanosarcina Mazei S-6T, and Methanosarcina Vacuolata Z-76IT GLORIA M
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1991, p. 267-274 Vol. 41, No. 2 0020-7713/91/020267-08$02.OO/O Copyright 0 1991, International Union of Microbiological Societies Characterization of Methanosarcina barkeri MST and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-76IT GLORIA M. MAESTROJUAN' AND DAVID R. BOONE172* Departments of Environmental Science and Engineering' and Chemical and Biological Science,2 Oregon Graduate Institute, 19600 N.W. von Neumann Drive, Beaverton, Oregon 97006-1999 Members of the genus Methanosarcina are recognized as major aceticlastic methanogens, and several species which thrive in low-salt, pH-neutral culture medium at mesophilic temperatures have been described. However, the environmental conditions which support the fastest growth of these species (Methanosarcina barkeri MST [T = type strain] and 227, Methanosarcina mazei S-6T, and Methanosarcina vacuolata Z-761T) have not been reported previously. Although the members of the genus Methanosarcina are widely assumed to grow best at pH values near neutrality, we found that some strains prefer acidic pH values. M. vacuolata and the two strains of M. barkeri which we tested were acidophilic when they were grown on H, plus methanol, growing most rapidly at pH 5 and growing at pH values as low as 4.3. M. mazei grew best at pH values near neutrality. We found that all of the strains tested grew most rapidly at 37 to 42°C on all of the growth substrates which we tested. None of the strains was strongly halophilic, although the growth of some strains was slightly stimulated by small amounts of added NaCI. -
History of the Department of Microbiology 1868 – 2009
June 2015 HISTORY OF THE DEPARTMENT OF MICROBIOLOGY 1868 – 2009 University of Illinois at Urbana-Champaign 1 A HISTORY OF THE DEPARTMENT OF MICROBIOLOGY 1868 – 2009 This 141 year history of the Department of Microbiology includes an article (Chapter 1), written and published in 1959 by the Department, which covers the period 1868 to 1959. I joined the Department in 1953, and my recounting of the Department’s history includes personal observations as well as anecdotes told to me by H. O. Halvorson and others. Later I realized what a unique experience it had been to join a first-class department, and I resolved to play a role in maintaining its research stature. Ralph Wolfe 2 Department of Microbiology History of the Headship: 1950 – 1959 Halvor Halvorson 1960 – 1963 Kim Atwood 1963 – 1972 Leon Campbell 1972 – 1982 Ralph DeMoss 1982 – 1987 Samuel Kaplan 1987 – 1990 Jordan Konisky 1990 – 1991 Ralph Wolfe (Acting Head) 1991 – 1997 Charles Miller 1997 – 2002 John Cronan 2003 – 2004 Jeffrey Gardner (Acting Head) 2005 – Present John Cronan 3 Organization of the History of the Department In Chapters 2 to 6 the data are divided into Academic Decades, each containing the following sections: Section I, an overview of the decade; Section II, some events for each year of the decade; Section III, a summary of the research interests, honors received, publications, and invited off-campus lectures or seminars for each faculty member. These data have been obtained from the annual reports of the faculty submitted to the departmental secretary. 4 CHAPTER 1 1868 – 1959 During this time period the name of the Department was Department of Bacteriology (Anecdotes by Ralph Wolfe) A SHORT HISTORY OF THE DEPARTMENT OF BACTERIOLOGY H. -
Characterization of Methanosarcina Mazei JL01 Isolated from Holocene
Proceedings Characterization of Methanosarcina mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta associata GLS2T † Viktoriia Oshurkova 1,*, Olga Troshina 1, Vladimir Trubitsyn 1, Yana Ryzhmanova 1, Olga Bochkareva 2 and Viktoria Shcherbakova 1 1 Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, prospect Nauki 5, Pushchino, 142290 Moscow, Russia; [email protected] (O.T.); [email protected] (V.T.); [email protected] (Y.R.); [email protected] (V.S.) 2 Institute of Science and Technology (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria; [email protected] * Correspondence: [email protected] † Presented at the 1st International Electronic Conference on Microbiology, 2–30 November 2020; Available online: https://ecm2020.sciforum.net/. Published: 18 December 2020 Abstract: A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic. After long-term extensive cultivation at 15 °C, it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate, and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stain-positive. Optimum conditions for growth were 24–28 °C, pH 6.8–7.3, and 0.075–0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein- coding genes revealed 16S rRNA’s close relation to Methanosarcina mazei S-6T (similarity 99.5%). -
Chapter 6 of Discover the World of Microbes
Some like it hot I.A.L. Diamond and Billy Wilder Chapter 6 Life in b oiling w ater The press most likely did not highlight the report of Thomas Brock (Bloomington, Indiana; later Madison, Wisconsin, USA) in 1969 on the isolation of a bacterium from a pond in Yellowstone National Park. This bacterium, Thermus aquaticus, grows at 70 ° C (nearly 160 ° F). Every molecular biologist or microbiologist is famil- iar with the enzyme Taq polymerase, which was isolated from T. aquaticus and has proved essential for the PCR technique used for analysis of trace amounts of DNA (see Chapter 25 ). Growth at 70 ° C s ounds p retty e xciting, b ut i t ’ s f ar from the 100 ° C (212 ° F ) at w hich w ater b oils! Just wait a few minutes. Brock then isolated an organism that grows at 80 ° C, Sul- folobus acidocaldarius . Among microbiologists, these reports aroused an interest in microorganisms growing at high temperatures, so sites in the immediate vicinity of volcanoes or geysers, where it spits and sputters, became the hunting grounds of microbiologists. Two German microbiologists from Munich, Wolfgang Zillig (1925 – 2005) and Karl Otto Stetter, were especially eager to isolate and characterize microorganisms growing in boiling water. First, they studied the sulfur - oxidizing Sulfolobus species from the Solfatara volcanic crater near Naples, Italy, then they concentrated on hot springs in Iceland. It is no easy task to take samples at such hostile sites and to then demonstrate in the samples the presence of living organ- isms that can be grown in cultures and are able to yield a suffi cient cell mass for detailed studies.