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Vascular Plant and Vertebrate Inventory of Montezuma Castle National Monument Vascular Plant and Vertebrate Inventory of Montezuma Castle National Monument
Schmidt, Drost, Halvorson In Cooperation with the University of Arizona, School of Natural Resources Vascular Plant and Vertebrate Inventory of Montezuma Castle National Monument Vascular Plant and Vertebrate Inventory of Montezuma Castle National Monument Plant and Vertebrate Vascular U.S. Geological Survey Southwest Biological Science Center 2255 N. Gemini Drive Flagstaff, AZ 86001 Open-File Report 2006-1163 Southwest Biological Science Center Open-File Report 2006-1163 November 2006 U.S. Department of the Interior U.S. Geological Survey National Park Service In cooperation with the University of Arizona, School of Natural Resources Vascular Plant and Vertebrate Inventory of Montezuma Castle National Monument By Cecilia A. Schmidt, Charles A. Drost, and William L. Halvorson Open-File Report 2006-1163 November, 2006 USGS Southwest Biological Science Center Sonoran Desert Research Station University of Arizona U.S. Department of the Interior School of Natural Resources U.S. Geological Survey 125 Biological Sciences East National Park Service Tucson, Arizona 85721 U.S. Department of the Interior Dirk Kempthorne, Secretary U.S. Geological Survey Mark Myers, Director U.S. Geological Survey, Reston, Virginia: 2006 Note: This document contains information of a preliminary nature and was prepared primarily for internal use in the U.S. Geological Survey. This information is NOT intended for use in open literature prior to publication by the investigators named unless permission is obtained in writing from the investigators named and from the Station Leader. Suggested Citation Schmidt, C. A., C. A. Drost, and W. L. Halvorson 2006. Vascular Plant and Vertebrate Inventory of Montezuma Castle National Monument. USGS Open-File Report 2006-1163. -
Vascular Plant and Vertebrate Inventory of Fort Bowie National Historic Site Vascular Plant and Vertebrate Inventory of Fort Bowie National Historic Site
Powell, Schmidt, Halvorson In Cooperation with the University of Arizona, School of Natural Resources Vascular Plant and Vertebrate Inventory of Fort Bowie National Historic Site Vascular Plant and Vertebrate Inventory of Fort Bowie National Historic Site Plant and Vertebrate Vascular U.S. Geological Survey Southwest Biological Science Center 2255 N. Gemini Drive Flagstaff, AZ 86001 Open-File Report 2005-1167 Southwest Biological Science Center Open-File Report 2005-1167 February 2007 U.S. Department of the Interior U.S. Geological Survey National Park Service In cooperation with the University of Arizona, School of Natural Resources Vascular Plant and Vertebrate Inventory of Fort Bowie National Historic Site By Brian F. Powell, Cecilia A. Schmidt , and William L. Halvorson Open-File Report 2005-1167 December 2006 USGS Southwest Biological Science Center Sonoran Desert Research Station University of Arizona U.S. Department of the Interior School of Natural Resources U.S. Geological Survey 125 Biological Sciences East National Park Service Tucson, Arizona 85721 U.S. Department of the Interior DIRK KEMPTHORNE, Secretary U.S. Geological Survey Mark Myers, Director U.S. Geological Survey, Reston, Virginia: 2006 For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod Telephone: 1-888-ASK-USGS For more information on the USGS-the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment: World Wide Web:http://www.usgs.gov Telephone: 1-888-ASK-USGS Suggested Citation Powell, B. F, C. A. Schmidt, and W. L. Halvorson. 2006. Vascular Plant and Vertebrate Inventory of Fort Bowie National Historic Site. -
Regulation and Evolution of Alternative Splicing in Plants
Regulation and evolution of alternative splicing in plants DISSERTATION zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) vorgelegt dem Rat der Biologisch-Pharmazeutischen Fakultät der Friedrich-Schiller-Universität Jena von Zhihao Ling, M.S. geboren am 10.08.1988 in China Max-Planck-Institut für chemische Ökologie Gutachter: Prof. Ian T. Baldwin, Max Planck Institut für Chemische Ökologie, Jena Prof. Günter Theissen, Friedrich Schiller Universität Jena Prof. Dorothee Staiger, Universität Bielefeld Beginn der Promotion: 26. September 2012 Dissertation eingereicht am: 25. November 2016 Tag der Verteidigung: 28. June 2017 Table of Contents 1. General Introduction ................................................................................................................ 1 1.1 Alternative splicing is widespread in plants .......................................................................... 1 1.2 AS contributes to biological regulation processes in plants .................................................. 2 1.3 Abiotic stresses induced AS changes in plants ..................................................................... 4 1.4 Biotic stresses induced AS changes in plants ....................................................................... 7 1.5 The splicing code and determinants of AS in plants is largely unknown ............................. 8 1.6 The rapid evolution of AS ................................................................................................... 10 1.7 Thesis outline ..................................................................................................................... -
Transgressive Phenotypes and Generalist Pollination in the Floral Evolution of Nicotiana Polyploids
Title Transgressive phenotypes and generalist pollination in the floral evolution of Nicotiana polyploids Authors McCarthy, EW; Chase, MW; Knapp, S; Litt, A; Leitch, AR; Le Comber, SC Description This is the author's proof Date Submitted 2017-02-23 ARTICLES PUBLISHED: XX XX 2016 | ARTICLE NUMBER: 16119 | DOI: 10.1038/NPLANTS.2016.119 Transgressive phenotypes and generalist pollination in the floral evolution of Q1 Nicotiana polyploids Elizabeth W. McCarthy1,2,3†,MarkW.Chase2, Sandra Knapp3,AmyLitt4, Andrew R. Leitch1 and Steven C. Le Comber1* Polyploidy is an important driving force in angiosperm evolution, and much research has focused on genetic, epigenetic and transcriptomic responses to allopolyploidy. Nicotiana is an excellent system in which to study allopolyploidy because half of the species are allotetraploids of different ages, allowing us to examine the trajectory of floral evolution over time. Here, we study the effects of allopolyploidy on floral morphology in Nicotiana, using corolla tube measurements and geometric morphometrics to quantify petal shape. We show that polyploid morphological divergence from the intermediate phenotype expected (based on progenitor morphology) increases with time for floral limb shape and tube length, and that most polyploids are distinct or transgressive in at least one trait. In addition, we show that polyploids tend to evolve shorter and wider corolla tubes, suggesting that allopolyploidy could provide an escape from specialist pollination via reversion to more generalist pollination strategies. 1 olyploidy, or whole genome duplication (WGD), is an impor- transgressively larger14. In addition, autopolyploidy alone can 33 2 Ptant driving force in the evolution of angiosperms. Ancient yield floral changes even without the diversity generated by hybrid- 34 3 polyploid events are shared by all seed plants, all angiosperms ization. -
Wild Tobacco Genomes Reveal the Evolution of Nicotine Biosynthesis
Wild tobacco genomes reveal the evolution of nicotine biosynthesis Shuqing Xua,1,2, Thomas Brockmöllera,1, Aura Navarro-Quezadab, Heiner Kuhlc, Klaus Gasea, Zhihao Linga, Wenwu Zhoua, Christoph Kreitzera,d, Mario Stankee, Haibao Tangf, Eric Lyonsg, Priyanka Pandeyh, Shree P. Pandeyi, Bernd Timmermannc, Emmanuel Gaquerelb,2, and Ian T. Baldwina,2 aDepartment of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; bCentre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany; cSequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; dInstitute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria; eInstitute for Mathematics and Computer Science, Universität Greifswald, 17489 Greifswald, Germany; fCenter for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China; gSchool of Plant Sciences, BIO5 Institute, CyVerse, University of Arizona, Tucson, AZ 85721; hNational Institute of Biomedical Genomics, Kalyani, 741251 West Bengal, India; and iDepartment of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, 700064 West Bengal, India Edited by Joseph R. Ecker, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, and approved April 27, 2017 (received for review January 4, 2017) Nicotine, the signature alkaloid of Nicotiana -
Chemistry& Metabolism Chemical Information National Library Of
Chemistry& Metabolism Chemical Information National Library of Medicine Chemical Resources of the Environmental Health & Toxicology Information Program chemistry.org: American Chemical Society - ACS HomePage Identified Compounds — Metabolomics Fiehn Lab AOCS > Publications > Online Catalog > Modern Methods for Lipid Analysis by Liquid Chromatography/Mass Spectrometry and Related Techniques (Lipase Database) Lipid Library Lipid Library Grom Analytik + HPLC GmbH: Homepage Fluorescence-based phospholipase assays—Table 17,3 | Life Technologies Phosphatidylcholine | PerkinElmer MetaCyc Encyclopedia of Metabolic Pathways MapMan Max Planck Institute of Molecular Plant Physiology MS analysis MetFrag Scripps Center For Metabolomics and Mass Spectrometry - XCMS MetaboAnalyst Lipid Analysis with GC-MS, LC-MS, FT-MS — Metabolomics Fiehn Lab MetLIn LOX and P450 inhibitors Lipoxygenase inhibitor BIOMOL International, LP - Lipoxygenase Inhibitors Lipoxygenase structure Lypoxygenases Lipoxygenase structure Plant databases (see also below) PlantsDB SuperSAGE & SAGE Serial Analysis of Gene Expression: Information from Answers.com Oncology: The Sidney Kimmel Comprehensive Cancer Center EMBL Heidelberg - The European Molecular Biology Laboratory EMBL - SAGE for beginners Human Genetics at Johns Hopkins - Kinzler, K Serial Analysis of Gene Expression The Science Creative Quarterly » PAINLESS GENE EXPRESSION PROFILING: SAGE (SERIAL ANALYSIS OF GENE EXPRESSION) IDEG6 software home page (Analysis of gene expression) GenXPro :: GENome-wide eXpression PROfiling -
Technical Report Literature Review on the Use of Biotechnology and Omics
Tobacco Biotechnology and Omics Task Force Technical Report Literature Review on the Use of Biotechnology and Omics December 2020 Task Force Coordinator and Author: David Zaitlin Kentucky Tobacco Research and Development Center University of Kentucky, Lexington, KY U.S.A. Table of Contents 0. Background ......................................................................................................................... 3 1. Introduction ......................................................................................................................... 3 1.1 Plant biotechnology ................................................................................................... 4 1.2 Tobacco biotechnology .............................................................................................. 5 2. Biotech/GMO crops ............................................................................................................ 6 2.1 Historical background ................................................................................................ 6 2.2 Benefits, risks, and outcomes of biotech crops .......................................................... 7 2.2.1 GM/Biotech crops and plant breeding ........................................................... 7 2.3 Impact of genomics, proteomics, transcriptomics, and metabolomics on modern crop breeding ........................................................................................................... 14 2.3.1 Genomics .................................................................................................... -
Annotated Checklist of the Vascular Plant Flora of Grand Canyon-Parashant National Monument Phase II Report
Annotated Checklist of the Vascular Plant Flora of Grand Canyon-Parashant National Monument Phase II Report By Dr. Terri Hildebrand Southern Utah University, Cedar City, UT and Dr. Walter Fertig Moenave Botanical Consulting, Kanab, UT Colorado Plateau Cooperative Ecosystems Studies Unit Agreement # H1200-09-0005 1 May 2012 Prepared for Grand Canyon-Parashant National Monument Southern Utah University National Park Service Mojave Network TABLE OF CONTENTS Page # Introduction . 4 Study Area . 6 History and Setting . 6 Geology and Associated Ecoregions . 6 Soils and Climate . 7 Vegetation . 10 Previous Botanical Studies . 11 Methods . 17 Results . 21 Discussion . 28 Conclusions . 32 Acknowledgments . 33 Literature Cited . 34 Figures Figure 1. Location of Grand Canyon-Parashant National Monument in northern Arizona . 5 Figure 2. Ecoregions and 2010-2011 collection sites in Grand Canyon-Parashant National Monument in northern Arizona . 8 Figure 3. Soil types and 2010-2011 collection sites in Grand Canyon-Parashant National Monument in northern Arizona . 9 Figure 4. Increase in the number of plant taxa confirmed as present in Grand Canyon- Parashant National Monument by decade, 1900-2011 . 13 Figure 5. Southern Utah University students enrolled in the 2010 Plant Anatomy and Diversity course that collected during the 30 August 2010 experiential learning event . 18 Figure 6. 2010-2011 collection sites and transportation routes in Grand Canyon-Parashant National Monument in northern Arizona . 22 2 TABLE OF CONTENTS Page # Tables Table 1. Chronology of plant-collecting efforts at Grand Canyon-Parashant National Monument . 14 Table 2. Data fields in the annotated checklist of the flora of Grand Canyon-Parashant National Monument (Appendices A, B, C, and D) . -
Checklist of the Vascular Plants of San Diego County 5Th Edition
cHeckliSt of tHe vaScUlaR PlaNtS of SaN DieGo coUNty 5th edition Pinus torreyana subsp. torreyana Downingia concolor var. brevior Thermopsis californica var. semota Pogogyne abramsii Hulsea californica Cylindropuntia fosbergii Dudleya brevifolia Chorizanthe orcuttiana Astragalus deanei by Jon P. Rebman and Michael G. Simpson San Diego Natural History Museum and San Diego State University examples of checklist taxa: SPecieS SPecieS iNfRaSPecieS iNfRaSPecieS NaMe aUtHoR RaNk & NaMe aUtHoR Eriodictyon trichocalyx A. Heller var. lanatum (Brand) Jepson {SD 135251} [E. t. subsp. l. (Brand) Munz] Hairy yerba Santa SyNoNyM SyMBol foR NoN-NATIVE, NATURaliZeD PlaNt *Erodium cicutarium (L.) Aiton {SD 122398} red-Stem Filaree/StorkSbill HeRBaRiUM SPeciMeN coMMoN DocUMeNTATION NaMe SyMBol foR PlaNt Not liSteD iN THE JEPSON MANUAL †Rhus aromatica Aiton var. simplicifolia (Greene) Conquist {SD 118139} Single-leaF SkunkbruSH SyMBol foR StRict eNDeMic TO SaN DieGo coUNty §§Dudleya brevifolia (Moran) Moran {SD 130030} SHort-leaF dudleya [D. blochmaniae (Eastw.) Moran subsp. brevifolia Moran] 1B.1 S1.1 G2t1 ce SyMBol foR NeaR eNDeMic TO SaN DieGo coUNty §Nolina interrata Gentry {SD 79876} deHeSa nolina 1B.1 S2 G2 ce eNviRoNMeNTAL liStiNG SyMBol foR MiSiDeNtifieD PlaNt, Not occURRiNG iN coUNty (Note: this symbol used in appendix 1 only.) ?Cirsium brevistylum Cronq. indian tHiStle i checklist of the vascular plants of san Diego county 5th edition by Jon p. rebman and Michael g. simpson san Diego natural history Museum and san Diego state university publication of: san Diego natural history Museum san Diego, california ii Copyright © 2014 by Jon P. Rebman and Michael G. Simpson Fifth edition 2014. isBn 0-918969-08-5 Copyright © 2006 by Jon P. -
A Homology-Guided, Genome-Based Proteome for Improved Proteomics in the Alloploid Nicotiana Benthamiana Jiorgos Kourelis1, Farnusch Kaschani2, Friederike M
Kourelis et al. BMC Genomics (2019) 20:722 https://doi.org/10.1186/s12864-019-6058-6 RESEARCH ARTICLE Open Access A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana Jiorgos Kourelis1, Farnusch Kaschani2, Friederike M. Grosse-Holz1, Felix Homma1, Markus Kaiser2 and Renier A. L. van der Hoorn1* Abstract Background: Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Results: Here we present an improved proteome based on the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. Due to the fragmented nature of the Niben1.0.1 draft genome, many protein- encoding genes are missing or partial. We complement these missing proteins by similarly annotating other draft genome assemblies. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis- assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53, 411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better in assigning spectra than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously predicted to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal inactivation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. Finally, we use this new proteome annotation to characterize the extracellular proteome as compared to a total leaf proteome, which highlights the enrichment of hydrolases in the apoplast. -
Homology-Guided Re-Annotation Improves the Gene Models of the Alloploid Nicotiana Benthamiana
bioRxiv preprint doi: https://doi.org/10.1101/373506; this version posted March 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana Jiorgos Kourelis1, Farnusch Kaschani2, Friederike M. Grosse-Holz1, Felix Homma1, Markus Kaiser2, Renier A. L. van der Hoorn1 1Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK; 2Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany. Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Here we present an improved re-annotation of the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously mis-annotated to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal a pseudogenisation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. -
Vascular Plant and Vertebrate Inventory of Tonto National Monument
In Cooperation with the University of Arizona, School of Natural Resources Vascular Plant and Vertebrate Inventory of Tonto National Monument Open-File Report 2007-1295 U.S. Department of the Interior U.S. Geological Survey National Park Service This page left intentionally blank. In cooperation with the University of Arizona, School of Natural Resources Vascular Plant and Vertebrate Inventory of Tonto National Monument By Eric W. Albrecht, Brian F. Powell, William L. Halvorson, and Cecilia A. Schmidt Open-File Report 2007-1295 U.S. Geological Survey Southwest Biological Science Center Sonoran Desert Research Station U.S. Department of the Interior University of Arizona U.S. Geological Survey School of Natural Resources National Park Service 125 Biological Sciences East Tucson, Arizona 85721 U.S. Department of the Interior DIRK KEMPTHORNE, Secretary U.S. Geological Survey Mark Myers, Director U.S. Geological Survey, Reston, Virginia: 2007 For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod Telephone: 1-888-ASK-USGS For more information on the USGS—the federal source for science about the Earth, its natural and living resources, natural hazards, and the environment: World Wide Web: http://www.usgs.gov Telephone: 1-888-ASK-USGS Suggested Citation Albrecht, E.W., Powell, B.F., Halvorson, W.L., and Schmidt, C.A., 2007, Vascular plant and vertebrate inventory of Tonto National Monument: U.S. Geological Survey Open-File Report 2007-1295, 57 p. [http://pubs.usgs.gov/of/2007/1295/]. Cover photo: Jeff Balmat, National Park Service Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S.