From Algae to Flowering Plants
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Chapter 1-1 Introduction
Glime, J. M. 2017. Introduction. Chapt. 1. In: Glime, J. M. Bryophyte Ecology. Volume 1. Physiological Ecology. Ebook sponsored 1-1-1 by Michigan Technological University and the International Association of Bryologists. Last updated 25 April 2021 and available at <http://digitalcommons.mtu.edu/bryophyte-ecology/>. CHAPTER 1-1 INTRODUCTION TABLE OF CONTENTS Thinking on a New Scale .................................................................................................................................... 1-1-2 Adaptations to Land ............................................................................................................................................ 1-1-3 Minimum Size..................................................................................................................................................... 1-1-5 Do Bryophytes Lack Diversity?.......................................................................................................................... 1-1-6 The "Moss".......................................................................................................................................................... 1-1-7 What's in a Name?............................................................................................................................................... 1-1-8 Phyla/Divisions............................................................................................................................................ 1-1-8 Role of Bryology................................................................................................................................................ -
Origin of Gibberellin-Dependent Transcriptional Regulation by Molecular Exploitation of a Transactivation Domain in DELLA Proteins
bioRxiv preprint doi: https://doi.org/10.1101/398883; this version posted December 10, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC 4.0 International license. Article - Discoveries Origin of gibberellin-dependent transcriptional regulation by molecular exploitation of a transactivation domain in DELLA proteins Jorge Hernández-García1, Asier Briones-Moreno1, Renaud Dumas2, and Miguel A. Blázquez1 1Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Valencia, Spain 2Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives/Biosciences and Biotechnology Institute of Grenoble, Institut National de la Recherche Agronomique (INRA), Grenoble, France Corresponding author: Miguel A. Blázquez ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/398883; this version posted December 10, 2018. 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-NC 4.0 International license. Abstract DELLA proteins are land-plant specific transcriptional regulators known to interact through their C-terminal GRAS domain with over 150 transcription factors in Arabidopsis thaliana. Besides, DELLAs from vascular plants can interact through the N-terminal domain with the gibberellin receptor encoded by GID1, through which gibberellins promote DELLA degradation. However, this regulation is absent in non-vascular land plants, which lack active gibberellins or a proper GID1 receptor. -
The Chloroplast Rpl23 Gene Cluster of Spirogyra Maxima (Charophyceae) Shares Many Similarities with the Angiosperm Rpl23 Operon
Algae Volume 17(1): 59-68, 2002 The Chloroplast rpl23 Gene Cluster of Spirogyra maxima (Charophyceae) Shares Many Similarities with the Angiosperm rpl23 Operon Jungho Lee* and James R. Manhart Department of Biology, Texas A&M University, College Station, TX, 77843-3258, U.S.A. A phylogenetic affinity between charophytes and embryophytes (land plants) has been explained by a few chloro- plast genomic characters including gene and intron (Manhart and Palmer 1990; Baldauf et al. 1990; Lew and Manhart 1993). Here we show that a charophyte, Spirogyra maxima, has the largest operon of angiosperm chloroplast genomes, rpl23 operon (trnI-rpl23-rpl2-rps19-rpl22-rps3-rpl16-rpl14-rps8-infA-rpl36-rps11-rpoA) containing both embryophyte introns, rpl16.i and rpl2.i. The rpl23 gene cluster of Spirogyra contains a distinct eubacterial promoter sequence upstream of rpl23, which is the first gene of the green algal rpl23 gene cluster. This sequence is completely absent in angiosperms but is present in non-flowering plants. The results imply that, in the rpl23 gene cluster, early charophytes had at least two promoters, one upstream of trnI and another upstream of rpl23, which partially or completely lost its function in land plants. A comparison of gene clusters of prokaryotes, algal chloroplast DNAs and land plant cpDNAs indicated a loss of numerous genes in chlorophyll a+b eukaryotes. A phylogenetic analysis using presence/absence of genes and introns as characters produced trees with a strongly supported clade contain- ing chlorophyll a+b eukaryotes. Spirogyra and embryophytes formed a clade characterized by the loss of rpl5 and rps9 and the gain of trnI (CAU) and introns in rpl2 and rpl16. -
General Botany Lab Review Fungi, Algae, Bryophytes, Ferns & Fern Allies
General Botany Lab Review Fungi, Algae, Bryophytes, Ferns & Fern Allies You have looked at a lot of stuff – both live and via prepared slides. You’ve also labeled at least one Life Cycle Diagram for each of the groups. Know what your benchmarks are for a general life cycle diagram and be able to label them. I will not ask you to identify anything to species or genus; be able to identify things to “group” (i.e., ascomycete, bryophyta, etc.) Be able to identify growth form (e.g., unicell, filamentous, etc.). Recognize the differences between sexual and asexual reroductive structures. All questions will be multiple choice. Material looked at: UNIT 1: FUNGI EXERCISE 1: CHYTRIDS/ CHYTRIDOMYCOTA: Allmyces arbusculus – life and prepared slides EXERCISE 2: ZYGOMYCETES/ ZYGOMYCOTA: Rhizopus stolonifer – live and prepared slides EXERCISE 2: MYCORRHIZA and the GLOMEROMYCETES/ GLOMEROMYCOTA – prepared slides only EXERCISE 3: ASCOMYCETES/ ASCOMYCOTA Aspergillus sp., Penicillium sp., Saccharomyces cerevisiae, Peziza sp., Sordaria fimicola, and Morchella sp. – a mixture of live and prepared materials EXERCISE 4: BASIDIOMYCETES/BASIDIOMYCETES Agaricus, Coprinus, Cronartium (a rust), Ustilago (a smut) – slides, fresh, and dried EXERCISE 5: SLIME MOLDS – live and prepared Physarum EXERCISE 6: LICHENS – live and prepared slides be able to identify the various growth forms UNIT 2: ALGAE EXERCISE 1: CYANOBACTERIA Anabaena sp., Nostoc, and Oscillaroria – live and prepared material EXERCISE 2: SUPERGROUP EXCAVATA (Phylum Euglenophyta) – live and prepared material -
Xylans of Red and Green Algae: What Is Known About Their Structures and How They Are Synthesised?
polymers Review Xylans of Red and Green Algae: What Is Known about Their Structures and How They Are Synthesised? Yves S.Y. Hsieh 1,* and Philip J. Harris 2,* 1 Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden 2 School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, New Zealand * Correspondence: [email protected] (Y.S.Y.H.); [email protected] (P.J.H.); Tel.: +46-8-790-9937 (Y.S.Y.H.); +64-9-923-8366 (P.J.H.) Received: 30 January 2019; Accepted: 17 February 2019; Published: 18 February 2019 Abstract: Xylans with a variety of structures have been characterised in green algae, including chlorophytes (Chlorophyta) and charophytes (in the Streptophyta), and red algae (Rhodophyta). Substituted 1,4-β-D-xylans, similar to those in land plants (embryophytes), occur in the cell wall matrix of advanced orders of charophyte green algae. Small proportions of 1,4-β-D-xylans have also been found in the cell walls of some chlorophyte green algae and red algae but have not been well characterised. 1,3-β-D-Xylans occur as triple helices in microfibrils in the cell walls of chlorophyte algae in the order Bryopsidales and of red algae in the order Bangiales. 1,3;1,4-β-D-Xylans occur in the cell wall matrix of red algae in the orders Palmariales and Nemaliales. In the angiosperm Arabidopsis thaliana, the gene IRX10 encodes a xylan 1,4-β-D-xylosyltranferase (xylan synthase), and, when heterologously expressed, this protein catalysed the production of the backbone of 1,4-β-D-xylans. -
Plant Evolution an Introduction to the History of Life
Plant Evolution An Introduction to the History of Life KARL J. NIKLAS The University of Chicago Press Chicago and London CONTENTS Preface vii Introduction 1 1 Origins and Early Events 29 2 The Invasion of Land and Air 93 3 Population Genetics, Adaptation, and Evolution 153 4 Development and Evolution 217 5 Speciation and Microevolution 271 6 Macroevolution 325 7 The Evolution of Multicellularity 377 8 Biophysics and Evolution 431 9 Ecology and Evolution 483 Glossary 537 Index 547 v Introduction The unpredictable and the predetermined unfold together to make everything the way it is. It’s how nature creates itself, on every scale, the snowflake and the snowstorm. — TOM STOPPARD, Arcadia, Act 1, Scene 4 (1993) Much has been written about evolution from the perspective of the history and biology of animals, but significantly less has been writ- ten about the evolutionary biology of plants. Zoocentricism in the biological literature is understandable to some extent because we are after all animals and not plants and because our self- interest is not entirely egotistical, since no biologist can deny the fact that animals have played significant and important roles as the actors on the stage of evolution come and go. The nearly romantic fascination with di- nosaurs and what caused their extinction is understandable, even though we should be equally fascinated with the monarchs of the Carboniferous, the tree lycopods and calamites, and with what caused their extinction (fig. 0.1). Yet, it must be understood that plants are as fascinating as animals, and that they are just as important to the study of biology in general and to understanding evolutionary theory in particular. -
Biology and Systematics of Heterokont and Haptophyte Algae1
American Journal of Botany 91(10): 1508±1522. 2004. BIOLOGY AND SYSTEMATICS OF HETEROKONT AND HAPTOPHYTE ALGAE1 ROBERT A. ANDERSEN Bigelow Laboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, Maine 04575 USA In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classi®ed into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed signi®cantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heter- okont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas). Key words: chromalveolate; chromist; chromophyte; ¯agella; phylogeny; stramenopile; tree of life. Heterokont algae are a monophyletic group that includes all (Phaeophyceae) by Linnaeus (1753), and shortly thereafter, photosynthetic organisms with tripartite tubular hairs on the microscopic chrysophytes (currently 5 Oikomonas, Anthophy- mature ¯agellum (discussed later; also see Wetherbee et al., sa) were described by MuÈller (1773, 1786). The history of 1988, for de®nitions of mature and immature ¯agella), as well heterokont algae was recently discussed in detail (Andersen, as some nonphotosynthetic relatives and some that have sec- 2004), and four distinct periods were identi®ed. -
Acidotropic Probes and Flow Cytometry: a Powerful Combination for Detecting Phagotrophy in Mixotrophic and Heterotrophic Protists
AQUATIC MICROBIAL ECOLOGY Vol. 44: 85–96, 2006 Published August 16 Aquat Microb Ecol Acidotropic probes and flow cytometry: a powerful combination for detecting phagotrophy in mixotrophic and heterotrophic protists Wanderson F. Carvalho*, Edna Granéli Marine Science Department, University of Kalmar, 391 82 Kalmar, Sweden ABSTRACT: Studies with phagotrophic organisms are hampered by a series of methodological con- straints. To overcome problems related to the detection and enumeration of mixotrophic and hetero- trophic cells containing food vacuoles, we combined flow cytometry and an acidotropic blue probe as an alternative method. Flow cytometry allows the analysis of thousands of cells per minute with high sensitivity to the autofluorescence of different groups of cells and to probe fluorescence. The method was first tested in a grazing experiment where the heterotrophic dinoflagellate Oxyrrhis marina fed on Rhodomonas salina. The maximum ingestion rate of O. marina was 1.7 prey ind.–1 h–1, and the fre- quency of cells with R. salina in the food vacuoles increased from 0 to 2.4 ± 0.5 × 103 cells ml–1 within 6 h. The blue probe stained 100% of O. marina cells that had R. salina in the food vacuoles. The acidotropic blue probe was also effective in staining food vacuoles in the mixotrophic dinoflagellate Dinophysis norvegica. We observed that 75% of the D. norvegica population in the aphotic zone pos- sessed food vacuoles. Overall, in cells without food vacuoles, blue fluorescence was as low as in cells that were kept probe free. Blue fluorescence in O. marina cells with food vacuoles was 6-fold higher than in those without food vacuoles (20 ± 4 and 3 ± 0 relative blue fluorescence cell–1, respectively), while in D. -
Complete Plastome Sequences Of
Karol et al. BMC Evolutionary Biology 2010, 10:321 http://www.biomedcentral.com/1471-2148/10/321 RESEARCH ARTICLE Open Access Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages Kenneth G Karol1*, Kathiravetpillai Arumuganathan2, Jeffrey L Boore3,4, Aaron M Duffy5, Karin DE Everett6, John D Hall1, S Kellon Hansen5, Jennifer V Kuehl7, Dina F Mandoli6,8, Brent D Mishler9, Richard G Olmstead6, Karen S Renzaglia10, Paul G Wolf5 Abstract Background: Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results: We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida,a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). -
Antimicrobial Peptides Expression for Defense System in Chicken Gastrointestinal and Reproductive Organs
The 6th International Seminar on Tropical Animal Production Integrated Approach in Developing Sustainable Tropical Animal Production October 20-22, 2015, Yogyakarta, Indonesia Antimicrobial Peptides Expression for Defense System in Chicken Gastrointestinal and Reproductive Organs Yukinori Yoshimura1, 2 Bambang Ariyadi3 and Naoki Isobe1, 2 1Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739- 8528, Japan; 2Research Center for Animal Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan; 3Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, 55281 Indonesia. Email address: [email protected] ABSTRACT: Maintenance of animal health is essential to obtain their maximum productivity and safe products. Avian β-defensins (AvBDs) are the member of antimicrobial peptides, and Toll-like receptors (TLRs) are the primary receptors that recognize pathogen-associated molecular patterns (PAMPs) of microbes. The aim of this study was to characterize the innate immune system with the focus on the expression of AvBDs in the gastrointestinal tract and reproductive organs for the strategy to enhance the disease resistance of chickens. The proventriculus and cecum of broiler chicks expressed TLRs and AvBDs. It is suggested that a variety of PAMPs of microbes are recognized by different TLRs, probably leading to regulate the synthesis of innate immune factors including AvBDs. In laying hens, TLRs and AvBDs were expressed in the theca and granulosa layers of ovarian follicles and in the oviduct. In vivo LPS challenge increased the expression of several AvBDs in the theca tissue. In contrast, in the cultured theca tissue, LPS upregulated the expression of IL1β and IL6, but did not affect the AvBDs expression; whereas IL1β upregulated the expression of the AvBD12 gene and protein. -
CH28 PROTISTS.Pptx
9/29/14 Biosc 41 Announcements 9/29 Review: History of Life v Quick review followed by lecture quiz (history & v How long ago is Earth thought to have formed? phylogeny) v What is thought to have been the first genetic material? v Lecture: Protists v Are we tetrapods? v Lab: Protozoa (animal-like protists) v Most atmospheric oxygen comes from photosynthesis v Lab exam 1 is Wed! (does not cover today’s lab) § Since many of the first organisms were photosynthetic (i.e. cyanobacteria), a LOT of excess oxygen accumulated (O2 revolution) § Some organisms adapted to use it (aerobic respiration) Review: History of Life Review: Phylogeny v Which organelles are thought to have originated as v Homology is similarity due to shared ancestry endosymbionts? v Analogy is similarity due to convergent evolution v During what event did fossils resembling modern taxa suddenly appear en masse? v A valid clade is monophyletic, meaning it consists of the ancestor taxon and all its descendants v How many mass extinctions seem to have occurred during v A paraphyletic grouping consists of an ancestral species and Earth’s history? Describe one? some, but not all, of the descendants v When is adaptive radiation likely to occur? v A polyphyletic grouping includes distantly related species but does not include their most recent common ancestor v Maximum parsimony assumes the tree requiring the fewest evolutionary events is most likely Quiz 3 (History and Phylogeny) BIOSC 041 1. How long ago is Earth thought to have formed? 2. Why might many organisms have evolved to use aerobic respiration? PROTISTS! Reference: Chapter 28 3. -
Botany Without Bias
editorial Botany without bias In the Gospel According to Matthew Chapter seven, Verse fve, Jesus says “frst cast out the beam out of thine own eye; and then shalt thou see clearly to cast out the mote out of thy brother’s eye”. We should remember this entreaty before too casually casting accusations of ‘plant blindness’. anguage usage helps maintain unconscious biases. In plant biology Lfor example, there is the careless use of the term ‘higher plants’, without thinking about its meaning or implication. If there is a definition of ‘higher plants’ then it is synonymous with vascular plants, but the image it conjures is of upstanding, leafy land-dwelling plants. The problem is that ‘higher’ is a charged term implying superiority of this group over their non-vascular cousins. This stratification is a manifestation of orthogenesis, the idea that evolution has both a direction and a goal. A perfect illustration of orthogenesis is the frequent meme of The Road to Homo Sapiens, the original version of which was drawn by Rudolph Zallinger for a 1965 edition of Life Nature Library1. Also known as The March of Progress, it shows a line of assumed human ancestors, starting with a gibbon-like in their News and Views3, “innovations spend much of their discussions on what Pliopithecus, processing from left to right, associated with improving water use the similarities of these organisms to becoming taller and more upright in stance, efficiency […] may be more fundamental angiosperms can tell about the history and culminating in a modern human. to the evolution of vascular plants than the of plants’ colonization of dry land, and The implication is clear, our evolutionary vascular system from which they derive much less on their characteristics and ancestors are only of interest as waypoints their name”.