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Algal Accessory Pigment Detection Using Aviris Image
ALGAL ACCESSORY PIGMENT DETECTION USING AVIRIS IMAGE-DERIVED SPECTRAL RADIANCE DATA hurie L. Richardson, Florida International University, Miami, Florida, and Vincent G. Ambrosia, JCWS, Inc., NASA Ames Research Center, Moffett Field, California. 1. INTRODUCTION Visual and derivative analyses of AVIRIS spectral data can be used to detect algal accessory pigments in squat ic communities (Richardson et al. 1994). This capability extends the use of remote sensing for the study of aquatic ecosystems by allowing detection of taxonomically significant pigment signatures which yield information about the type of algae present. Such information allows remote sensing-based assessment of squat ic ecosystem health, as in the detection of nuisance blooms of cyanobacteria (Dekker et al., 1992) or toxic blooms of dinoflagellates (Carder and Steward, 1985). Remote sensing of aquatic systems has traditionally focused on quantification of chlorophyll a, a photoreactive (and light-harvesting) pigment which is common to all algae as well as cyanobacteria (bIuegrcxm algae). Due to the ubiquitousness of this pigment within algae, chl a is routinely measured to estimate algal biomass both during ground-truthing and using various airborne or satellite based sensors (Clark, 1981; Smith and Baker, 1982; Galat and Verdin, 1989; Mittenzwey et al., 1992), including AVIRIS (Hamilton et al., 1993). Within the remote sensing and aquatic sciences communities, ongoing research has been performed to detect algal accessory pigments for assessment of algal population composition (Gieskew 1991; Millie et al., 1993; Richardson, 1996). This research is based on the fact that many algal accessory pigments are taxonomically significant, and all are spectrally unique (Foppen, 1971; Morton, 1975; Bj#mland and Liaaen- Jensen, 1989; Rowan, 1989), Aquatic scientists have been refining pigment analysis techniques, primarily high performance liquid chromatography, or HPLC, (e.g. -
Superorganisms of the Protist Kingdom: a New Level of Biological Organization
Foundations of Science https://doi.org/10.1007/s10699-020-09688-8 Superorganisms of the Protist Kingdom: A New Level of Biological Organization Łukasz Lamża1 © The Author(s) 2020 Abstract The concept of superorganism has a mixed reputation in biology—for some it is a conveni- ent way of discussing supra-organismal levels of organization, and for others, little more than a poetic metaphor. Here, I show that a considerable step forward in the understand- ing of superorganisms results from a thorough review of the supra-organismal levels of organization now known to exist among the “unicellular” protists. Limiting the discussion to protists has enormous advantages: their bodies are very well studied and relatively sim- ple (as compared to humans or termites, two standard examples in most discussions about superorganisms), and they exhibit an enormous diversity of anatomies and lifestyles. This allows for unprecedented resolution in describing forms of supra-organismal organiza- tion. Here, four criteria are used to diferentiate loose, incidental associations of hosts with their microbiota from “actual” superorganisms: (1) obligatory character, (2) specifc spatial localization of microbiota, (3) presence of attachment structures and (4) signs of co-evolu- tion in phylogenetic analyses. Three groups—that have never before been described in the philosophical literature—merit special attention: Symbiontida (also called Postgaardea), Oxymonadida and Parabasalia. Specifcally, it is argued that in certain cases—for Bihos- pites bacati and Calkinsia aureus (symbiontids), Streblomastix strix (an oxymonad), Joe- nia annectens and Mixotricha paradoxa (parabasalids) and Kentrophoros (a ciliate)—it is fully appropriate to describe the whole protist-microbiota assocation as a single organism (“superorganism”) and its elements as “tissues” or, arguably, even “organs”. -
New Perspectives on Analysing Data from Biological Collections Based on Social Network Analytics Pedro C
www.nature.com/scientificreports OPEN New perspectives on analysing data from biological collections based on social network analytics Pedro C. de Siracusa, Luiz M. R. Gadelha Jr. & Artur Ziviani Biological collections have been historically regarded as fundamental sources of scientifc information on biodiversity. They are commonly associated with a variety of biases, which must be characterized and mitigated before data can be consumed. In this work, we are motivated by taxonomic and collector biases, which can be understood as the efect of particular recording preferences of key collectors on shaping the overall taxonomic composition of biological collections they contribute to. In this context, we propose two network models as the frst steps towards a network-based conceptual framework for understanding the formation of biological collections as a result of the composition of collectors’ interests and activities. Building upon the defned network models, we present a case study in which we use our models to explore the community of collectors and the taxonomic composition of the University of Brasília herbarium. We describe topological features of the networks and point out some of the most relevant collectors in the biological collection as well as their taxonomic groups of interest. We also investigate their collaborative behaviour while recording specimens. Finally, we discuss future perspectives for incorporating temporal and geographical dimensions to the models. Moreover, we indicate some possible investigation directions that could beneft from our approach based on social network analytics to model and analyse biological collections. How data is classifed in information infrastructures directly impacts our potential knowledge about diferent domains1–3. -
Trichonympha Cf
MOLECULAR PHYLOGENETICS OF TRICHONYMPHA CF. COLLARIS AND A PUTATIVE PYRSONYMPHID: THE RELEVANCE TO THE ORIGIN OF SEX by JOEL BRYAN DACKS B.Sc. The University of Alberta, 1995 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER'S OF SCIENCE in THE FACULTY OF GRADUATE STUDIES (Department of Zoology) We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA April 1998 © Joel Bryan Dacks, 1998 In presenting this thesis in partial fulfilment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. Department of ~2—oc)^Oa^ The University of British Columbia Vancouver, Canada Date {X^ZY Z- V. /^P DE-6 (2/88) Abstract Why sex evolved is one of the central questions in evolutionary genetics. To address this question I have undertaken a molecular phylogenetic study of two candidate lineages to determine the first sexual line. In my thesis the hypermastigotes are confirmed as closely related to the trichomonads in the phylum Parabasalia and found to be more deeply divergent than a putative pyrsonymphid. This means that the Parabasalia are the first sexual lineage. From this I go on to infer that the ancestral sexual cycle included facultative sex. -
APOSTILA DIDATICA 402 Protozoa
UNIVERSIDADE FEDERAL RURAL DO RIO DE JANEIRO INSTITUTO DE VETERINÁRIA CLASSIFICAÇÃO E MORFOLOGIA DE PROTOZOÁRIOS E RICKÉTTSIAS EM MEDICINA VETERINÁRIA SEROPÉDICA 2016 PREFÁCIO Este material didático foi produzido como parte do projeto intitulado “Desenvolvimento e produção de material didático para o ensino de Parasitologia Animal na Universidade Federal Rural do Rio de Janeiro: atualização e modernização”. Este projeto foi financiado pela Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) Processo 2010.6030/2014-28 e coordenado pela professora Maria de Lurdes Azevedo Rodrigues (IV/DPA). SUMÁRIO Caracterização morfológica dos táxons superiores de eukaryota 08 1. Império Eukaryota 08 1.1. Reino Protozoa 08 1.2. Reino Chromista 08 1.3. Reino Fungi 08 1.4. Reino Animalia 08 1.5. Reino Plantae 08 Caracterização morfológica de parasitos do reino Protozoa 08 1.1.A. Filo Metamonada 09 A.1. Classe Trepomonadea 09 A.1.1. Ordem Diplomonadida 09 1. Família Hexamitidae 09 a. Gênero Giardia 09 a.1. Espécie Giardia intestinalis 09 1.2.B. Filo Rhizopoda 09 A.1. Classe Entamoebidea 10 A.1.1. Ordem Amoebida 10 1. Família Endamoebidae 10 a. Gênero Entamoeba 10 a.1. Espécie Entamoeba histolytica 10 a.2. Espécie Entomoeba coli 10 1.2.C. Filo Parabasala 11 A.1. Classe Trichomonadea 11 A.1.1. Ordem Trichomonadida 11 1. Família Trichomonadidae 11 a. Gênero Tritrichomonas 11 a.1. Espécie Tritrichomonas foetus 11 2. Família Monocercomonadidae 12 a. Gênero Histomonas 12 a.2. Espécie Histomonas meleagridis 12 1.2.D. Filo Euglenozoa 13 C.1. Classe Kinotoplastidea 13 C.1.1. -
"Phycology". In: Encyclopedia of Life Science
Phycology Introductory article Ralph A Lewin, University of California, La Jolla, California, USA Article Contents Michael A Borowitzka, Murdoch University, Perth, Australia . General Features . Uses The study of algae is generally called ‘phycology’, from the Greek word phykos meaning . Noxious Algae ‘seaweed’. Just what algae are is difficult to define, because they belong to many different . Classification and unrelated classes including both prokaryotic and eukaryotic representatives. Broadly . Evolution speaking, the algae comprise all, mainly aquatic, plants that can use light energy to fix carbon from atmospheric CO2 and evolve oxygen, but which are not specialized land doi: 10.1038/npg.els.0004234 plants like mosses, ferns, coniferous trees and flowering plants. This is a negative definition, but it serves its purpose. General Features Algae range in size from microscopic unicells less than 1 mm several species are also of economic importance. Some in diameter to kelps as long as 60 m. They can be found in kinds are consumed as food by humans. These include almost all aqueous or moist habitats; in marine and fresh- the red alga Porphyra (also known as nori or laver), an water environments they are the main photosynthetic or- important ingredient of Japanese foods such as sushi. ganisms. They are also common in soils, salt lakes and hot Other algae commonly eaten in the Orient are the brown springs, and some can grow in snow and on rocks and the algae Laminaria and Undaria and the green algae Caulerpa bark of trees. Most algae normally require light, but some and Monostroma. The new science of molecular biology species can also grow in the dark if a suitable organic carbon has depended largely on the use of algal polysaccharides, source is available for nutrition. -
Characterizing the Absorption Properties for Remote Sensing of Three Small Optically-Diverse South African Reservoirs
Remote Sens. 2013, 5, 4370-4404; doi:10.3390/rs5094370 OPEN ACCESS Remote Sensing ISSN 2072-4292 www.mdpi.com/journal/remotesensing Article Characterizing the Absorption Properties for Remote Sensing of Three Small Optically-Diverse South African Reservoirs Mark William Matthews 1;* and Stewart Bernard 1;2 1 Marine Remote Sensing Unit, Department of Oceanography, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa 2 Earth Systems Earth Observation, Council for Scientific and Industrial Research, 15 Lower Hope Street, Rosebank, 7700 Cape Town, South Africa; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +27-216-505-775. Received: 16 July 2013; in revised form: 30 August 2013 / Accepted: 3 September 2013 / Published: 9 September 2013 Abstract: Characterizing the specific inherent optical properties (SIOPs) of water constituents is fundamental to remote sensing applications. Therefore, this paper presents the absorption properties of phytoplankton, gelbstoff and tripton for three small, optically-diverse South African inland waters. The three reservoirs, Hartbeespoort, Loskop and Theewaterskloof, are challenging for remote sensing, due to differences in phytoplankton assemblage and the considerable range of constituent concentrations. Relationships between the absorption properties and biogeophysical parameters, chlorophyll-a (chl-a), TChl (chl-a plus phaeopigments), seston, minerals and tripton, are established. The value determined for the mass-specific tripton absorption coefficient ∗ 2 −1 at 442 nm, atr(442), ranges from 0.024 to 0.263 m ·g . The value of the TChl-specific ∗ phytoplankton absorption coefficient (aφ) was strongly influenced by phytoplankton species, ∗ 2 −1 size, accessory pigmentation and biomass. -
Pigment Signatures of Phytoplankton Communities in the Beaufort Sea
Biogeosciences, 12, 991–1006, 2015 www.biogeosciences.net/12/991/2015/ doi:10.5194/bg-12-991-2015 © Author(s) 2015. CC Attribution 3.0 License. Pigment signatures of phytoplankton communities in the Beaufort Sea P. Coupel1, A. Matsuoka1, D. Ruiz-Pino2, M. Gosselin3, D. Marie4, J.-É. Tremblay1, and M. Babin1 1Joint International ULaval-CNRS Laboratory Takuvik, Québec-Océan, Département de Biologie, Université Laval, Québec, Québec G1V 0A6, Canada 2Laboratoire d’Océanographie et du Climat: Expérimentation et Approches Numériques (LOCEAN), UPMC, CNRS, UMR 7159, Paris, France 3Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec G5L 3A1, Canada 4Station Biologique, CNRS, UMR 7144, INSU et Université Pierre et Marie Curie, Place George Teissier, 29680 Roscoff, France Correspondence to: P. Coupel ([email protected]) Received: 11 August 2014 – Published in Biogeosciences Discuss.: 13 October 2014 Revised: 15 December 2014 – Accepted: 30 December 2014 – Published: 17 February 2015 Abstract. Phytoplankton are expected to respond to recent potentially leads to incorrect group assignments and some environmental changes of the Arctic Ocean. In terms of misinterpretation of CHEMTAX. Thanks to the high repro- bottom-up control, modifying the phytoplankton distribution ducibility of pigment analysis, our results can serve as a base- will ultimately affect the entire food web and carbon export. line to assess change and spatial or temporal variability in However, detecting and quantifying changes in phytoplank- several phytoplankton populations that are not affected by ton communities in the Arctic Ocean remains difficult be- these misinterpretations. cause of the lack of data and the inconsistent identification methods used. -
Photosynthetic Action Spectra of Marine Algae*
PHOTOSYNTHETIC ACTION SPECTRA OF MARINE ALGAE* BY F. T. HAXO~ AND L. IL BLINKS (From the Hopkins Marine Station of Stanford University, Pacific C-ro~e) (Received for publication,October 26, 1949) INTRODUC'rION Englemann (1883, 1884) showed by an ingenious, though not strictlyquanti- tative method (migration of motile bacteria to regions of higher oxygen con- centration), that various algae displayed high photosynthetic activity in spectral regions in which light absorption was due mainly to pigments other than chlorophyll. From these now classic experiments it was concluded that, in addition to chlorophyll, other characteristicpigments of blue-green, red, and brown algae participate in photosynthesis. Substantial proof of Engclmann's contention has come from the more ex- tensive and exacting studies of this problem carried out in recent years. Dutton and Manning (1941) and Wassink and Kerstcn (1946) have shown that light absorbed by fucoxanthin, the major accessory pigment of diatoms, is utilized for photosynthesis with about the same efficiencyas that absorbed by chloro- phyll. However, the carotenoids of some other plants (which lack the fucoxan- thin protein) appear to be relativelyinactive; this situation has been reported for purple bacteria (French, 1937), Chlorella (Emerson and Lewis, 1943), and Chroococcus (Emerson and Lewis, 1942). In the latter blue-green alga the de- tailed study by these workers of quantum yield throughout the spectrum pro- vided conclusive proof that another pigment, the water-soluble chromoprotein phycocyanin, is an efficientparticipant in photosynthesis. The red algae, being in most cases macroscopic in form and marine in habitat, have not been studied by the quantitative methods applied to the aforemen- tioned unicellularalgae (cf.,however, the manometric studies of Emerson and Grcen, 1934, on Gigartina). -
Next Generation Sequencing, Assembly, and Analysis of Bovine
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2018 Next Generation Sequencing, Assembly, and Analysis of Bovine and Feline Tritrichomonas foetus Genomes Toward Taxonomic Clarification And Improved Therapeutic and Preventive Targets Ellen Ann Fleetwood University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Fleetwood, Ellen Ann, "Next Generation Sequencing, Assembly, and Analysis of Bovine and Feline Tritrichomonas foetus Genomes Toward Taxonomic Clarification And Improved Therapeutic and Preventive Targets. " PhD diss., University of Tennessee, 2018. https://trace.tennessee.edu/utk_graddiss/4925 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Ellen Ann Fleetwood entitled "Next Generation Sequencing, Assembly, and Analysis of Bovine and Feline Tritrichomonas foetus Genomes Toward Taxonomic Clarification And Improved Therapeutic and Preventive Targets." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the -
Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic ‘‘Supergroups’’
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘‘supergroups’’ Vladimir Hampla,b,c, Laura Huga, Jessica W. Leigha, Joel B. Dacksd,e, B. Franz Langf, Alastair G. B. Simpsonb, and Andrew J. Rogera,1 aDepartment of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5; bDepartment of Biology, Dalhousie University, Halifax, NS, Canada B3H 4J1; cDepartment of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; dDepartment of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; eDepartment of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7; and fDepartement de Biochimie, Universite´de Montre´al, Montre´al, QC, Canada H3T 1J4 Edited by Jeffrey D. Palmer, Indiana University, Bloomington, IN, and approved January 22, 2009 (received for review August 12, 2008) Nearly all of eukaryotic diversity has been classified into 6 strong support for an incorrect phylogeny (16, 19, 24). Some recent suprakingdom-level groups (supergroups) based on molecular and analyses employ objective data filtering approaches that isolate and morphological/cell-biological evidence; these are Opisthokonta, remove the sites or taxa that contribute most to these systematic Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Exca- errors (19, 24). vata. However, molecular phylogeny has not provided clear evi- The prevailing model of eukaryotic phylogeny posits 6 major dence that either Chromalveolata or Excavata is monophyletic, nor supergroups (25–28): Opisthokonta, Amoebozoa, Archaeplastida, has it resolved the relationships among the supergroups. To Rhizaria, Chromalveolata, and Excavata. With some caveats, solid establish the affinities of Excavata, which contains parasites of molecular phylogenetic evidence supports the monophyly of each of global importance and organisms regarded previously as primitive Rhizaria, Archaeplastida, Opisthokonta, and Amoebozoa (16, 18, eukaryotes, we conducted a phylogenomic analysis of a dataset of 29–34). -
EBS 566/555 Lecture 14: Phytoplankton Functional
EBS 566/555 3/3/2010 Lecture 15 Blooms, primary production and types of phytoplankton (Ch 2, 3) Topics – Finish blooms – Major taxa of phytoplankton – How to measure phytoplankton – Primary production http://cmore.soest.hawaii.edu EBS566/666-Lecture 13 1 Alternatives to the Spring Bloom • Polar and tropical seas • Shallow water case: stratification not important for bloom initiation, only light is important • Estuaries (Cloern and Jassby 2008, 2009) • Extremely oligotrophic regions • Iron limitation (e.g. subarctic North Pacific) – But also applies to spring bloom! • Grazing regime • Upwelling systems (coastal, equatorial) EBS566/666-Lecture 13 2 Global comparison of phytoplankton biomass In South Pacific Gyre, chl a is highest in winter compared to summer Green = chl a Red = mixed layer depth (determined from Argo float) Claustre, unpubl. EBS566/666-Lecture 13 4 Annually averaged chl a HNLC HNLC HNLC EBS566/666-Lecture 13 5 Fate of bloom phytoplankton • Shallow decomposition ( microbial loop, regeneration) • Export – To deep ocean – Burial in sediments ( sedimentary record) • Grazing – Mesozooplankton – Microzooplankton – Excretion regenerated nutrients EBS566/666-Lecture 13 6 We can estimate algal biomass using the photosynthetic pigment, chlorophyll a micro.magnet.fsu.edu http://www.agen.ufl.edu hypnea.botany.uwc.ac.za left: Chloroplast of Chlamydomonas, a unicellular green alga. Note the chloroplast (Chl) with stacked thylakoids, and starch (s). TEM image by Richard Pienaar stroma grana lamellae/stroma thylakoids The ‘Z’ scheme Non-cyclic