Transcriptome Reconstruction and Functional Analysis of Eukaryotic Marine Plankton Communities Via High-Throughput Metagenomics and Metatranscriptomics
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Amyloodinium Ocellatum (Dinoflagellata) in Mississippi Sound: Natural and Experimental Hosts
Gulf and Caribbean Research Volume 6 Issue 4 January 1980 Studies on Amyloodinium ocellatum (Dinoflagellata) in Mississippi Sound: Natural and Experimental Hosts Adrian R. Lawler Gulf Coast Research Laboratory Follow this and additional works at: https://aquila.usm.edu/gcr Part of the Marine Biology Commons Recommended Citation Lawler, A. R. 1980. Studies on Amyloodinium ocellatum (Dinoflagellata) in Mississippi Sound: Natural and Experimental Hosts. Gulf Research Reports 6 (4): 403-413. Retrieved from https://aquila.usm.edu/gcr/vol6/iss4/8 DOI: https://doi.org/10.18785/grr.0604.08 This Article is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Gulf and Caribbean Research by an authorized editor of The Aquila Digital Community. For more information, please contact [email protected]. Gulf Research Reports, Vol. 6,No. 4,403-413, 1980. STUDIES ON AMYLOODINIUM OCELLA TUM (DINOFLAGELLATA) IN MISSISSIPPI SOUND: NATURAL AND EXPERIMENTAL HOSTS' ADRIAN R. LAWLER Parasitology Section, Gulf Coast Research Laboratory, Ocean Springs, Mississippi 39564 ABSTRACT Four species of parasitic dinoflagellates have been found to occur naturally on the gills and fins of Missis- sippi Sound fishes: Amyloodinium ocellatum (Brown 1931) Brown and Hovasse 1946, Oodinium cyprinodontum Lawler 1967, and two undescribed species. Sixteen of 43 species of fishes examined had natural gill infections of A. ocellatum. Seventy-one of 79 species of fishes exposed to A. ocellatum dinospores were susceptible, and succumbed, to the dinoflagel- late. Eight did not die even though exposed to numerous dinospores. The most common signs in an infested fish were spasmodic gasping and uncoordinated movements. -
Chromerid Genomes Reveal the Evolutionary Path From
RESEARCH ARTICLE elifesciences.org Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites Yong H Woo1*, Hifzur Ansari1,ThomasDOtto2, Christen M Klinger3†, Martin Kolisko4†, Jan Michalek´ 5,6†, Alka Saxena1†‡, Dhanasekaran Shanmugam7†, Annageldi Tayyrov1†, Alaguraj Veluchamy8†§, Shahjahan Ali9¶,AxelBernal10,JavierdelCampo4, Jaromır´ Cihla´ rˇ5,6, Pavel Flegontov5,11, Sebastian G Gornik12,EvaHajduskovˇ a´ 5, AlesHorˇ ak´ 5,6,JanJanouskovecˇ 4, Nicholas J Katris12,FredDMast13,DiegoMiranda- Saavedra14,15, Tobias Mourier16, Raeece Naeem1,MridulNair1, Aswini K Panigrahi9, Neil D Rawlings17, Eriko Padron-Regalado1, Abhinay Ramaprasad1, Nadira Samad12, AlesTomˇ calaˇ 5,6, Jon Wilkes18,DanielENeafsey19, Christian Doerig20, Chris Bowler8, 4 10 3 21,22 *For correspondence: yong. Patrick J Keeling , David S Roos ,JoelBDacks, Thomas J Templeton , 12,23 5,6,24 5,6,25 1 [email protected] (YHW); arnab. Ross F Waller , Julius Lukesˇ , Miroslav Obornık´ ,ArnabPain* [email protected] (AP) 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering † These authors contributed Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; equally to this work 2Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Present address: ‡Vaccine and Cambridge, United Kingdom; 3Department of Cell Biology, University of Alberta, Infectious Disease Division, Fred Edmonton, Canada; 4Canadian Institute for Advanced Research, Department of Botany, -
MBI Volume 70 Issue 2 Cover and Back Matter
MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM RESEARCH AWARDS Applications are invited for research awards to enable scientists from the United Kingdom, or from abroad, to work at the Association's Citadel Hill Laboratory, either as independent visitors or to collaborate in work currently being undertaken as part of the Association's Research Programme. Two levels of award are available: RESEARCH BURSARIES available for visitors at all levels of experience from graduate students to senior scientists. Several awards are made each year with a maximum value of £2,500. RAY LANKESTERINVESTIGATORSHIP available to postdoctoral research workers with several years of research experience in some aspect of marine biology or marine physiology. One award is made each year to a value of £5,000 to enable visitors to work at the Laboratory for a minimum of 5 months over an 18-month period. Applications or enquiries are invited for 1990 and 1991. Successful applicants will be expected to become members of the Association. Further details may be obtained from: Dr Gerald Boalch, The Bursar Marine Biological Association of the United Kingdom The Laboratory Citadel Hill Plymouth PL1 2PB UK or by telephoning: 0752-222772 ext. 211 Downloaded from https://www.cambridge.org/core. IP address: 170.106.35.93, on 26 Sep 2021 at 17:38:53, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0025315400035359 Cover: The photograph on the outside of the cover was taken by David Nicholson at Pedney Beach, Cornwall. Inside front cover: Second zoea of velvet fiddler crab Portunus puber (L.) (height 3 mm). -
Microbes and Metagenomics in Human Health an Overview of Recent Publications Featuring Illumina® Technology TABLE of CONTENTS
Microbes and Metagenomics in Human Health An overview of recent publications featuring Illumina® technology TABLE OF CONTENTS 4 Introduction 5 Human Microbiome Gut Microbiome Gut Microbiome and Disease Inflammatory Bowel Disease (IBD) Metabolic Diseases: Diabetes and Obesity Obesity Oral Microbiome Other Human Biomes 25 Viromes and Human Health Viral Populations Viral Zoonotic Reservoirs DNA Viruses RNA Viruses Human Viral Pathogens Phages Virus Vaccine Development 44 Microbial Pathogenesis Important Microorganisms in Human Health Antimicrobial Resistance Bacterial Vaccines 54 Microbial Populations Amplicon Sequencing 16S: Ribosomal RNA Metagenome Sequencing: Whole-Genome Shotgun Metagenomics Eukaryotes Single-Cell Sequencing (SCS) Plasmidome Transcriptome Sequencing 63 Glossary of Terms 64 Bibliography This document highlights recent publications that demonstrate the use of Illumina technologies in immunology research. To learn more about the platforms and assays cited, visit www.illumina.com. An overview of recent publications featuring Illumina technology 3 INTRODUCTION The study of microbes in human health traditionally focused on identifying and 1. Roca I., Akova M., Baquero F., Carlet J., treating pathogens in patients, usually with antibiotics. The rise of antibiotic Cavaleri M., et al. (2015) The global threat of resistance and an increasingly dense—and mobile—global population is forcing a antimicrobial resistance: science for interven- tion. New Microbes New Infect 6: 22-29 1, 2, 3 change in that paradigm. Improvements in high-throughput sequencing, also 2. Shallcross L. J., Howard S. J., Fowler T. and called next-generation sequencing (NGS), allow a holistic approach to managing Davies S. C. (2015) Tackling the threat of anti- microbial resistance: from policy to sustainable microbes in human health. -
Working Group Reports
2.0 WORKING GROUPS REPORTS Expenditures by SCOR Working Groups (1996-2005), p. 2-1 2.1 Disbanded Working Groups, p. 2-2 2.1.1 WG 78 on Determination of Photosynthetic Pigments in Seawater, p. 2-2 Urban 2.2 Current Working Groups— The Executive Committee Reporter for each working group will present an update on working group activities and progress, and will make recommendations on actions to be taken. Working groups expire at each General Meeting, but can be renewed at the meeting and can be disbanded whenever appropriate. 2.2.1 WG 111—Coupling Winds, Waves and Currents in Coastal Models, p. 2-16 Wainer 2.2.2 WG 115—Standards for the Survey and Analysis of Plankton, p. 2-18 Pierrot-Bults 2.2.3 WG 116—Sediment Traps and 234Th Methods for Carbon Export Flux Determination, p. 2-29 Labeyrie 2.2.4 WG 119—Quantitative Ecosystems Indicators for Fisheries Management, p. 2-31 Taniguchi 2.2.5 WG 120—Marine Phytoplankton and Global Climate Regulation: The Phaeocystis spp. Cluster As Model, p. 2-33 Hall 2.2.6 WG 121—Ocean Mixing, p. 2-35 Akulichev 2.2.7 WG 122—Mechanisms of Sediment Retention in Estuaries, p. 2-39 Labeyrie 2.2.8 WG 123—Reconstruction of Past Ocean Circulation (PACE), p. 2-40 Labeyrie 2.2.9 WG 124—Analyzing the Links Between Present Oceanic Processes and Paleo-Records (LINKS), p. 2-43 Wainer 2.2.10 WG 125—Global Comparisons of Zooplankton Time Series, p. 2-52 Pierrot-Bults 2.2.11 WG 126—Role of Viruses in Marine Ecosystems, p. -
Bioinformatics Tools for RNA-Seq Gene and Isoform Quantification
on: Sequ ati en er c n in e g G & t x A Journal of e p Zhang, et al., Next Generat Sequenc & Applic p N l f i c o 2016, 3:3 a l t a i o n r ISSN: 2469-9853n u s DOI: 10.4172/2469-9853.1000140 o Next Generation Sequencing & Applications J Review Article Open Access Bioinformatics Tools for RNA-seq Gene and Isoform Quantification Chi Zhang1, Baohong Zhang1, Michael S Vincent2 and Shanrong Zhao1* 1Early Clinical Development, Pfizer Worldwide R&D, Cambridge, MA, USA 2Inflammation and Immunology RU, Pfizer Worldwide R&D, Cambridge, MA, USA *Corresponding author: Shanrong Zhao, Early Clinical Development, Pfizer Worldwide R&D, Cambridge, MA, 02139, USA, Tel: + 1-212-733-2323; E-mail: [email protected] Rec date: Oct 27, 2016; Acc date: Dec 15, 2016; Pub date: Dec 17, 2016 Copyright: © 2016 Zhang C, et al. This is an open-access article distributed under the terms of the creative commons attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression. ‘Union-exon’ and transcript based approaches are widely used in gene quantification. The ‘Union-exon’ based approach is simple, but it does not distinguish between isoforms when multiple alternatively spliced transcripts are expressed from the same gene. Because a gene is expressed in one or more transcript isoforms, the transcript based approach is more biologically meaningful than the ‘union exon’-based approach. -
The Chromosome-Centric Human Proteome Project for Cataloging Proteins Encoded in the Genome
CORRESPONDENCE The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome To the Editor: utility for biological and disease studies. Table 1 Features of salient genes on The Chromosome-Centric Human With development of new tools for in- chromosomes 13 and 17 Proteome Project (C-HPP) aims to define depth characterization of the transcriptome Genea AST nsSNPs the full set of proteins encoded in each and proteome, the HPP is well positioned Chromosome 13 chromosome through development of a to have a strategic role in addressing the BRCA2 3 54 standardized approach for analyzing the complexity of human phenotypes. With this RB1 2 3 massive proteomic data sets currently being in mind, the HUPO has organized national IRS2 1 3 generated from dedicated efforts of national chromosome teams that will collaborate and international teams. The initial goal with well-established laboratories building Chromosome 17 of the C-HPP is to identify at least one complementary proteotypic peptides, BRCA1 24 24 representative protein encoded by each of antibodies and informatics resources. ERBB2 6 13 the approximately 20,300 human genes1,2. An important C-HPP goal is to encourage TP53 14 5 aEnsembl protein and AST information can be found at The proteins will be characterized for tissue capture and open sharing of proteomic http://www.ensembl.org/Homo_sapiens/. localization and major isoforms, including data sets from diverse samples to enhance AST, alternative splicing transcript; nsSNP, nonsyno- mous single-nucleotide polyphorphism assembled from post-translational modifications (PTMs), a gene- and chromosome-centric display data from the 1000 Genomes Projects. -
Downloaded As a CSV Dump file
cells Article Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus Metamorphosis Nicolas Buisine 1,† , Alexis Grimaldi 1,†, Vincent Jonchere 1,† , Muriel Rigolet 1, Corinne Blugeon 2 , Juliette Hamroune 2 and Laurent Marc Sachs 1,* 1 UMR7221 Molecular Physiology and Adaption, CNRS, Museum National d’Histoire Naturelle, 57 Rue Cuvier, CEDEX 05, 75231 Paris, France; [email protected] (N.B.); [email protected] (A.G.); [email protected] (V.J.); [email protected] (M.R.) 2 Genomics Core Facility, Département de Biologie, Institut de Biologie de l’ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; [email protected] (C.B.); [email protected] (J.H.) * Correspondence: [email protected] † Co-first authors, alphabetic order. Abstract: Background: Most work in endocrinology focus on the action of a single hormone, and very little on the cross-talks between two hormones. Here we characterize the nature of interactions between thyroid hormone and glucocorticoid signaling during Xenopus tropicalis metamorphosis. Methods: We used functional genomics to derive genome wide profiles of methylated DNA and measured changes of gene expression after hormonal treatments of a highly responsive tissue, tailfin. Clustering classified the data into four types of biological responses, and biological networks were Citation: Buisine, N.; Grimaldi, A.; modeled by system biology. Results: We found that gene expression is mostly regulated by either Jonchere, V.; Rigolet, M.; Blugeon, C.; T or CORT, or their additive effect when they both regulate the same genes. A small but non- Hamroune, J.; Sachs, L.M. -
APPENDIX 1 Classified List of Fishes Mentioned in the Text, with Scientific and Common Names
APPENDIX 1 Classified list of fishes mentioned in the text, with scientific and common names. ___________________________________________________________ Scientific names and classification are from Nelson (1994). Families are listed in the same order as in Nelson (1994), with species names following in alphabetical order. The common names of British fishes mostly follow Wheeler (1978). Common names of foreign fishes are taken from Froese & Pauly (2002). Species in square brackets are referred to in the text but are not found in British waters. Fishes restricted to fresh water are shown in bold type. Fishes ranging from fresh water through brackish water to the sea are underlined; this category includes diadromous fishes that regularly migrate between marine and freshwater environments, spawning either in the sea (catadromous fishes) or in fresh water (anadromous fishes). Not indicated are marine or freshwater fishes that occasionally venture into brackish water. Superclass Agnatha (jawless fishes) Class Myxini (hagfishes)1 Order Myxiniformes Family Myxinidae Myxine glutinosa, hagfish Class Cephalaspidomorphi (lampreys)1 Order Petromyzontiformes Family Petromyzontidae [Ichthyomyzon bdellium, Ohio lamprey] Lampetra fluviatilis, lampern, river lamprey Lampetra planeri, brook lamprey [Lampetra tridentata, Pacific lamprey] Lethenteron camtschaticum, Arctic lamprey] [Lethenteron zanandreai, Po brook lamprey] Petromyzon marinus, lamprey Superclass Gnathostomata (fishes with jaws) Grade Chondrichthiomorphi Class Chondrichthyes (cartilaginous -
Relationships Between Oceanographic Factors and the Distribution of Juvenile Coho Salmon
AN ABSTRACT OF THE THESIS OF Alton W. Chung for the degree of Master of Science in Oceanography presented on March 1, 1985 Title: Relationships Between Oceanographic Factors and the Distribution of Juvenile Coho Salmon (Oncorhynchus kisutch) Of f Oregon and Washington, 1982-1983 Redacted for Privacy Abstract approved: Dr. William G. Pearc Juvenile coho salmon (101-400 mm) were sampled by purse seine off the Pacific Coast from Waatch Point, Washington to Four Mile Creek, Oregon, out to 30 mi offshore, during the months of May, June, and September in 1982 and 1983. Sea surface temperature, surface salinity, surface chlorophyll-a concentration, and Secchi depth were measured at each station. Sea surface temperatures were higher in 1983 than in 1982, while surface chlorophyll-a concentrations and surface salinities were lower. Catch data were not highly correlated with any of the four physical parameters measured. Strong northerly winds and strong upwelling tended to disperse juvenile coho offshore and south. Fish were found closer inshore during periods of weak winds and weak upwelling. In both years the center of distribution of the fish appeared to shift northward as the summer progressed. Larger fish, in general, were found farther north and offshore throughout the year. Relationships Between Oceanographic Factors and the Distribution of Juvenile Coho Salmon Oncorhynchus kisutch Off Oregon and Washington, 1982-1983 by Alton W. Chung A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree -
Algae Becomes UNCW Project
Established in 1867 / Volume 71, Number 20 January 21, 2001 Wilmington, N.C. $1.50¢ Home delivery 36¢ water, indicate whether a certain The blooms can kill people as well, toxin is present. as UNCW chemist Jeff Wright knows. They envision a dipstick-type Algae becomes Dr. Wright led an emergency effort device that changes colors much like by the Canadian government in 1987 a pregnancy test. to figure out what poisoned more Dr. Baden has developed a method than 100 people in Montreal, of testing for brevetoxin, the killer in UNCW project including four who eventually died. red tides, and submitted it to the The victims had eaten mussels at Food and Drug Administration. exactly what it was like two days ago local restaurants. As it is now, officials screening BY BRIAN FEAGANS when the fish died,” Dr. Tomas said. A group of 30 scientists worked shellfish for the toxin have only one Staff Writer “Marine systems are very dynamic. around the clock for 104 hours before federally approved method: inject More than 5 million fish had died They’re constantly changing. You fingering little-known microscopic samples into a mouse and see if it in creeks feeding Rehoboth Bay have to be thinking like the ocean, algae as the killer. dies. when puzzled Delaware officials got a the way the tides are going in and The Pseudo-nitzschia were pro- Florida is funding the research as a phone call from UNCW researcher out.” ducing a potent acid that causes way to save mice and time. Carmelo Tomas in September. -
Living Resources Report Texas A&M University-Corpus Christi Results - Open Bay Habitat
Center for Coastal Studies CCBNEP Living Resources Report Texas A&M University-Corpus Christi Results - Open Bay Habitat B. Living Resources - Habitats Detailed community profiles of estuarine habitats within the CCBNEP study area are not available. Therefore, in the following sections, the organisms, community structure, and ecosystem processes and functions of the major estuarine habitats (Open Bay, Oyster Reef, Hard Substrate, Seagrass Meadow, Coastal Marsh, Tidal Flat, Barrier Island, and Gulf Beach) within the CCBNEP study area are presented. The following major subjects will be addressed for each habitat: (1) Physical setting and processes; (2) Producers and Decomposers; (3) Consumers; (4) Community structure and zonation; and (5) Ecosystem processes. HABITAT 1: OPEN BAY Table Of Contents Page 1.1. Physical Setting & Processes ............................................................................ 45 1.1.1 Distribution within Project Area ......................................................... 45 1.1.2 Historical Development ....................................................................... 45 1.1.3 Physiography ...................................................................................... 45 1.1.4 Geology and Soils ................................................................................ 46 1.1.5 Hydrology and Chemistry ................................................................... 47 1.1.5.1 Tides .................................................................................... 47 1.1.5.2 Freshwater