Bacterial Bioluminescence: Applications in Food Microbiology
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Understanding Bioluminescence in Dinoflagellates—How Far Have We Come?
Microorganisms 2013, 1, 3-25; doi:10.3390/microorganisms1010003 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Review Understanding Bioluminescence in Dinoflagellates—How Far Have We Come? Martha Valiadi 1,* and Debora Iglesias-Rodriguez 2 1 Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse, Plӧn 24306, Germany 2 Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected] or [email protected]; Tel.: +49-4522-763277; Fax: +49-4522-763310. Received: 3 May 2013; in revised form: 20 August 2013 / Accepted: 24 August 2013 / Published: 5 September 2013 Abstract: Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms’ lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence in dinoflagellates, highlighting significant discoveries of the last quarter of a century. We identify significant gaps in our knowledge and conflicting information and propose some important research questions -
Ecological Characterization of Bioluminescence in Mangrove Lagoon, Salt River Bay, St. Croix, USVI
Ecological Characterization of Bioluminescence in Mangrove Lagoon, Salt River Bay, St. Croix, USVI James L. Pinckney (PI)* Dianne I. Greenfield Claudia Benitez-Nelson Richard Long Michelle Zimberlin University of South Carolina Chad S. Lane Paula Reidhaar Carmelo Tomas University of North Carolina - Wilmington Bernard Castillo Kynoch Reale-Munroe Marcia Taylor University of the Virgin Islands David Goldstein Zandy Hillis-Starr National Park Service, Salt River Bay NHP & EP 01 January 2013 – 31 December 2013 Duration: 1 year * Contact Information Marine Science Program and Department of Biological Sciences University of South Carolina Columbia, SC 29208 (803) 777-7133 phone (803) 777-4002 fax [email protected] email 1 TABLE OF CONTENTS INTRODUCTION ............................................................................................................................................... 4 BACKGROUND: BIOLUMINESCENT DINOFLAGELLATES IN CARIBBEAN WATERS ............................................... 9 PROJECT OBJECTIVES ..................................................................................................................................... 19 OBJECTIVE I. CONFIRM THE IDENTIY OF THE BIOLUMINESCENT DINOFLAGELLATE(S) AND DOMINANT PHYTOPLANKTON SPECIES IN MANGROVE LAGOON ........................................................................ 22 OBJECTIVE II. COLLECT MEASUREMENTS OF BASIC WATER QUALITY PARAMETERS (E.G., TEMPERATURE, SALINITY, DISSOLVED O2, TURBIDITY, PH, IRRADIANCE, DISSOLVED NUTRIENTS) FOR CORRELATION WITH PHYTOPLANKTON -
Determining the Depth Limit of Bioluminescent Sources in Scattering Media
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.21.044982; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Determining the Depth Limit of Bioluminescent Sources in Scattering Media. Ankit Raghuram1,*, Fan Ye1, Jesse K. Adams1,2, Nathan Shaner3, Jacob T. Robinson1,2,4,5, Ashok Veeraraghavan1,2,6 1 Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA 2 Applied Physics Program, Rice University, Houston, TX 77005, USA 3 Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA 4 Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA 5 Department of Bioengineering, Rice University, Houston, TX 77005, USA 6 Department of Computer Science, Rice University, Houston TX 77005, USA * [email protected] Abstract Bioluminescence has several potential advantages compared to fluorescence microscopy for in vivo biological imaging. Because bioluminescence does not require excitation light, imaging can be performed for extended periods of time without phototoxicity or photobleaching, and optical systems can be smaller, simpler, and lighter. Eliminating the need for excitation light may also affect how deeply one can image in scattering biological tissue, but the imaging depth limits for bioluminescence have yet to be reported. Here, we perform a theoretical study of the depth limits of bioluminescence microscopy and find that cellular resolution imaging should be possible at a depth of 5-10 mean free paths (MFPs). This limit is deeper than the depth limit for confocal microscopy and slightly lower than the imaging limit expected for two-photon microscopy under similar conditions. -
Pathogenic Mechanisms of Photobacterium Damselae Subspecies Piscicida in Hybrid Striped Bass Ahmad A
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2002 Pathogenic mechanisms of Photobacterium damselae subspecies piscicida in hybrid striped bass Ahmad A. Elkamel Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Veterinary Pathology and Pathobiology Commons Recommended Citation Elkamel, Ahmad A., "Pathogenic mechanisms of Photobacterium damselae subspecies piscicida in hybrid striped bass" (2002). LSU Doctoral Dissertations. 773. https://digitalcommons.lsu.edu/gradschool_dissertations/773 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. PATHOGENIC MECHANISMS OF PHOTOBACTERIUM DAMSELAE SUBSPECIES PISCICIDA IN HYBRID STRIPED BASS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Pathobiological Sciences by Ahmad A. Elkamel B.V. Sc., Assiut University, 1993 May 2002 DEDICATION This work is dedicated to the people in my life who encouraged each step of my academic career. My mother was anxious as I was for each exam or presentation. I have been always looking to my Dad as a model, and trying to follow his footsteps in academic career. My wife stood by me like no other one in the world, and her love and support helped me see one of my dreams come true. -
Who Glows There? Bioluminescence of Fireflies, Mushrooms, and Jellyfish Detailed Project Description
Who Glows there? Bioluminescence of Fireflies, Mushrooms, and Jellyfish Glenna Smith Anthony Todd Background: Most people think of fireflies when it comes to bioluminescent or glow- in-the-dark organisms, but many other organisms use bioluminescence as well to communicate, ward off predators, or attract their meal. On land and in fresh water, it is fairly rare with only a handful of bioluminescent mushrooms and insects (not including the recently developed abundance of transgenic glowing organisms like tobacco or rabbits). In the ocean, however, and the deep sea in particular where it is the only source of light, bioluminescence is used by a multitude of creatures: fish, squid, jellyfish, sponges, algae. We propose construction of a small exhibit which will teach children about bioluminescence and allow them to ‘draw’ the bioluminescence onto glow-in-the- dark cutouts of the organisms using fiber optic ‘pens’. This exhibit could be positioned in SciTech near the “shadowbox”. Goals: Teach children about the utility of bioluminescence by various organisms (it isn’t just for show!). Children would learn how creatures communicate with and relate to each other using bioluminescence, and how bioluminescence is particularly useful in their environment (counterillumination camouflage). Target Museum: SciTech Target Audience: Grades K-10 (benchmarks addressed in appendix 1) Big Idea: Fireflies, jellyfish, and other organisms are using bioluminescence to communicate, protect themselves, and feed themselves. Detailed Project Description: This demo will be a fun, hands-on small exhibit to showcase several bioluminescent organisms, and explain why glowing is useful to their survival. The exhibit would feature a series of pictures of glowing fish, mushrooms, insects, (the pictures could be backlit). -
Shedding Light on the Bioluminescence “Paradox” Although Luminescence Provides Host Squids with Obvious Advantages, How Does It Benefit Light-Producing Bacteria?
Shedding Light on the Bioluminescence “Paradox” Although luminescence provides host squids with obvious advantages, how does it benefit light-producing bacteria? Eric V. Stabb he fascinating biochemistry, genetics, have special significance for this bacterium. Bi- and cell density-dependent regula- oluminescence offers many such puzzles, and it tion of bacterial bioluminescence is unlikely a single solution will solve them all. T provoke a challenging question. Nonetheless, it is an exciting moment in bio- What good is it to bioluminescent luminescence research, with recent advances of- bacteria? fering the promise of answering the longstand- There may be no single answer to this seem- ing question, “how can bioluminescence ingly simple question. However, two recent ad- help bacteria?” Although researchers learned vances shed new light on the problem. First, nearly a century ago that luminescence reduces studies of the symbiosis between the biolumines- oxygen and that symbiotic bacteria inhabit the cent bacterium Vibrio fischeri and the Hawaiian light organs of squids, what was unimaginable bobtail squid bring an ecologically relevant until very recently is our ability to analyze the V. niche for a bioluminescent bacterium into focus fischeri genome sequence and to combine this under the discerning lens of controlled labora- knowledge with the ability to genetically manip- tory experimentation. Second, progress in under- ulate these bacteria and observe them under standing the genetics of V. fischeri, including controlled laboratory conditions in the ecologi- genomic sequencing of a squid symbiont, is en- cally relevant environment of a natural squid abling researchers to analyze how luminescence host. integrates into the physiology of this bacterial species and to test specific hypotheses about Biochemistry and Genetics of what advantage light production confers on the V. -
Articles and Detrital Matter
Biogeosciences, 7, 2851–2899, 2010 www.biogeosciences.net/7/2851/2010/ Biogeosciences doi:10.5194/bg-7-2851-2010 © Author(s) 2010. CC Attribution 3.0 License. Deep, diverse and definitely different: unique attributes of the world’s largest ecosystem E. Ramirez-Llodra1, A. Brandt2, R. Danovaro3, B. De Mol4, E. Escobar5, C. R. German6, L. A. Levin7, P. Martinez Arbizu8, L. Menot9, P. Buhl-Mortensen10, B. E. Narayanaswamy11, C. R. Smith12, D. P. Tittensor13, P. A. Tyler14, A. Vanreusel15, and M. Vecchione16 1Institut de Ciencies` del Mar, CSIC. Passeig Mar´ıtim de la Barceloneta 37-49, 08003 Barcelona, Spain 2Biocentrum Grindel and Zoological Museum, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany 3Department of Marine Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy 4GRC Geociencies` Marines, Parc Cient´ıfic de Barcelona, Universitat de Barcelona, Adolf Florensa 8, 08028 Barcelona, Spain 5Universidad Nacional Autonoma´ de Mexico,´ Instituto de Ciencias del Mar y Limnolog´ıa, A.P. 70-305 Ciudad Universitaria, 04510 Mexico,` Mexico´ 6Woods Hole Oceanographic Institution, MS #24, Woods Hole, MA 02543, USA 7Integrative Oceanography Division, Scripps Institution of Oceanography, La Jolla, CA 92093-0218, USA 8Deutsches Zentrum fur¨ Marine Biodiversitatsforschung,¨ Sudstrand¨ 44, 26382 Wilhelmshaven, Germany 9Ifremer Brest, DEEP/LEP, BP 70, 29280 Plouzane, France 10Institute of Marine Research, P.O. Box 1870, Nordnes, 5817 Bergen, Norway 11Scottish Association for Marine Science, Scottish Marine Institute, Oban, -
The Spot 42 RNA: a Regulatory Small RNA with Roles in the Central
1 The Spot 42 RNA: A regulatory small RNA with roles in the central 2 metabolism 3 Cecilie Bækkedal and Peik Haugen* 4 5 Department of Chemistry, The Norwegian Structural Biology Centre (NorStruct) and Centre for 6 Bioinformatics (SfB), UiT – The Arctic University of Norway, 9037 Tromsø, Norway 7 8 Key words: sRNA, small RNA, Spot 42, spf, non-coding RNA, gamma proteobacteria, pirin. 9 *Correspondence to: Peik Haugen; E-mail: [email protected] 10 Disclosure statement: the authors have no conflict of interest and nothing to disclose. 11 12 The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA 13 (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the 14 majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently 15 Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate 16 metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP 17 complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution 18 of spf, show family-specific secondary structural features of Spot 42, and link highly conserved 19 structural regions to mRNA target binding. 20 Introduction 21 The spf gene is highly conserved in Escherichia, Shigella, Klebsiella, Salmonella and Yersinia 22 (genera) within the Enterobacteriacea family.1 In E. coli the spf gene is flanked by polA 23 (upstream) and yihA (downstream),2,3 and a CRP binding sequence and -10 and -35 promoter 24 sequences are found upstream of spf. -
To See Or Not to See
Bioluminescence 2009: ocean Living Light on the Deep Sea Floor Expedition To See or Not to See www.oceanexplorer.noaa.gov Focus Bioluminescence, color, and camouflage in deep ocean organisms Grade Level 9-12 (Life Science) Focus Question Image credit: NOAA. How are light and color important to organisms in deep ocean environments? Learning Objectives ] Students will be able to identify and discuss key factors that determine the effectiveness of color camouflage in pelagic and benthic habitats. ] Students will be able to describe how ambient light changes with Image credit: NOAA. increasing depth in the ocean. ] Students will be able to explain how the wavelength of light that illuminates an organism may determine the most effective camouflage coloration. ] Students will be able to explain how an organism that has effective camouflage coloration under ambient illumination may not be effectively camouflaged when it is illuminated by Image credit: NOAA. bioluminescence. Materials @ Copies of “Bioluminescence and Color Camouflage Inquiry Guide,” one copy for each student group @ Flashlights; one for each student group @ Blue filters (see Learning Procedure Step 1c) Audio/Visual Materials 9 (Optional) Images showing light and color in deep-sea Image credit: NOAA. environments and organisms (see Learning Procedure, Step 1d) Image captions on Page 2. Teaching Time Two 45-minute class periods, plus time for student research 1 www.oceanexplorer.noaa.gov Bioluminescence 2009: To See or Not to See Grades 9-12 (Life Science) Seating Arrangement Groups of 2-4 students Maximum Number of Students 30 Key Words Light Vision Bioluminescence Electromagnetic spectrum Color Wavelength Camouflage The lobate ctenophore Ocyropsis maculata as viewed under unpolarized light (top) and polarized light (bottom). -
Light and Vision in the Deep-Sea Benthos: I
Nova Southeastern University NSUWorks Marine & Environmental Sciences Faculty Articles Department of Marine and Environmental Sciences 10-1-2012 Light and Vision in the Deep-Sea Benthos: I. Bioluminescence at 500-1000 m Depth in the Bahamian Islands Sönke Johnsen Duke University Tamara M. Frank Nova Southeastern University, [email protected] Steven H.D. Haddock Monterey Bay Aquarium Research Institute Edith A. Widder Ocean Research and Conservation Association Charles G. Messing Nova Southeastern University, [email protected] Find out more information about Nova Southeastern University and the Halmos College of Natural Sciences and Oceanography. Follow this and additional works at: https://nsuworks.nova.edu/occ_facarticles Part of the Marine Biology Commons, and the Oceanography and Atmospheric Sciences and Meteorology Commons Recommended Citation Johnsen, Sönke, Tamara M. Frank, Steven HD Haddock, Edith A. Widder, and Charles G. Messing. "Light and vision in the deep-sea benthos: I. Bioluminescence at 500–1000 m depth in the Bahamian Islands." The ourJ nal of experimental biology 215, no. 19 (2012): 3335-3343. This Article is brought to you for free and open access by the Department of Marine and Environmental Sciences at NSUWorks. It has been accepted for inclusion in Marine & Environmental Sciences Faculty Articles by an authorized administrator of NSUWorks. For more information, please contact [email protected]. 3335 The Journal of Experimental Biology 215, 3335-3343 © 2012. Published by The Company of Biologists Ltd doi:10.1242/jeb.072009 RESEARCH ARTICLE Light and vision in the deep-sea benthos: I. Bioluminescence at 500–1000m depth in the Bahamian Islands Sönke Johnsen1,*, Tamara M. -
16.2 the WORLD of PERPETUAL DARKNESS the Lack of Food
Final PDF to printer 376 Part Three Structure and Function of Marine Ecosystems O2 abyssopelagic zone lies from 4,000 to 6,000 m (13,000 to 20,000 ft). The hadopelagic, or hadal pelagic, zone consists of the waters of the ocean trenches, from below 6,000 m to Amount of dissolved oxygen just above the sea floor, as deep as 11,000 m (36,000 ft). Low High Each of the depth zones supports a distinct community of animals, but they also have much in common. Here we hotosynthesi CO P s Organic 2 stress the similarities, rather than the differences, among the + matter H O + Epipelagic depth zones of the deep sea. 2 n O Respiratio 2 The conditions of life in the deep pelagic environment Decomposition change very little. Not only is it always dark, it is always 200 m cold: The temperature remains nearly constant, typically at 1 to 2 °C (35 °F). Salinity and other chemical properties of the water are also remarkably uniform. Oxygen minimum zone CO Organic 2 matter The deep sea also includes the ocean bottom beyond + H O Respiration + the continental shelf. Bottom-living organisms are covered 2 O Decomposition 2 Mesopelagic separately (see “The Deep-Ocean Floor,” below). The deep sea includes the bathypelagic, from 1,000 to 4,000 m; the abyssopelagic, 4,000 to 6,000 m; and the hadopelagic, 6,000 m to 1,000 m the bottom of trenches. The physical environment in these zones is quite constant. The deep sea also includes the deep-sea floor. -
Expression Profiling Reveals Spot 42 Small RNA As a Key Regulator in The
Hansen et al. BMC Genomics 2012, 13:37 http://www.biomedcentral.com/1471-2164/13/37 RESEARCH ARTICLE Open Access Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida Geir Å Hansen1, Rafi Ahmad1,2, Erik Hjerde1, Christopher G Fenton3, Nils-Peder Willassen1,2 and Peik Haugen1,2* Abstract Background: Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio salmonicida, causes cold-water vibriosis in farmed Atlantic salmon. Its genome encodes Spot 42 with 84% identity to E. coli Spot 42. Results: We generated a A. salmonicida spf deletion mutant. We then used microarray and Northern blot analyses to monitor global effects on the transcriptome in order to provide insights into the biological roles of Spot 42 in this bacterium. In the presence of glucose, we found a surprisingly large number of ≥ 2X differentially expressed genes, and several major cellular processes were affected. A gene encoding a pirin-like protein showed an on/off expression pattern in the presence/absence of Spot 42, which suggests that Spot 42 plays a key regulatory role in the central metabolism by regulating the switch between fermentation and respiration. Interestingly, we discovered an sRNA named VSsrna24, which is encoded immediately downstream of spf.