Open Maresca Thesis F.Pdf

Total Page:16

File Type:pdf, Size:1020Kb

Open Maresca Thesis F.Pdf The Pennsylvania State University The Graduate School Eberly College of Science THE GENETIC BASIS FOR PIGMENT VARIATION AMONG GREEN SULFUR BACTERIA A Thesis in Biochemistry and Molecular Biology by Julia A. Maresca Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2007 The thesis of Julia A. Maresca was reviewed and approved by the following committee members* Donald A. Bryant Ernest C. Pollard Professor of Biotechnology and Professor of Biochemistry and Molecular Biology Thesis Advisor Chair of Committee John H. Golbeck Professor of Biochemistry and Biophysics Sarah E. Ades Assistant Professor of Biochemistry and Molecular Biology Squire J. Booker Associate Professor of Biochemistry and Molecular Biology Lee R. Kump Professor of Geosciences Robert A. Schlegel Professor of Biochemistry and Molecular Biology Department Head, Department of Biochemistry and Molecular Biology *Signatures are on file with the Graduate School ii Abstract The pigmentation differences between green-colored and brown-colored green sulfur bacteria (GSB) are more than cosmetic: species with different pigmentation inhabit different parts of the photic zone. Green-colored species, which make bacteriochlorophyll (BChl) c or d as their primary antenna BChl and chlorobactene as their main carotenoid, tend to be found in the upper layer of anaerobic photic zones. Brown-colored species, which make BChl e and the dicyclic carotenoid isorenieratene, are usually found deeper in the water column. These pigment pairs are invariant, which means that for a green species to become a brown one or vice versa, changes in two unrelated biosynthetic pathways must occur. In this work, comparative genomics has been used to identify the genes unique to pigment biosynthesis in green-colored and brown-colored green sulfur bacterial species. The gene encoding the C-20 methyltransferase, responsible for the difference between BChls c and d, has been identified and inactivated, and detailed analysis of BChl c- and d- producing strains has provided a molecular explanation for the observation that BChl c-containing species tend to live in darker environments. Additionally, a cluster of genes found exclusively in the genomes of brown-colored GSB species has been identified, and fragments of this cluster have been inserted into the chromosome of Chlorobium (Chl.) tepidum to investigate their role in BChl e biosynthesis. Using phylogenetic profiling, carotenoid cyclases specific to chlorobactene or isorenieratene biosynthesis were identified. These cyclases are responsible for the difference between mono- and dicyclic carotenoids, and their activity has been characterized both in GSB and in a heterologous expression system in Escherichia coli. Based on these analyses, the biosynthetic pathway for chlorobactene was established and a similar pathway for isorenieratene biosynthesis is demonstrated. Lastly, analysis of genome regions has identified chlorobactene-modifying enzymes which synthesize the membrane-associated OH-chlorobactene acyl glycosides in both green-colored and brown-colored GSB. These genes have been inactivated in Chl. tepidum and their roles in synthesizing glycosylated and acylated carotenoids have been confirmed. The investigations described in this work explain the genetic basis for stratification of green- colored species in the environment, complete the biosynthetic pathway for chlorobactene, identify the first known isorenieratene-specific carotenoid cyclase, and explain some of iii the natural variation in carotenoid end products seen in different species of green sulfur bacteria. Four of these proteins, the carotenoid cyclases, the carotenoid glycosyltransferase, and the carotenoid acyltransferase, are the first-characterized members of what appear to be large families of carotenoid-modifying enzymes. iv Table of Contents List of Tables x List of Figures xi Acknowledgements xiv CHAPTER 1. Introduction. 1 1.1 Green sulfur bacteria 2 1.2 Phylogeny of green sulfur bacteria 2 1.3 Ecology of green sulfur bacteria 4 1.4 Carbon and sulfur metabolism 5 1.5 Bacteriochlorophylls in the chlorosome: the antenna of green sulfur bacteria 6 1.6 (Bacterio)chlorophylls associated with the chlorosome baseplate, the FMO protein, and the photosynthetic reaction center. 8 1.7 Carotenoids in green sulfur bacteria 9 1.8 Genome sequences of green sulfur bacteria 10 1.9 Identification of genes unique to pigment biosynthesis in green sulfur bacteria 12 CHAPTER 2. Identification of a new class of carotenoid cyclases in photosynthetic organisms 38 Abstract 39 2.1 Introduction 40 2.2 Methods 2.2.1 Bacterial strains and growth conditions 43 2.2.2. Phylogenetic profiling 43 2.2.3 Preparation of genomic library and identification v of gene 43 2.2.4 Construct for inactivation of cruA (CT0456) in Chl. tepidum 44 2.2.5 Pigment analysis 44 2.3 Results 2.3.1 Phylogenetic profiling 45 2.3.2 Identification of lycopene cyclase in Chl. tepidum 45 2.3.3 Inactivation of Lycopene Cyclase in Chl. tepidum 45 2.3.4 Phylogenetic Analyses of Lycopene Cyclases 46 2.4 Discussion 47 2.5 References 50 CHAPTER 3. Heterologous expression of CruA-type carotenoid cyclases and proposed biosynthetic pathway for isorenieratene 71 Abstract 72 3.1 Introduction 73 3.2 Methods 3.2.1 Strains and growth conditions 75 3.2.2 Constructs for expression of CruA and CruB in E. coli 75 3.2.3 Assays of CruA and CruB activity in E. coli 75 3.2.4 Expression of cruB in Chl. tepidum 76 3.2.5 Inhibition of carotenoid cyclization 76 3.2.6 Pigment analysis 76 3.3 Results vi 3.3.1 Activity of cruA and cruB on lycopene in E. coli 78 3.3.2 Activity of cruA and cruB on neurosporene in E. coli 78 3.3.3 Expression of cruB in Chl. tepidum 78 3.3.4 Inhibition of lycopene cyclase activity 79 3.4 Discussion 80 3.5 References 84 CHAPTER 4: Identification of two genes encoding carotenoid- modifying enzymes in Chlorobium tepidum 104 Abstract 105 4.1 Introduction 106 4.2 Materials and Methods 4.2.1 Identification of candidate genes and phylogenetic comparisons 107 4.2.2 Construction of mutant strains 108 4.3 Results 4.3.1 Identification of candidate genes for the terminal steps of carotenogenesis in Chl. tepidum 108 4.3.2 Insertional inactivation of CT1987 and CT0976 109 4.3.3 Characterization of mutant strains 109 4.3.4 Growth rates of mutants 110 4.3.5 Sequence comparisons and phylogenetic analyses 110 4.4 Discussion 110 4.5 References 114 CHAPTER 5: Identification of the bacteriochlorophyll c C-20 methyl- transferase in Chl. tepidum 128 vii Abstract 129 5.1 Introduction 130 5.2 Materials and Methods 5.2.1 Strains and growth conditions 132 5.2.2 Inactivation of CT0028 132 5.2.3 Chlorosome preparation and analysis 132 5.2.4 Growth rate measurements 133 5.2.5 Competition experiments 133 5.3 Results 5.3.1 Identification of genes potentially encoding the BChl c C-20 methyltransferase 135 5.3.2 Sequence analysis of bchU and crtF genes 136 5.3.3 Construction and verification of a CT0028 mutant of Chl. tepidum 137 5.3.4 Pigment analysis of Chl. tepidum CT0028 (bchU) mutant 137 5.3.5 Analysis of molar extinction coefficients of BChl c and d 138 5.3.6 Growth characteristics of BChl c and BChl d strains 139 5.3.7 Competition between BChl c- and d- containing strains 139 5.4 Discussion 141 5.5 References 146 CHAPTER 6: Oxidation of the C71 position of bacteriochlorophyll e 166 Abstract 167 viii 6.1 Introduction 168 6.2 Materials and Methods 6.2.1 Genomic comparisons 170 6.2.2 Dot-blot analysis of distribution of putative BChl e- and isorenieratene-specific genes in a culture collection 170 6.2.3 Expression of genes from Pld. phaeoclathrati- forme in Chl. tepidum 170 6.2.4 Pigment analysis 171 6.3 Results 6.3.1 “In silico” subtractive hybridization 171 6.3.2 Distribution of BE1 and cruB among brown- colored species of GSB 172 6.3.3 Expression of genes from Pld. phaeoclathrati- forme in Chl. tepidum 172 6.4 Discussion 173 6.5 References 176 APPENDICES Appendix A. The biochemical basis for structural asymmetry in carotenoids. 196 Appendix B. Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. 231 Appendix C. Attempts to transform Chlorobium phaeobacteroides strain 1549 with exogenous DNA. 243 Appendix D. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat 264 Appendix E. Identification of a homoserine lactonase in Sulfolobus solfataricus 276 ix Appendix F. Complete curriculum vitae for Julia Maresca 296 x List of Tables Chapter 2. Table 2.1 Primers used Table 2.2 Protocols for HPLC analysis of pigments Chapter 3. Table 3.1 Primers used in this work Table 3.2 Plasmid combinations in E. coli strain BL21(DE3): pAC-LYC Table 3.3 Plasmid combinations in E. coli strain BL21(DE3): pAC-NEUR Chapter 4. Table 4.1 Primers used in this work Chapter 5. Table 5.1 Absorption maxima in vivo and in methanol of bacteriochlorophylls c, d, and e. Table 5.2 Primers used in this work Table 5.3 Growth rates of bacteriochlorophyll c- and d-producing strains of Chl. tepidum and Chl. vibrioforme Chapter 6. Table 6.1 Primers used in this work Table 6.2 Genes possibly specific to BChl e biosynthesis in the region around cruB in the genomes of 3 brown-colored GSB Table 6.3 Distribution of genes BE1 and cruB among green-colored and brown-colored GSB species in a culture collection xi List of Figures Chapter 1. Figure 1.1 Phylogeny of the major eubacterial taxa based on RecA sequences Figure 1.2 Phylogeny of GSB based on 16S rDNA sequences Figure 1.3 Micrograph of Chl. tepidum cells and extracellularly deposited S0 Figure 1.4 Transmission electron micrograph of Chl.
Recommended publications
  • Isolation and Characterization of Achromobacter Sp. CX2 From
    Ann Microbiol (2015) 65:1699–1707 DOI 10.1007/s13213-014-1009-6 ORIGINAL ARTICLE Isolation and characterization of Achromobacter sp. CX2 from symbiotic Cytophagales, a non-cellulolytic bacterium showing synergism with cellulolytic microbes by producing β-glucosidase Xiaoyi Chen & Ying Wang & Fan Yang & Yinbo Qu & Xianzhen Li Received: 27 August 2014 /Accepted: 24 November 2014 /Published online: 10 December 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract A Gram-negative, obligately aerobic, non- degradation by cellulase (Carpita and Gibeaut 1993). There- cellulolytic bacterium was isolated from the cellulolytic asso- fore, efficient degradation is the result of multiple activities ciation of Cytophagales. It exhibits biochemical properties working synergistically to efficiently solubilize crystalline cel- that are consistent with its classification in the genus lulose (Sánchez et al. 2004;Lietal.2009). Most known Achromobacter. Phylogenetic analysis together with the phe- cellulolytic organisms produce multiple cellulases that act syn- notypic characteristics suggest that the isolate could be a novel ergistically on native cellulose (Wilson 2008)aswellaspro- species of the genus Achromobacter and designated as CX2 (= duce some other proteins that enhance cellulose hydrolysis CGMCC 1.12675=CICC 23807). The strain CX2 is the sym- (Wang et al. 2011a, b). Synergistic cooperation of different biotic microbe of Cytophagales and produces β-glucosidase. enzymes is a prerequisite for the efficient degradation of cellu- The results showed that the non-cellulolytic Achromobacter lose (Jalak et al. 2012). Both Trichoderma reesi and Aspergillus sp. CX2 has synergistic activity with cellulolytic microbes by niger were co-cultured to increase the levels of different enzy- producing β-glucosidase.
    [Show full text]
  • Basin Geochemical Evolution of the Eagle Ford and Effects On
    BASIN GEOCHEMICAL EVOLUTION OF THE EAGLE FORD AND EFFECTS ON TRACE ELEMENT RELEASE A Thesis by IVAN MAULANA Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Chair of Committee, Michael Tice Co-chair of Committee, Bruce Herbert Committee Members, Franco Marcantonio Terry Wade Head of Department, Michael Pope May 2016 Major Subject: Geology Copyright 2016 Ivan Maulana ABSTRACT The Ocean Anoxic Event 2 (OAE-2) at the Cenomanian-Turonian boundary is recognized from a carbon isotope excursion (CIE) in the Eagle Ford (EF) Group, and commonly attributed to global anoxic conditions in deeper marine settings. Whereas OAE are typically marked by widespread deposition of organic-rich shales, previous work shows diachroneity between the CIE and the organic-rich Lower EF, as well as anoxia- euxinia in the Western Interior Seaway of North America. We found evidence for periodic photic zone euxinia from an EF core, based on ratios of biomarkers and redox-sensitive trace elements. Sedimentary structures suggest depositional environments above storm wave base. Integration with a sequence-stratigraphic framework emphasizes the role of estuarine-style salinity stratification, subject to redox shifts caused by storm mixing in relatively shallow water depths. Independent zircon ages indicate that transition from the Lower to Upper EF occurs in the south before the north, consistent with a northward migration of this stratification mechanism as sea level rose. This implies that the redox states during deposition of the EF leading up to the CIE were influenced by regionally distinct mechanisms at relatively shallow water depths, instead of global anoxic conditions in deeper marine settings.
    [Show full text]
  • Identification of Active Methylotroph Populations in an Acidic Forest Soil
    Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria.
    [Show full text]
  • Exploring Bacteria Diatom Associations Using Single-Cell
    Vol. 72: 73–88, 2014 AQUATIC MICROBIAL ECOLOGY Published online April 4 doi: 10.3354/ame01686 Aquat Microb Ecol FREEREE ACCESSCCESS Exploring bacteria–diatom associations using single-cell whole genome amplification Lydia J. Baker*, Paul F. Kemp Department of Oceanography, University of Hawai’i at Manoa, 1950 East West Road, Center for Microbial Oceanography: Research and Education (C-MORE), Honolulu, Hawai’i 96822, USA ABSTRACT: Diatoms are responsible for a large fraction of oceanic and freshwater biomass pro- duction and are critically important for sequestration of carbon to the deep ocean. As with most surfaces present in aquatic systems, bacteria colonize the exterior of diatom cells, and they inter- act with the diatom and each other. The ecology of diatoms may be better explained by conceptu- alizing them as composite organisms consisting of the host cell and its bacterial associates. Such associations could have collective properties that are not predictable from the properties of the host cell alone. Past studies of these associations have employed culture-based, whole-population methods. In contrast, we examined the composition and variability of bacterial assemblages attached to individual diatoms. Samples were collected in an oligotrophic system (Station ALOHA, 22° 45’ N, 158° 00’ W) at the deep chlorophyll maximum. Forty eukaryotic host cells were isolated by flow cytometry followed by multiple displacement amplification, including 26 Thalassiosira spp., other diatoms, dinoflagellates, coccolithophorids, and flagellates. Bacteria were identified by amplifying, cloning, and sequencing 16S rDNA using primers that select against chloroplast 16S rDNA. Bacterial sequences were recovered from 32 of 40 host cells, and from parallel samples of the free-living and particle-associated bacteria.
    [Show full text]
  • Molecular Biogeochemistry, Lecture 8
    12.158 Lecture Pigment-derived Biomarkers (1) Colour, structure, distribution and function (2) Biosynthesis (3) Nomenclature (4) Aromatic carotenoids ● Biomarkers for phototrophic sulfur bacteria ● Alternative biological sources (5) Porphyrins and maleimides Many of the figures in this lecture were kindly provided by Jochen Brocks, RSES ANU 1 Carotenoid pigments ● Carotenoids are usually yellow, orange or red coloured pigments lutein β-carotene 17 18 19 2' 2 4 6 8 3 7 9 16 1 5 lycopenelycopene 2 Structural diversity ● More than 600 different natural structures are known, ● They are derived from the C40 carotenoid lycopene by varied hydrogenation, dehydrogenation, cyclization and oxidation reaction 17 18 19 2' 2 4 6 8 3 7 9 16 1 5 lycopene neurosporene α-carotene γ -carotene spirilloxanthin siphonaxanthin canthaxanthin spheroidenone 3 Structural diversity Purple non-sulfur bacteria peridinin 7,8-didehydroastaxanthin okenone fucoxanthin Biological distribution ● Carotenoids are biosynthesized de novo by all phototrophic bacteria, eukaryotes and halophilic archaea ● They are additionally synthesized by a large variety of non-phototrophs ● Vertebrates and invertebrates have to incorporate carotenoids through the diet, but have often the capacity to structurally modifiy them 4 Carotenoid function (1) Accessory pigments in Light Harvesting Complex (LHC) (annual production by marine phytoplancton alone: 4 million tons) e.g. LH-II Red and blue: protein complex Green: chlorophyll Yellow: lycopene (2) Photoprotection (3) photoreceptors for phototropism
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Taxonomy JN869023
    Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075
    [Show full text]
  • Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
    Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively).
    [Show full text]
  • Lipidomic and Genomic Investigation of Mahoney Lake, B.C
    Lipidomic and Genomic Investigation of Mahoney Lake, B.C. The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Bovee, Roderick. 2014. Lipidomic and Genomic Investigation of Mahoney Lake, B.C.. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11745724 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Lipidomic and Genomic Investigation of Mahoney Lake, B.C. A dissertation presented by Roderick Bovee to The Department of Earth and Planetary Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Earth and Planetary Sciences Harvard University Cambridge, Massachusetts December, 2013 © 2013 – Roderick Bovee All rights reserved. Dissertation Adviser: Professor Ann Pearson Roderick Bovee Lipidomic and Genomic Investigation of Mahoney Lake, B.C. Abstract Photic-zone euxinia (PZE) is associated with several times in Earth's history including Phanerozoic extinction events and long parts of the Proterozoic. One of the best modern analogues for extreme PZE is Mahoney Lake in British Columbia, Canada where a dense layer of purple sulfur bacteria separate the oxic mixolimnion from one of the most sulfidic monimolimnions in the world. These purple sulfur bacteria are known to produce the carotenoid okenone. Okenone's diagenetic product, okenane, has potential as a biomarker for photic-zone euxinia, so understanding its production and transport is important for interpreting the geologic record.
    [Show full text]
  • This Article Was Published in an Elsevier Journal. the Attached Copy
    This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and education use, including for instruction at the author’s institution, sharing with colleagues and providing to institution administration. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 72 (2008) 1396–1414 www.elsevier.com/locate/gca Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation Jochen J. Brocks a,*, Philippe Schaeffer b a Research School of Earth Sciences and Centre for Macroevolution and Macroecology, The Australian National University, Canberra, ACT 0200, Australia b Laboratoire de Ge´ochimie Bio-organique, CNRS UMR 7177, Ecole Europe´enne de Chimie, Polyme`res et Mate´riaux, 25 rue Becquerel, 67200 Strasbourg, France Received 20 June 2007; accepted in revised form 12 December 2007; available online 23 December 2007 Abstract Carbonates of the 1640 million years (Ma) old Barney Creek Formation (BCF), McArthur Basin, Australia, contain more than 22 different C40 carotenoid derivatives including lycopane, c-carotane, b-carotane, chlorobactane, isorenieratane, b-iso- renieratane, renieratane, b-renierapurpurane, renierapurpurane and the monoaromatic carotenoid okenane.
    [Show full text]
  • Human Milk Microbiota Profiles in Relation to Birthing Method, Gestation and Infant Gender Camilla Urbaniak1,2, Michelle Angelini3, Gregory B
    Urbaniak et al. Microbiome (2016) 4:1 DOI 10.1186/s40168-015-0145-y RESEARCH Open Access Human milk microbiota profiles in relation to birthing method, gestation and infant gender Camilla Urbaniak1,2, Michelle Angelini3, Gregory B. Gloor4 and Gregor Reid1,2* Abstract Background: Human milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonate, which in turn can affect disease risk later in life. Very little is known about what factors shape the human milk microbiome. The goal of the present study was to examine the milk microbiota from a range of women who delivered vaginally or by caesarean (C) section, who gave birth to males or females, at term or preterm. Methods: Milk was collected from 39 Caucasian Canadian women, and microbial profiles were analyzed by 16S ribosomal RNA (rRNA) sequencing using the Illumina platform. Results: A diverse community of milk bacteria was found with the most dominant phyla being Proteobacteria and Firmicutes and at the genus level, Staphylococcus, Pseudomonas, Streptococcus and Lactobacillus. Comparison of bacterial profiles between preterm and term births, C section (elective and non-elective) and vaginal deliveries, and male and female infants showed no statistically significant differences. Conclusions: The study revealed the diverse bacterial types transferred to newborns. We postulate that there may be a fail-safe mechanism whereby the mother is “ready” to pass along her bacterial imprint irrespective of when and how the baby is born. Keywords: Human milk, Milk microbiota, Factors affecting the milk microbiota Background levels of Bifidobacterium in human milk correlate with With the incidence of various non-infectious diseases on low levels of Bifidobacterium in the neonatal gut [3], the rise, there is much interest in the developmental ori- allowing for higher than normal levels of Bacteroides to gins of health and disease and the potential role of early be established [4].
    [Show full text]
  • Microbial Diversity of Soda Lake Habitats
    Microbial Diversity of Soda Lake Habitats Von der Gemeinsamen Naturwissenschaftlichen Fakultät der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Susanne Baumgarte aus Fritzlar 1. Referent: Prof. Dr. K. N. Timmis 2. Referent: Prof. Dr. E. Stackebrandt eingereicht am: 26.08.2002 mündliche Prüfung (Disputation) am: 10.01.2003 2003 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Gemeinsamen Naturwissenschaftlichen Fakultät, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Baumgarte, S., Moore, E. R. & Tindall, B. J. (2001). Re-examining the 16S rDNA sequence of Halomonas salina. International Journal of Systematic and Evolutionary Microbiology 51: 51-53. Tagungsbeiträge Baumgarte, S., Mau, M., Bennasar, A., Moore, E. R., Tindall, B. J. & Timmis, K. N. (1999). Archaeal diversity in soda lake habitats. (Vortrag). Jahrestagung der VAAM, Göttingen. Baumgarte, S., Tindall, B. J., Mau, M., Bennasar, A., Timmis, K. N. & Moore, E. R. (1998). Bacterial and archaeal diversity in an African soda lake. (Poster). Körber Symposium on Molecular and Microsensor Studies of Microbial Communities, Bremen. II Contents 1. Introduction............................................................................................................... 1 1.1. The soda lake environment .................................................................................
    [Show full text]