DOCSLIB.ORG

KEGG Orthology-Based Annotation of the Predicted

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
KEGG Orthology-Based Annotation of the Predicted Dunlap et al. BMC Genomics 2013, 14:509 http://www.biomedcentral.com/1471-2164/14/509 DATABASE Open Access KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome Walter C Dunlap1,2, Antonio Starcevic4, Damir Baranasic4, Janko Diminic4, Jurica Zucko4, Ranko Gacesa4, Madeleine JH van Oppen1, Daslav Hranueli4, John Cullum5 and Paul F Long2,3* Abstract Background: Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. Description: Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. Conclusions: We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives. Keywords: Acropora digitifera, KEGG orthology, Database, Annotation, Proteome, Genome, Coral, Symbiosis, Cnidaria * Correspondence: [email protected] 2Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom 3Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom Full list of author information is available at the end of the article © 2013 Dunlap et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Dunlap et al. BMC Genomics 2013, 14:509 Page 2 of 59 http://www.biomedcentral.com/1471-2164/14/509 Background estimate levels of mRNA expression, and by direct analysis All of the reef-building corals (Scleractinia; phylum using next-generation, high-throughput sequencing. How- Cnidaria) that create the vast calcium carbonate de- ever, much of this work has been conducted using the posits of coral reefs have evolved an endosymbiotic aposymbiotic state of pre-settlement coral larvae, so partnership with photosynthetic dinoflagellates of the transcribed genes relevant to metamorphosis and the genus Symbiodinium (Dinophyceae), commonly known cytobiology of the adult polyp are limited to a few recent as zooxanthellae, which reside within the gastrodermal studies [33-36]. The transcriptome additionally does not cells of their scleractinian host [1-3]. Coral-algal symbiosis provide the structural framework and essential regulatory is a cooperative metabolic adaptation necessary for sur- elements of the functional genome for comprehensive vival in the shallow oligotrophic (nutrient-poor) waters of evaluation. Recently, deep metatranscriptomic sequencing tropical and subtropical marine environments [4,5] that of two adult coral holobiomes has been made available drives the productivity of coral reefs [6]. Coral reefs pro- on searchable databases: PocilloporaBase for Pocillopora vide habitat and trophic support for many thousands of damicornis [36] and PcarnBase for Platygyra carnosus marine species, the richness of which rival the biological [37]. In contrast, high-throughput metaproteomic analyses biodiversity of tropical rainforests [7]. Underlying the basic to quantify the product yield of stress-response genes of requirements of corals for growth, reproduction and sur- the coral holobiome are yet to be widely adopted by the vival are special needs to accommodate symbiont-specific coral reef scientific community, despite the proteome be- host recognition, to control innate and responsive im- ing the ultimate measure of the coral phenotype [38,39]. mune systems, and what is likely to emerge from future The early accumulation of transcriptomic data revealed research is the extent to which the host is involved in that a small proportion of coral ESTs matched genes direct regulation of its endosymbiont populations. known previously only from other kingdoms of life, imply- Much is understood about the cellular biology of ing that the ancestral animal genome contained many cnidarian-dinoflagellate symbiosis (reviewed in [8]), genes traditionally regarded as ‘non-animal’ that have been but less is known at the molecular level of coral symbiology. lost from most animal genomes [40]. Furthermore, an un- There is little opposition to the contention that envi- expected revelation from EST data is the greater extent to ronmental and anthropogenic disturbances are causing which coral sequences resemble human genes than those alarming losses to coral reefs ([9] and reference therein). of the Drosophila and Caenorhabditis model invertebrate Threats to productivity are being imposed by the disruption genomes [41,42]. Comparative genomic analysis has of coral symbiosis (apparent as “coral bleaching”)causedin revealed higher genetic divergence and massive gene loss response to increasing thermal stress attributed to global within the ecdysozoan lineages. Hence, many genes warming [10,11], from an increase in stress-related coral assumed to have much later evolutionary origins are likely disease [12-14], from the discharge of domestic and indus- to have been present in an ancestral or early-diverged trial wastes, pollutants from agricultural development and metazoan [43]. While much of the animal kingdom the transport of sediments in terrestrial runoff [15,16], and remains yet to be explored, examples of the metazoan potentially from imminent declines in coral calcification phylum Cnidaria provide a unique insight into the deep owing to rising ocean acidification [17-19]. Accordingly, we evolutionary origins of at least some vertebrate gene fa- requireabetterunderstandingofthemolecularstressre- milies [42]. Thus, the complete genomic sequence of a sponses and adaptive potential of corals. Such information coral is likely to reveal many genes previously assumed to is necessary to predict bleaching events and so better in- be strictly vertebrate innovations. To date, cnidarian ge- form effective management policies for the conservation of nomes have been published for the sea anemone N. coral reef ecosystems [20-24]. vectensis [42] and the hydroid Hydra magnipapillata [44]. To understand how coral holobionts respond to envi- Only the coral genome of Acropora digitifera is available ronmental change at the molecular level, the identification without restriction on use of its published sequence [45], of genes that may respond by transcription to stress is of but the compiled sequence has not been fully annotated. primary importance [25]. Thus, the use of transcriptomic At the time of this writing, the genome assembly of methodologies to identify stress-responsive genes has been Acropora millepora has been released to the public do- highly successful [26-32]. Transcriptome high-throughput main [46], also without full annotation, but an embargo is profiling has allowed changes in gene expression across imposed on use of this data that is highly restrictive to the thousands of genes to be measured simultaneously. Fuel- progress of further studies. Understanding how genomic led by data-generating power, the number of coral based variation affects molecular and organismal biology is the studies utilising transcriptomics to investigate molecular ultimate justification of genome sequencing, and annota- responses to environmental stressors has expanded greatly tion is an essential step in this process. We envisage that by the acquisition of expressed sequence tag (EST) gene li- unrestricted access to annotation of the A. digitifera gen- braries, the fabrication of microarray biochips used to ome will provide an unprecedented foundation to freely Dunlap et al. BMC Genomics 2013, 14:509 Page 3 of 59 http://www.biomedcentral.com/1471-2164/14/509 interrogatethegenericmolecularstructure,possible
Load more

Recommended publications
  • WO 2018/009838 Al 11 January 2018 (11.01.2018) W !P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/009838 Al 11 January 2018 (11.01.2018) W !P O PCT (51) International Patent Classification: Declarations under Rule 4.17: C12N 5/075 (2010.01) — as to applicant's entitlement to apply for and be granted a (21) International Application Number: patent (Rule 4.1 7(H)) PCT/US2017/041 155 — as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(Hi)) (22) International Filing Date: 07 July 2017 (07.07.2017) Published: — with international search report (Art. 21(3)) (25) Filing Language: English — before the expiration of the time limit for amending the (26) Publication Langi English claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (30) Priority Data: — with sequence listing part of description (Rule 5.2(a)) 62/359,416 07 July 2016 (07.07.2016) US (71) Applicant: RUBIUS THERAPEUTICS, INC. [US/US]; 620 Memorial Dr #100W, Cambridge, MA 02139 (US). (72) Inventors; and (71) Applicants: HARANDI, Omid [US/US]; 39 Rowena Road, Newton, MA 02459 (US). KHANWALKAR, Ur- jeet [IN/US]; 2 11 Elm Street, Apt. 3, Cambridge, MA 02139 (US). HARIHARAN, Sneha [IN/US]; 18 Hamilton Road, Apt. 407, Arlington, MA 02472 (US). (72) Inventors: KAHVEJIAN, Avak; 2 Beverly Road, Arling ton, MA 02474 (US). MATA-FINK, Jordi; 8 Windsor Rd #1, Somerville, MA 02144 (US).DEANS, Robert, J.; 1609 Ramsgate Court, Riverside, CA 92506 (US).
    [Show full text]
  • Chapter 5 High-Pressure Stopped-Flow Kinetic Studies of Nnos
    Probing the dynamics and conformational landscape of neuronal nitric oxide synthase A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2013 Anna Sobolewska-Stawiarz Contents Contents ...................................................................................................................... 2 List of Figures ............................................................................................................. 6 List of Tables ............................................................................................................ 10 Abstract ..................................................................................................................... 12 Declaration ................................................................................................................ 13 Copyright Statement ................................................................................................ 13 Acknowledgements ................................................................................................... 14 List of Abbreviations ............................................................................................... 15 List of Amino Acids Abbreviations ........................................................................ 17 CHAPTER 1. INTRODUCTION ........................................................................... 18 1.1 Nitric oxide synthase .........................................................................................
    [Show full text]
  • Protein S-Nitrosylation: Methods of Detection and Cellular Regulation
    Protein S-Nitrosylation: Methods of Detection and Cellular Regulation by Michael Tcheupdjian Forrester Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Jonathan S. Stamler, MD (Supervisor) ___________________________ Irwin Fridovich, PhD ___________________________ K. V. Rajagopalan, PhD ___________________________ Dennis J. Thiele, PhD ___________________________ Eric J. Toone, PhD Dissertation submitted in partial fulfillment of the requirements for the degree of doctor of philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 i v ABSTRACT Protein S-Nitrosylation: Methods of Detection and Cellular Regulation by Michael Tcheupdjian Forrester Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Jonathan S. Stamler, MD (Supervisor) ___________________________ Irwin Fridovich, PhD ___________________________ K. V. Rajagopalan, PhD ___________________________ Dennis J. Thiele, PhD ___________________________ Eric J. Toone, PhD An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of doctor of philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 i v Copyright by Michael T. Forrester 2009 Abstract Protein S-nitrosylation—the post-translational modification of cysteine thiols into S-nitrosothiols—is a principle mechanism of nitric oxide-based signaling. Studies have demonstrated myriad roles for S-nitrosylation in organisms from bacteria to humans, and recent efforts have begun to elucidate how this redox-based modification is regulated during physiological and pathophysiological conditions. This doctoral thesis is focused on the 1) analysis of existing methodologies for the detection of protein S-nitrosylation; 2) development of new methodologies for the detection of protein S-nitrosylation and 3) discovery of novel enzymatic mechanisms by which S-nitrosylation is regulated in vivo.
    [Show full text]
  • Rhodococcus Jostii Strain 8
    Functional characterisation of alkane-degrading monooxygenases in Rhodococcus jostii strain 8 Jindarat Ekprasert A thesis submitted to the School of Environmental Sciences in fulfilment of the requirements for the degree of Doctor of Philosophy September 2014 University of East Anglia Norwich, UK i Contents List of figures viii List of tables xiii Declaration xv Acknowledgements xvi Abbreviations xvii Abstract xxi Chapter 1 introduction 1 1.1. Significance of alkanes in the environment 2 1.1.1. Chemistry of alkanes 2 1.2. The Rhodococcus genus 3 1.2.1. Common characteristics of Rhodococcus spp. 3 1.2.2. Rhodococcus spp. are capable of degrading gaseous alkanes 4 1.2.3. Potential applications of Rhodococcus in biotechnology 5 1.3. Bacterial enzymes responsible for alkane degradation 6 1.3.1. Integral membrane, non-heme iron alkane hydroxylases (AlkB) 6 1.3.2. Soluble di-iron monooxygenases (SDIMO) 8 1.3.2.1. SDIMO classification 10 1.3.2.2. Molecular genetics of SDIMOs 13 1.3.2.3. Mutagenesis of soluble methane monooxygenase 13 1.3.3. Cytochrome P450 alkane hydroxylases 14 3.3.1. Class I P450 14 3.3.2. Class II P450 (CYP52) 15 3.3.3. Class II P450 (CYP2E, CYP4B) 15 1.3.4. Membrane bound copper-containing (and possibly iron-containing) monooxygenases 15 1.4. Alkane metabolisms in Rhodococcus spp. 16 1.4.1. Aerobic metabolism of C2-C4 gaseous alkanes in bacteria 16 1.4.1.1. Ethane (C2H6) metabolism 16 1.4.1.2. Propane (C3H8) metabolism 17 ii 1.4.1.3.
    [Show full text]
  • Biochemical and Cellular Studies of Vertebrate Globins
    Biochemical and Cellular Studies of Vertebrate Globins By Shun Wilford Tse Thesis submitted for the degree of Doctor of Philosophy School of Biological Sciences University of East Anglia September 2015 © This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that no quotations from the thesis, nor any information derived there-from may be published without the author's prior, written consent. Abstract Human cytoglobin is a small heme-containing protein in the globin superfamily with a wide range of tissue and organ distribution. Although several cellular functions have been proposed for cytoglobin, the exact physiological function is still not fully defined. Recently, cytoglobin has been implicated to have a regulatory role in cancer cells to control cell proliferation and migration depending on cellular oxygen level. In order to gain a better understanding of a structure-to-function relationship of cytoglobin as a heme-protein and to evaluate its possible physiological function(s) in cancer cells, a combination of techniques, including protein engineering and advanced spectroscopies, was deployed. In this study, recombinant human cytoglobin purified from E.coli was purified as a monomeric protein, but displayed a dimeric property in solution. An intra-molecular disulphide bond is formed within the protein which has a redox potential at ca -280 mV. Advanced spectroscopic studies confirmed a low-spin bis-histidyl heme in cytoglobin in both ferric and ferrous state regardless of the state of the disulphide bond. Furthermore, nitrite reductase activitiy in globins was investigated in detail using myoglobin as a model to explore the biochemical basis of the distal histidine residue in determining activity.
    [Show full text]
  • Nitric Oxide Dioxygenase: an Enzymic Function for Flavohemoglobin
    Proc. Natl. Acad. Sci. USA Vol. 95, pp. 10378–10383, September 1998 Biochemistry Nitric oxide dioxygenase: An enzymic function for flavohemoglobin PAUL R. GARDNER*, ANNE M. GARDNER,LORI A. MARTIN, AND ANDREW L. SALZMAN Division of Critical Care Medicine, Children’s Hospital Medical Center, and Department of Pediatrics, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229 Communicated by Irwin Fridovich, Duke University Medical Center, Durham, NC, July 7, 1998 (received for review June 9, 1998) ABSTRACT Nitric oxide (NO•) is a toxin, and various life Moreover, this aerobic cyanide-sensitive NO• consumption forms appear to have evolved strategies for its detoxification. activity appeared to constitute part of an adaptive defense NO•-resistant mutants of Escherichia coli were isolated that against NO• toxicity. Thus, we supposed that E. coli mutants rapidly consumed NO•.AnNO•-converting activity was re- containing elevated activity might be selected for resistance to • constituted in extracts that required NADPH, FAD, and O2, 2 NO -mediated killing, and furthermore, that they could be was cyanide-sensitive, and produced NO3 . This nitric oxide used to facilitate the biochemical and genetic characterization dioxygenase (NOD) contained 19 of 20 N-terminal amino of the NO• scavenging activity. acids identical to those of the E. coli flavohemoglobin. Fur- Here, we describe the isolation and characterization of an thermore, NOD activity was produced by the flavohemoglobin O2-dependent and cyanide-sensitive nitric oxide dioxygenase gene and was inducible by NO•. FlavohemoglobinyNOD- (NOD) from NO•-resistant E. coli, which is a flavohemoglo- deficient mutants were also sensitive to growth inhibition by bin. The identification of NOD with flavohemoglobin is sig- gaseous NO•.
    [Show full text]
  • Current Advances of Nitric Oxide in Cancer and Anticancer Therapeutics
    Review Current Advances of Nitric Oxide in Cancer and Anticancer Therapeutics Joel Mintz 1,†, Anastasia Vedenko 2,†, Omar Rosete 3 , Khushi Shah 4, Gabriella Goldstein 5 , Joshua M. Hare 2,6,7 , Ranjith Ramasamy 3,6,* and Himanshu Arora 2,3,6,* 1 Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL 33328, USA; [email protected] 2 John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; [email protected] (A.V.); [email protected] (J.M.H.) 3 Department of Urology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; [email protected] 4 College of Arts and Sciences, University of Miami, Miami, FL 33146, USA; [email protected] 5 College of Health Professions and Sciences, University of Central Florida, Orlando, FL 32816, USA; [email protected] 6 The Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA 7 Department of Medicine, Cardiology Division, Miller School of Medicine, University of Miami, Miami, FL 33136, USA * Correspondence: [email protected] (R.R.); [email protected] (H.A.) † These authors contributed equally to this work. Abstract: Nitric oxide (NO) is a short-lived, ubiquitous signaling molecule that affects numerous critical functions in the body. There are markedly conflicting findings in the literature regarding the bimodal effects of NO in carcinogenesis and tumor progression, which has important consequences for treatment. Several preclinical and clinical studies have suggested that both pro- and antitumori- Citation: Mintz, J.; Vedenko, A.; genic effects of NO depend on multiple aspects, including, but not limited to, tissue of generation, the Rosete, O.; Shah, K.; Goldstein, G.; level of production, the oxidative/reductive (redox) environment in which this radical is generated, Hare, J.M; Ramasamy, R.; Arora, H.
    [Show full text]
  • The Hydrozoan Coral Millepora Dichotoma: Speciation Or Phenotypic Plasticity?
    Marine Biology (2003) 143: 1175–1183 DOI 10.1007/s00227-003-1135-3 Efrat Meroz-Fine Æ Itzchak Brickner Æ Yossi Loya Micha Ilan The hydrozoan coral Millepora dichotoma: speciation or phenotypic plasticity? Received: 31 January 2003 / Accepted: 14 May 2003 / Published online: 26 August 2003 Ó Springer-Verlag 2003 Abstract This article describes ecological and biological biological and molecular data thus attest to the two differences between two morphs of the Red Sea fire coral morphs being distinguishable. Contrary to previous re- Millepora dichotoma. The species is divided into two ports, we consequently suggest that the two morphs of main morphs: branching and encrusting, which were M. dichotoma found in the Gulf of Elat are actually two found to differ both in color and morphology. Each distinct species. morph has two or more sub-morphs. A total of 372 M. dichotoma colonies were examined in a census at two study sites in the Gulf of Elat. Colony size and abun- Introduction dance of the two morphs were found to differ signifi- cantly between sites. Experimental examination of each Hydrozoan corals of the genus Millepora are among the morph’s morphological plasticity revealed different major contributors of calcium carbonate skeletons on growth rates and difference in growth plasticity between coral reefs (Edmunds 1999). Wide variability in colony the branching and the encrusting morph. Most of the morphology of Millepora has traditionally been viewed fragments from the branching colonies (94%) attached as a phenotypic response to variation in environmental to experimentally placed Plexiglas substrate, compared conditions (de Weerdt 1981, 1984; Lewis 1989; Vago with much less attachment by the encrusting fragments et al.
    [Show full text]
  • Modelling of the Melissa Artificial Ecosystem
    ESTEC/CONTRACT 8125/88/NL/‘FG PRF 141315 Modelling of the MELiSSA artificial ecosystem Toward a structured model of the nitrifying compartment - Description of the respiratory chain of nitrifying organisms - Development of assumptions for the reverse electron flow in the respiratory electron transport chain - Stoichiometric description of the nitrification - Determination of KL~ for oxygen transfer limitation TECHNICAL NOTE 23.2 L. Poughon Laboratoire de Genie Chimique Biologique 63177 AUBIERE Cedex, FRANCE April 1995 Technical note 23.2 Toward a structured model of the nitrifying compartment T.N. 23.2: Modelling of the MELiSSA artificial ecosystem TOWARD A STRUCl-URJZD MODEL OF THE NITRIFYING COMPARTMENT L. Poughon. Laboratoire de Genie Chimique Biologique 63177 AUBIERE Cedex. France. INTRODUCTION In the MELiSSA loop the nitrifying compartment has the same function than the nitrifying process in the terrestrial ecosystem (figure 1) which is to provide an edible N-source for plants or micro-organisms (as Spirulines in the case of the MELiSSA loop). The ammoniflcation processes from organic waste (as for example the human waste faeces and urea) are performed in the MELiSSA loop by the 2 first compartments (liquefying and anoxygenic phototrophs compartments). It must be noted that there are some structural differences between the MELiSSA N-loop and the terrestrial ecosystem: l- the MELiSSA loop represent a very simplified part of the N loop encountered on earth; 2- the denitrification process (N mineral -> N2) or the N2 removing (N2 -> N mineral) are not considered 3- the sole N - source is N03- for Spirulina, it is NlQ+ for phototrophs and it is organic N for the crew.
    [Show full text]
  • Relating Metatranscriptomic Profiles to the Micropollutant
    1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles.
    [Show full text]
  • Comparison of Physiology and Genome-Wide Expression in Two Nitrosomonas Spp
    Comparison of physiology and genome-wide expression in two Nitrosomonas spp. under batch cultivation By Mohammad Ghashghavi A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science In Microbiology and Biotechnology Department of Biological Sciences University of Alberta © Mohammad Ghashghavi, 2014 Abstract: Ammonia oxidizing bacteria (AOB) play a central role in the nitrogen cycle by oxidizing ammonia to nitrite. Nitrosomonas europaea ATCC 19718 has been the single most studied AOB that has contributed to our understanding of chemolithotrophic ammonia oxidation. As a closely related species, Nitrosomonas eutropha C91 has also been extensively studied. Both of these bacteria are involved in wastewater treatment systems and play a crucial part in major losses of ammonium-based fertilizers globally. Although comparative genome analysis studies have been done before, change in genome-wide expression between closely related organisms are scarce. In this study, we compared these two organisms through physiology and transcriptomic experiments during exponential and early stationary growth phase. We found that under batch cultivation, N. europaea produces more N2O while N. eutropha consumes more nitrite. From transcriptomic analysis, we also found that there are selections of motility genes that are highly expressed in N. eutropha during early stationary growth phase and such observation was completely absent in N. europaea. Lastly, principle homologous genes that have been well studied had different patterns of expression in these strains. This study not only gives us a better understanding regarding physiology and genome-wide expression of these two AOB, it also opens a wide array of opportunities to further our knowledge in understanding other closely related species with regards to their evolution, physiology and niche preference.
    [Show full text]
  • Comparative Studies of the Venom of a New Taipan Species, Oxyuranus Temporalis, with Other Members of Its Genus
    Toxins 2014, 6, 1979-1995; doi:10.3390/toxins6071979 OPEN ACCESS toxins ISSN 2072-6651 www.mdpi.com/journal/toxins Article Comparative Studies of the Venom of a New Taipan Species, Oxyuranus temporalis, with Other Members of Its Genus Carmel M. Barber 1, Frank Madaras 2, Richard K. Turnbull 3, Terry Morley 4, Nathan Dunstan 5, Luke Allen 5, Tim Kuchel 3, Peter Mirtschin 2 and Wayne C. Hodgson 1,* 1 Monash Venom Group, Department of Pharmacology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3168, Australia; E-Mail: [email protected] 2 Venom Science Pty Ltd, Tanunda, South Australia 5352, Australia; E-Mails: [email protected] (F.M.); [email protected] (P.M.) 3 SA Pathology, IMVS Veterinary Services, Gilles Plains, South Australia 5086, Australia; E-Mails: [email protected] (R.K.T.); [email protected] (T.K.) 4 Adelaide Zoo, Adelaide, South Australia 5000, Australia; E-Mail: [email protected] 5 Venom Supplies, Tanunda, South Australia, South Australia 5352, Australia; E-Mails: [email protected] (N.D.); [email protected] (L.A.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +61-3-9905-4861; Fax: +61-3-9905-2547. Received: 5 May 2014; in revised form: 11 June 2014 / Accepted: 16 June 2014 / Published: 2 July 2014 Abstract: Taipans are highly venomous Australo-Papuan elapids. A new species of taipan, the Western Desert Taipan (Oxyuranus temporalis), has been discovered with two specimens housed in captivity at the Adelaide Zoo. This study is the first investigation of O.
    [Show full text]