Exploring Polar Microbiomes As Source of Bioactive Molecules
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The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil
THE ROLE OF EARTHWORM GUT-ASSOCIATED MICROORGANISMS IN THE FATE OF PRIONS IN SOIL Von der Fakultät für Lebenswissenschaften 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 Taras Jur’evič Nechitaylo aus Krasnodar, Russland 2 Acknowledgement I would like to thank Prof. Dr. Kenneth N. Timmis for his guidance in the work and help. I thank Peter N. Golyshin for patience and strong support on this way. Many thanks to my other colleagues, which also taught me and made the life in the lab and studies easy: Manuel Ferrer, Alex Neef, Angelika Arnscheidt, Olga Golyshina, Tanja Chernikova, Christoph Gertler, Agnes Waliczek, Britta Scheithauer, Julia Sabirova, Oleg Kotsurbenko, and other wonderful labmates. I am also grateful to Michail Yakimov and Vitor Martins dos Santos for useful discussions and suggestions. I am very obliged to my family: my parents and my brother, my parents on low and of course to my wife, which made all of their best to support me. 3 Summary.....................................................………………………………………………... 5 1. Introduction...........................................................................................................……... 7 Prion diseases: early hypotheses...………...………………..........…......…......……….. 7 The basics of the prion concept………………………………………………….……... 8 Putative prion dissemination pathways………………………………………….……... 10 Earthworms: a putative factor of the dissemination of TSE infectivity in soil?.………. 11 Objectives of the study…………………………………………………………………. 16 2. Materials and Methods.............................…......................................................……….. 17 2.1 Sampling and general experimental design..................................................………. 17 2.2 Fluorescence in situ Hybridization (FISH)………..……………………….………. 18 2.2.1 FISH with soil, intestine, and casts samples…………………………….……... 18 Isolation of cells from environmental samples…………………………….………. -
Bacillus Pycnus Spa Nov. and Bacillus Neidei Spa Nov., Round-Spored
674 International Journal ofSystematic and Evolutionary Microbiology (2002),52,501-505 DOl: 10.1099/ijs.0.01836-0 Bacillus pycnus Spa nov. and Bacillus neidei Spa NOTE nov., round-spored bacteria from soil 1 Microbial Properties L. K. Nakamura,1 O. Shida/ H. Takagi2 and K. Komagata3 Research Unit, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, Author for correspondence: L K. Nakamura. Tel: + 13096816395. Fax: + 13096816672. IL 61604, USA e-mail: nakamulki"mail.ncaur.usda.gov 2 Research Laboratory, Higeta Shoyu Co. Ltd, Bacillus sphaericus sensu lato currently consists of seven or more groups of Choshi, Chiba 288, Japan unrelated taxa, one of which is B. sphaericus sensu stricto and another of 3 Department of which is Bacillus fusiformis. Members of two groups (groups 6 and 7), in Agricultural Chemistry, Tokyo University of common with all other B. sphaericus-like organisms, are unable to grow Agriculture, Setagaya-ku, anaerobically or to use common hexoses, pentoses and hexitols as sources of Tokyo 156, Japan carbon, have G+C contents of 34-36 mol % and form round spores. Groups 6 and 7 can be differentiated from other B. sphaericus-like organisms by low DNA relatedness and by variations in whole-cell fatty acid composition. Unique characteristics of group 6 include the ability to oxidize fi-hydroxybutyrate, the non-requirement for biotin and thiamin and failure to grow in 5 % NaCI. Distinctive traits of group 7 include the inability to oxidize pyruvate and a requirement for biotin, thiamin and cystine for growth. These data show that groups 6 and 7 represent two novel species, for which the names Bacillus pycnus sp. -
Universidade Federal Do Pampa Campus São Gabriel Programa De Pós-Graduação Stricto Sensu Em Ciências Biológicas
UNIVERSIDADE FEDERAL DO PAMPA CAMPUS SÃO GABRIEL PROGRAMA DE PÓS-GRADUAÇÃO STRICTO SENSU EM CIÊNCIAS BIOLÓGICAS PABULO HENRIQUE RAMPELOTTO SEQUENCIAMENTO POR ION TORRENT REVELA PADRÕES DE INTERAÇÃO E DISTRIBUIÇÃO DE COMUNIDADES MICROBIANAS EM UM PERFIL DE SOLO ORNITOGÊNICO DA ILHA SEYMOUR, PENÍNSULA ANTÁRTICA SÃO GABRIEL, RS, BRASIL. 2014 PABULO HENRIQUE RAMPELOTTO SEQUENCIAMENTO POR ION TORRENT REVELA PADRÕES DE INTERAÇÃO E DISTRIBUIÇÃO DE COMUNIDADES MICROBIANAS EM UM PERFIL DE SOLO ORNITOGÊNICO DA ILHA SEYMOUR, PENÍNSULA ANTÁRTICA Dissertação apresentada ao programa de Pós- Graduação Stricto Sensu em Ciências Biológicas da Universidade Federal do Pampa, como requisito parcial para obtenção do Título de Mestre em Ciências Biológicas. Orientador: Prof. Dr. Luiz Fernando Wurdig Roesch São Gabriel 2014 AGRADECIMENTOS À Universidade Federal do Pampa e ao Programa de Pós-Graduação em Ciências Biológicas, por minha formação profissional. Ao Prof. Luiz Fernando Wurdig Roesch, pela orientação durante estes dois anos de mestrado. Ao Prof. Antônio Batista Pereira pela coleta do material durante a XXX Operação Antártica Brasileira (OPERANTAR). À FAPERGS/CAPES, pela concessão da bolsa. RESUMO Neste estudo, foram analisadas e comparadas comunidades bacterianas do solo de uma pinguineira da Ilha Seymour (Península Antártica) em termos de abundância, estrutura, diversidade e rede de interações, a fim de se identificar padrões de interação entre os vários grupos de bactérias presentes em solos ornitogênicos em diferentes profundidades (camadas). A análise das sequências revelou a presença de oito filos distribuídos em diferentes proporções entre as Camadas 1 (0-8 cm), 2 (20-25 cm) e 3 (35-40 cm). De acordo com os índices de diversidade, a Camada 3 apresentou os maiores valores de riqueza, diversidade e uniformidade quando comparado com as Camadas 1 e 2. -
Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
Kocuria (Micrococcus) and Cultivation Methods for Their Detection – Part 1
Kvasny Prum. 10 64 / 2018 (1) Brewing Microbiology – Kocuria (Micrococcus) and Cultivation Methods for their Detection – Part 1 DOI: 10.18832/kp201804 Brewing Microbiology – Kocuria (Micrococcus) and Cultivation Methods for their Detection – Part 1 Mikrobiologie pivovarské výroby – bakterie Kocuria (Micrococcus) a kultivační metody pro jejich detekci – 1. část Dagmar MATOULKOVÁ, Petra KUBIZNIAKOVÁ Mikrobiologické oddělení, Výzkumný ústav pivovarský a sladařský, a.s., / Department of Microbiology, Research Institute of Brewing and Malting, PLC, Lípová 15, 120 44 Prague, e-mail: [email protected], [email protected] Recenzovaný článek / Reviewed Paper Matoulková, D., Kubizniaková, P., 2018: Brewing microbiology – Kocuria (Micrococcus) and cultivation methods for their detection – Part 1. Kvasny Prum. 64(1): 10–13 Signifi cant brewery species of micrococcus were reclassifi ed to the genus Kocuria: Kocuria kristinae (previously Micrococcus kristinae) and Kocuria varians (previously Micrococcus varians). Bacteria of genus Kocuria belong to less risky microbial contaminants of beer and brewery plant. Species Kocuria kristinae may exceptionally cause beer spoilage. Signifi cant is their misplacement for pediococci. Here we present an overview of basic morphological and physiological properties of Kocuria (Micrococcus) species and describe their harmfulness in the brewing process. Matoulková, D., Kubizniaková, P., 2018: Mikrobiologie pivovarské výroby – bakterie Kocuria (Micrococcus) a kultivační metody pro jejich detekci – 1. část. Kvasny Prum. 64(1): 10–13 Pivovarsky významné druhy mikrokoků byly reklasifi kovány do rodu Kocuria: Kocuria kristinae (dříve Micrococcus kristinae) a Kocuria varians (dříve Micrococcus varians). Bakterie rodu Kocuria patří k méně rizikovým mikrobiálním kontaminacím piva a pivovarského pro- vozu. Výjimečně může být druh Kocuria kristinae původcem kažení piva. Význam těchto bakterií spočívá zejména v možnosti záměny s pediokoky. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Product Sheet Info
Product Information Sheet for HM-331 Sporosarcina sp., Strain 2681 Incubation: Temperature: 37°C Atmosphere: Aerobic Catalog No. HM-331 Propagation: 1. Keep vial frozen until ready for use, then thaw. For research use only. Not for human use. 2. Transfer the entire thawed aliquot into a single tube of broth. Contributor: 3. Use several drops of the suspension to inoculate an Kimberlee A. Musser, Ph.D., Chief, Bacterial Diseases, agar slant and/or plate. Division of Infectious Diseases, Wadsworth Center, New York 4. Incubate the tubes and plate at 37°C for 48 hours. State Department of Health, Albany, New York Citation: Manufacturer: NIH Biodefense and Emerging Infections Acknowledgment for publications should read “The following reagent was obtained through the NIH Biodefense and Research Resource Repository Emerging Infections Research Resources Repository, NIAID, NIH as part of the Human Microbiome Project: Sporosarcina Product Description: sp., Strain 2681, HM-331.” Bacteria Classification: Planococcaceae, Sporosarcina Species: Sporosarcina sp. Biosafety Level: 2 Strain: 2681 Original Source: Sporosarcina sp., strain 2681 was isolated Appropriate safety procedures should always be used with 1 this material. Laboratory safety is discussed in the following from human blood. Comments: Sporosarcina sp., strain 2681 is a reference publication: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and genome for The Human Microbiome Project (HMP). HMP Prevention, and National Institutes of Health. Biosafety in is an initiative to identify and characterize human microbial flora. The complete genome of Sporosarcina sp., strain Microbiological and Biomedical Laboratories. 5th ed. Washington, DC: U.S. Government Printing Office, 2007; see 2681 is currently being sequenced at the Human Genome www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm. -
Characterization of Pasteurized Fluid Milk Shelf-Life Attributes H.I
JFS M: Food Microbiology and Safety Characterization of Pasteurized Fluid Milk Shelf-life Attributes H.I. FROMM AND K.J. BOOR ABSTRACT: Pasteurized fluid milk samples were systematically collected from 3 commercial dairy plants. Samples were evaluated for microbial, chemical, and sensory attributes throughout shelf life. In general, product shelf lives were limited by multiplication of heat-resistant psychrotrophic organisms that caused undesirable flavors in milk. The predominant microorganisms identified were Gram-positive rods including Paenibacillus, Bacillus, and Mi- crobacterium. Principal component analysis of sensory data collected using quantitative descriptive analysis showed that attributes related to milk flavor defects explained the largest amount of variance. These findings highlight the need to develop specific strategies for excluding bacterial contaminants from milk to further extend product shelf lives. Keywords: shelf life, fluid milk, spoilage, quantitative descriptive analysis, principal component analysis Introduction teurization contamination has been controlled and longer product er capita consumption of fluid milk in the United States has shelf lives are expected (Champagne and others 1994; Ralyea and Pdecreased steadily over the past 30 years (ERS/USDA 2001). others 1998). These Gram-positive organisms can be present in raw Highly perishable fluid milk products must compete in the market- milk, but they also may enter milk products at various points during place against shelf-stable beverages that have captured a large pro- production and processing (Griffiths and Phillips 1990; Schraft and portion of the beverage market in recent years (IDFA 2003). Extend- others 1996; Svensson and others 1999). Further extension of prod- ing fluid milk shelf life may enable processors to maintain a uct shelf lives will require elimination of these heat-resistant, Gram- competitive position in the beverage market by facilitating the pro- positive contaminants. -
Identification of 129 Micrococcaceae Strains Isolated from Food of Animal Origin C
Identification of 129 Micrococcaceae strains isolated from food of animal origin C. Delarras, C. Guichaoua and M.-P. Caprais Code words: Staphylococcus- nitrofurantoin- aurease- ID 32 STAPH Tab. 1: List of 26 biochemical tests in the ID 32 STAPH-system - numerical identification Reaction/ Test Reaction/ Test substrate substrate 129 strains of Micrococcaceae novobiocin (5 11g/ml), 13 to 44% Urease URE Cellobiose (F) GEL were isolated from food of animal were identified with negative dis Aginin dihydrolase ADH Acetoin (production) VP origin (minced meat, cakes with cordant tests using this mi Ornithin decarboxylase ODC Nitrat (reduction) NIT confectioner's custard) on Baird cromethod. 44% produced no ac Esculin (hydrolysis) ESC B Galactosidase B GAL Glucose (F) GLU Arginin arylamidase ArgA Parker medium. etoin, 35 % had no urease and Fructose (F) FRU Alkaline phosphatase PAL 15 % no arginine dihydrolase. Maltose (F) MAL Pyrrolidonyl Arylamidase PyrA 120 were Staphylococcus and 9 Mannose (F) MNE Novobiocin (Resistance) NOVO Lactose (F) LAC Sucrose (F) SAC Micrococcus, according to the 10 48 Staphylococcus strains (40 %) Trehalose (F) TRE N-Acetyl Glucosamine (F) NAG 32 STAPH-System (1989). The re were identified as human coagula Mannitol (F) MAN Turanose (F) TUR sults were analyzed using a com se negative Staphylococcus spe Raffinose (F) RAF Arabinose (F) ARA Ribose (F) RIB B Glucoronidase B GUR puter program. cies (strains: 39; species: 9) or as animal species (strains: 4; spe (F) ~ Fermentation 60% of these 120 Staphylococcus cies: 1). 5 were Staphylococcus strains of animal origin were co sp S. epidermidis and S. warneri - similar colonies, but without reading of the biochemical tests agulase positive S. -
Potential Use of Soil-Born Fungi Isolated from Treated Soil in Indonesia to Degrade Glyphosate Herbicide
JOURNAL OF DEGRADED AND MINING LANDS MANAGEMENT ISSN: 2339-076X, Volume 1, Number 2 (January 2014): 63-68 Research Article Potential use of soil-born fungi isolated from treated soil in Indonesia to degrade glyphosate herbicide N. Arfarita1*, T. Imai 2, B. Prasetya3 1 Faculty of Agriculture, Malang Islamic University, Jl. M.T. Haryono, Malang 65144, Indonesia 2 Division of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi 755-8611, Japan 3 Faculty of Agriculture, Brawijaya University, Jl. Veteran, Malang 65145, Indonesia. * Corresponding author: [email protected] Abstract: The glyphosate herbicide is the most common herbicides used in palm-oil plantations and other agricultural in Indonesial. In 2020, Indonesian government to plan the development of oil palm plantations has reached 20 million hectares of which now have reached 6 million hectares. It means that a huge chemicals particularly glyphosate has been poured into the ground and continues to pollute the soil. However, there is no report regarding biodegradation of glyphosate-contaminated soils using fungal strain especially in Indonesia. This study was to observe the usage of Round Up as selection agent for isolation of soil-born fungi capable to grow on glyphosate as a sole source of phosphorus. Five fungal strains were able to grow consistently in the presence of glyphosate as the sole phosphorus source and identified as Aspergillus sp. strain KRP1, Fusarium sp. strain KRP2, Verticillium sp. strain KRP3, Acremoniumsp. strain GRP1 and Scopulariopsis sp. strain GRP2. This indicates as their capability to utilize and degrade this herbicide. We also used standard medium as control and get seventeen fungal strains. -
A Primary Assessment of the Endophytic Bacterial Community in a Xerophilous Moss (Grimmia Montana) Using Molecular Method and Cultivated Isolates
Brazilian Journal of Microbiology 45, 1, 163-173 (2014) Copyright © 2014, Sociedade Brasileira de Microbiologia ISSN 1678-4405 www.sbmicrobiologia.org.br Research Paper A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates Xiao Lei Liu, Su Lin Liu, Min Liu, Bi He Kong, Lei Liu, Yan Hong Li College of Life Science, Capital Normal University, Haidian District, Beijing, China. Submitted: December 27, 2012; Approved: April 1, 2013. Abstract Investigating the endophytic bacterial community in special moss species is fundamental to under- standing the microbial-plant interactions and discovering the bacteria with stresses tolerance. Thus, the community structure of endophytic bacteria in the xerophilous moss Grimmia montana were esti- mated using a 16S rDNA library and traditional cultivation methods. In total, 212 sequences derived from the 16S rDNA library were used to assess the bacterial diversity. Sequence alignment showed that the endophytes were assigned to 54 genera in 4 phyla (Proteobacteria, Firmicutes, Actinobacteria and Cytophaga/Flexibacter/Bacteroids). Of them, the dominant phyla were Proteobacteria (45.9%) and Firmicutes (27.6%), the most abundant genera included Acinetobacter, Aeromonas, Enterobacter, Leclercia, Microvirga, Pseudomonas, Rhizobium, Planococcus, Paenisporosarcina and Planomicrobium. In addition, a total of 14 species belonging to 8 genera in 3 phyla (Proteo- bacteria, Firmicutes, Actinobacteria) were isolated, Curtobacterium, Massilia, Pseudomonas and Sphingomonas were the dominant genera. Although some of the genera isolated were inconsistent with those detected by molecular method, both of two methods proved that many different endophytic bacteria coexist in G. montana. According to the potential functional analyses of these bacteria, some species are known to have possible beneficial effects on hosts, but whether this is the case in G.