DOCSLIB.ORG

Community Transcriptomics Reveals Drainage Effects on Paddy Soil Microbiome Across the Three Domains of Life

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Community Transcriptomics Reveals Drainage Effects on Paddy Soil Microbiome Across the Three Domains of Life Community transcriptomics reveals drainage effects on paddy soil microbiome across the three domains of life Dissertation zur Erlangung des akademischen Grades Doktor der Naturwissenschaften (Dr. rer. nat) dem Fachbereich Biologie der Philipps-Universität Marburg/Lahn vorgelegt von Rehab Abdallah aus Kairo, Ägypten Marburg an der Lahn | 2018 The experimental work for this thesis was carried out from October 2014 to April 2018 at the Max Planck Institute for Terrestrial Microbiology under supervision of PD Dr. Werner Liesack in the Department of Biogeochemistry and the Department of Organismic Interactions. The thesis was accepted by the Department of Biology of the Phillips University Marburg at the: 05/07/2018 First examiner: PD Dr. Werner Liesack Second examiner: Prof. Dr. Ralf Conrad Date of defense: 27/9/2018 Dedicated to my husband and my family Publication This thesis resulted in the following papers: Abdallah R. Z., Wegner C.E., Liesack W., Community transcriptomics reveals drainage effects on paddy soil microbiome across the three domains of life, (Submitted to Soil Biology and Biogeochemistry) Abdallah R. Z., Wegner C.E., Liesack W., The effect of incubation time on paddy soil microbial communities after drainage, (in preparation as short report) “Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world” Louis Pasteur Table of contents Summary ............................................................................................................... i Zusammenfassung .............................................................................................. iii 1 Introduction .................................................................................................. 1 1.1 Methane budget, emissions, and global warming ...................................................... 1 1.2 Paddy soil and rice farming......................................................................................... 2 1.3 Biogeochemistry of rice paddies .................................................................................. 2 1.3.1 Microbial-biogeochemical cycles in surface and bulk soil ........................................ 2 Bacterial nitrogen, iron, and sulphur cycles ....................................................... 4 Soil organic matter and bio-polymer degradation in paddy soil ........................ 5 Carbohydrate Active Enzymes ........................................................................... 7 Methanogens and methanotrophs ....................................................................... 8 1.3.2 Rhizosphere soil ....................................................................................................... 10 1.4 Drainage and its importance to paddy soil .............................................................. 11 1.5 Oxygen and desiccation as environmental variables of drainage .......................... 12 1.6 Current knowledge on the response of microbial communities in paddy soil to drainage ................................................................................................................................... 13 1.7 Desiccation and oxygen as environmental stressors in pure culture studies ........ 14 1.8 Desiccation and its effect on microbial communities in other soil systems ........... 15 1.9 Molecular-ecology techniques used to assess the responses of microbial communities to environmental cues...................................................................................... 17 1.10 Engineered systems (microcosms) to study environmental stress under controlled conditions ................................................................................................................................ 18 1.11 Aim of the study and working hypothesis ................................................................ 18 2 Material and Methods ................................................................................ 20 2.1 Materials ..................................................................................................................... 20 2.1.1 Soil sample ............................................................................................................... 20 2.1.2 Instruments used ....................................................................................................... 20 2.1.3 Chemicals and reagents ............................................................................................ 21 2.1.4 Kits ........................................................................................................................... 22 2.2 Methods ....................................................................................................................... 23 2.2.1 Microcosm preparation, incubation, and drainage ................................................... 23 2.2.2 Sampling ................................................................................................................... 23 2.2.3 Measurement of soil physical and chemical parameters .......................................... 25 2.2.4 DNA and total RNA extraction and quality assessment .......................................... 26 2.2.5 cDNA synthesis and Illumina sequencing ............................................................... 26 2.2.6 qPCR and RT-qPCR................................................................................................. 27 2.2.7 Computational analysis ............................................................................................ 28 Demultiplexing and quality control .................................................................. 28 Extraction of SSU rRNA and mRNA datasets ................................................. 28 Diversity analyses ............................................................................................ 28 Analysis of SSU rRNA reads ........................................................................... 28 Analysis of mRNA transcripts ......................................................................... 29 2.2.8 Analysis of differential drainage effects .................................................................. 30 2.2.9 Statistical analysis and figures generation ............................................................... 30 3 Results .......................................................................................................... 31 3.1 Soil physical and chemical parameters .................................................................... 31 3.2 Sampling, extraction and purification of total RNA ............................................... 32 3.3 Absolute abundance of Bacteria, Archaea, and Fungi ............................................ 33 3.4 cDNA synthesis for Illumina RNA-Seq .................................................................... 33 3.5 Sequencing statistics of Illumina RNA-Seq ............................................................. 34 3.6 Effect of drainage on the microbial community composition ................................ 37 3.6.1 Microbial diversity and richness .............................................................................. 37 3.6.2 Drainage effects on domain level (Bacteria, Archaea, and Eukarya) ..................... 38 3.6.3 Effect of drainage on bacterial community composition ......................................... 39 3.6.4 Effect of drainage on archaeal community composition .......................................... 41 3.6.5 Effect of drainage on eukaryotic community composition ...................................... 41 3.7 Effect of drainage on community functioning ......................................................... 42 3.7.1 Effect of drainage on the gene expression of particular functional categories ........ 42 General cellular processes and stress response genes ...................................... 42 Transcripts involved in methane cycling ......................................................... 44 Plant bio-polymer degradation ......................................................................... 44 3.8 The impact of the pre-incubation period on the community response to drainage 48 3.8.1 The effect of pre-incubation period on SSU rRNA level ......................................... 48 3.8.2 The effect of pre-incubation period on mRNA level ............................................... 53 4 Discussion .................................................................................................... 58 4.1 Effects of drainage on soil physical and chemical parameters............................... 59 4.2 Effects of drainage on absolute abundance of Bacteria, Archaea, and Fungi....... 59 4.3 The use of a ‘double RNA approach’ – Illumina RNA sequencing (RNA-Seq) and computational analysis ........................................................................................................... 60 4.4 The development of drainage-specific microbial communities in paddy soil ....... 61 4.5 SSU rRNA dynamics versus mRNA turnover ......................................................... 64 4.6 Environmental factors driving drainage-induced community change .................. 65 4.7 Drainage-induced changes in functional gene expression ...................................... 68 4.7.1 Cellular processes: Decrease in cell motility but increase in transcription and translation ............................................................................................................................
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • New Zealand's Genetic Diversity
    1.13 NEW ZEALAND’S GENETIC DIVERSITY NEW ZEALAND’S GENETIC DIVERSITY Dennis P. Gordon National Institute of Water and Atmospheric Research, Private Bag 14901, Kilbirnie, Wellington 6022, New Zealand ABSTRACT: The known genetic diversity represented by the New Zealand biota is reviewed and summarised, largely based on a recently published New Zealand inventory of biodiversity. All kingdoms and eukaryote phyla are covered, updated to refl ect the latest phylogenetic view of Eukaryota. The total known biota comprises a nominal 57 406 species (c. 48 640 described). Subtraction of the 4889 naturalised-alien species gives a biota of 52 517 native species. A minimum (the status of a number of the unnamed species is uncertain) of 27 380 (52%) of these species are endemic (cf. 26% for Fungi, 38% for all marine species, 46% for marine Animalia, 68% for all Animalia, 78% for vascular plants and 91% for terrestrial Animalia). In passing, examples are given both of the roles of the major taxa in providing ecosystem services and of the use of genetic resources in the New Zealand economy. Key words: Animalia, Chromista, freshwater, Fungi, genetic diversity, marine, New Zealand, Prokaryota, Protozoa, terrestrial. INTRODUCTION Article 10b of the CBD calls for signatories to ‘Adopt The original brief for this chapter was to review New Zealand’s measures relating to the use of biological resources [i.e. genetic genetic resources. The OECD defi nition of genetic resources resources] to avoid or minimize adverse impacts on biological is ‘genetic material of plants, animals or micro-organisms of diversity [e.g. genetic diversity]’ (my parentheses).
    [Show full text]
  • Analysis of Microbial Community Structure of Pit Mud for Chinese Strong-Flavor Liquor Fermentation Using Next Generation DNA Sequencing of Full-Length 16S Rrna
    bioRxiv preprint doi: https://doi.org/10.1101/380949; this version posted July 31, 2018. 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. Analysis of microbial community structure of pit mud for Chinese strong-flavor liquor fermentation using next generation DNA sequencing of full-length 16S rRNA Zuolin Liu1†, Ying Han1†, Junwei Li1,2, Runjie Cao2, Hongkui He2*, Anjun Li2 and Zhizhou Zhang1* 1School of Chemical Engineering and Chemistry, Harbin Institute of Technology, Harbin, China 150006 2The Center for Solid-state Fermentation Engineering of Anhui Province, The Anhui GujingTribute Liquor Ltd, Bozhou, Anhui, China, 236800 † *The corresponding author: [email protected]; [email protected] Equal contribution Contact: Zhizhou Zhang, PhD Prof [email protected] 86-631-5683176 Abstract. The pit is the necessary bioreactor for brewing process of Chinese strong-flavor liquor. Pit mud in pits contains a large number of microorganisms and is a complex ecosystem. The analysis of bacterial flora in pit mud is of great significance to understand liquor fermentation mechanisms. To overcome taxonomic limitations of short reads in 16S rRNA variable region sequencing, we used high-throughput DNA sequencing of near full-length 16S rRNA gene to analyze microbial compositions of different types of pit mud that produce different qualities of strong-flavor liquor. The results showed that the main species in pit mud were Pseudomonas extremaustralis 14-3, Pseudomonas veronii, Serratia marcescens WW4, and Clostridium leptum in Ruminiclostridium.
    [Show full text]
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (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 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Tenggerimyces Flavus Sp. Nov., Isolated from Soil in a Karst Cave, and Emended Description of the Genus Tenggerimyces
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1499–1505 DOI 10.1099/ijsem.0.000908 Tenggerimyces flavus sp. nov., isolated from soil in a karst cave, and emended description of the genus Tenggerimyces Xiao-Jun Li,1,2 Su-Juan Dai,1 Shao-Wei Liu,1 Jia-Meng Liu,1 Li Chen,3 Lin Hu3 and Cheng-Hang Sun1 Correspondence 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Cheng-Hang Sun Medical College, Beijing 100050, PR China [email protected] or 2College of laboratory Medical Science, Hebei North University, Zhangjiakou 075000, PR China [email protected] 3Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China A novel actinomycete, designated strain S6R2A4-9T, was isolated from a soil sample collected from a karst cave in Henan Province, China, and subjected to a polyphasic taxonomic study. This isolate grew optimally at 25–28 8C, pH 6.5–8.0 and in the absence of NaCl. The substrate mycelium of the isolate was well developed with irregular branches. Aerial mycelium fragmented into long, rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S6R2A4-9T resided in the cluster of the genus Tenggerimyces within the family Nocardioidaceae and shared the highest 16S rRNA gene sequence similarity (98.98 %) with Tenggerimyces mesophilus I12A-02601T. The G+C content of the genomic DNA was 67.0 mol%. The strain contained glucose, ribose and xylose in its whole-cell hydrolysates. Strain S6R2A4-9T possessed a novel variation of peptidoglycan derived from the type A1c meso-Dpm-direct.
    [Show full text]
  • Rhizosphere Soil Microbial Properties on Tetraena Mongolica in the Arid and Semi-Arid Regions, China
    International Journal of Environmental Research and Public Health Article Rhizosphere Soil Microbial Properties on Tetraena mongolica in the Arid and Semi-Arid Regions, China Mengying Ruan 1, Yuxiu Zhang 1,* and Tuanyao Chai 2 1 School of Chemical and Environmental Engineering, China University of Mining & Technology-Beijing, Beijing 100083, China; [email protected] 2 College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; [email protected] * Correspondence: [email protected]; Tel.: +86-010-62331792 Received: 26 June 2020; Accepted: 13 July 2020; Published: 16 July 2020 Abstract: Tetraena mongolica is a rare and endangered species unique to China. The total number and density of Tetraena mongolica shrubs in desertification areas have experienced a sharp decrease with increases in coal mining activities. However, available information on the T. mongolica rhizosphere soil quality and microbial properties is scarce. Here, we investigated the effect of coal mining on the soil bacterial community and its response to the soil environment in the T. mongolica region. The results showed that the closer to the coal mining area, the lower the vegetation coverage and species diversity. The electrical conductivity (EC) in the contaminated area increased, while the total nitrogen (TN), available phosphorus (AP), available potassium (AK), and soil organic carbon (SOC) decreased. The activity of NAG, sucrose, β-glucosidase, and alkaline phosphatase further decreased. In addition, the mining area could alter the soil’s bacterial abundance and diversity. The organic pollutant degradation bacteria such as Sphingomonas, Gemmatimonas, Nocardioides, and Gaiella were enriched in the soil, and the carbon-nitrogen cycle was changed.
    [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]
  • Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks
    Journal of Fungi Article Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks Yaping Wang 1,2,3, Yuhang Fu 3, Yuanyuan He 3, Muhammad Fakhar-e-Alam Kulyar 3 , Mudassar Iqbal 3,4, Kun Li 1,2,* and Jiaguo Liu 1,2,* 1 Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; [email protected] 2 MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China 3 College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; [email protected] (Y.F.); [email protected] (Y.H.); [email protected] (M.F.-e.-A.K.); [email protected] (M.I.) 4 Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan * Correspondence: [email protected] (K.L.); [email protected] (J.L.) Abstract: Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that Citation: Wang, Y.; Fu, Y.; He, Y.; matched the natural aging process from juvenile to natural aging.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Pila Genes. the Location of Alpha Helices (Represented by Red H) and Beta Strands (Represented by Yellow E) Was Predicted with Jpred 4 (Drozdetskiy Et Al, 2015)
    Supplementary Figure S1. Secondary structure of the N-terminus of PilA proteins from Desulfuromondales species and other bacteria that possess type IVa pilA genes. The location of alpha helices (represented by red H) and beta strands (represented by yellow E) was predicted with Jpred 4 (Drozdetskiy et al, 2015). Transmembrane helices (green background) were predicted with TmPred (Hofmann & Stoffel, 1993), TMHMM (Krogh et al, 2001), and HMMTOP (Tusnady & Simon, 2001). G. bemidjiensis (Gbem_2590) MLNKLRSNKGFTLIELLIVVAIIGILAAIAIPQFSAYREKAYNAASNSDLKNFKTGLEAFNADFQTYPAAYVASTN ---HHH----HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH-----HHHHHHHHHH-------EEEE--- G. bremensis (K419DRAFT_00801) MLNKLRSNKGFTLIELLIVVAIIGILAAIAIPQFSAYREKAYNAASNSDLKNWKTGQEAYQADFQAYPAAYDVH --HHHH----HHHHHHHHHHHHHHHHHHH----HHHHHHHHHH------HHHHHHHHHHHHHHH---------- Pelobacter seleniigenes (N909DRAFT_0006) MLKKFRKNEKGFTLIELLIVVAIIGILAAIAIPQFASYRQKAFNSASQSDLKTIKTSLEGYYTDEYYYPY --HHHHH-----HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------- Geobacter sp. OR-1 (WP_041974243) MLSKLRSNKGFTLIELLIVVAIIGILAAIAIPQFSAYREKAYNTAANADDKNAKTGEEAYNADNQKYPLAYDQH --HHHHH----HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------ Geobacter sp. M18 (GM18_2492) MLNKIRSNKGFTLIELLIVVAIIGILAAIAIPQFSAYRAKAYNAAANSDLKNIKTGMEAYMADRQAYPVSLDER --HHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------ Geobacter sp. M21 MLNKLRSNKGFTLIELLIVVAIIGILAAIAIPQFSAYRAKAYNSAANSDLKNMKTGMEAYMADRQAYPALLDQR --HHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------- Desulfuromonas
    [Show full text]
  • Supplementary Table 2
    Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942
    [Show full text]