Specific Adaptation of Ustilaginoidea Virens in Occupying Host
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Genome-Wide Transcriptional Changes and Lipid Profile
G C A T T A C G G C A T genes Article Genome-Wide Transcriptional Changes and Lipid Profile Modifications Induced by Medicago truncatula N5 Overexpression at an Early Stage of the Symbiotic Interaction with Sinorhizobium meliloti Chiara Santi 1, Barbara Molesini 1, Flavia Guzzo 1, Youry Pii 2 ID , Nicola Vitulo 1 and Tiziana Pandolfini 1,* ID 1 Department of Biotechnology, University of Verona, 37134 Verona, Italy; [email protected] (C.S.); [email protected] (B.M.); fl[email protected] (F.G.); [email protected] (N.V.) 2 Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bolzano BZ, Italy; [email protected] * Correspondence: tiziana.pandolfi[email protected]; Tel.: +39-045-8027918 Received: 30 October 2017; Accepted: 11 December 2017; Published: 19 December 2017 Abstract: Plant lipid-transfer proteins (LTPs) are small basic secreted proteins, which are characterized by lipid-binding capacity and are putatively involved in lipid trafficking. LTPs play a role in several biological processes, including the root nodule symbiosis. In this regard, the Medicago truncatula nodulin 5 (MtN5) LTP has been proved to positively regulate the nodulation capacity, controlling rhizobial infection and nodule primordia invasion. To better define the lipid transfer protein MtN5 function during the symbiosis, we produced MtN5-downregulated and -overexpressing plants, and we analysed the transcriptomic changes occurring in the roots at an early stage of Sinorhizobium meliloti infection. We also carried out the lipid profile analysis of wild type (WT) and MtN5-overexpressing roots after rhizobia infection. The downregulation of MtN5 increased the root hair curling, an early event of rhizobia infection, and concomitantly induced changes in the expression of defence-related genes. -
The ELIXIR Core Data Resources: Fundamental Infrastructure for The
Supplementary Data: The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences The “Supporting Material” referred to within this Supplementary Data can be found in the Supporting.Material.CDR.infrastructure file, DOI: 10.5281/zenodo.2625247 (https://zenodo.org/record/2625247). Figure 1. Scale of the Core Data Resources Table S1. Data from which Figure 1 is derived: Year 2013 2014 2015 2016 2017 Data entries 765881651 997794559 1726529931 1853429002 2715599247 Monthly user/IP addresses 1700660 2109586 2413724 2502617 2867265 FTEs 270 292.65 295.65 289.7 311.2 Figure 1 includes data from the following Core Data Resources: ArrayExpress, BRENDA, CATH, ChEBI, ChEMBL, EGA, ENA, Ensembl, Ensembl Genomes, EuropePMC, HPA, IntAct /MINT , InterPro, PDBe, PRIDE, SILVA, STRING, UniProt ● Note that Ensembl’s compute infrastructure physically relocated in 2016, so “Users/IP address” data are not available for that year. In this case, the 2015 numbers were rolled forward to 2016. ● Note that STRING makes only minor releases in 2014 and 2016, in that the interactions are re-computed, but the number of “Data entries” remains unchanged. The major releases that change the number of “Data entries” happened in 2013 and 2015. So, for “Data entries” , the number for 2013 was rolled forward to 2014, and the number for 2015 was rolled forward to 2016. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences 1 Figure 2: Usage of Core Data Resources in research The following steps were taken: 1. API calls were run on open access full text articles in Europe PMC to identify articles that mention Core Data Resource by name or include specific data record accession numbers. -
Bioinformatics Study of Lectins: New Classification and Prediction In
Bioinformatics study of lectins : new classification and prediction in genomes François Bonnardel To cite this version: François Bonnardel. Bioinformatics study of lectins : new classification and prediction in genomes. Structural Biology [q-bio.BM]. Université Grenoble Alpes [2020-..]; Université de Genève, 2021. En- glish. NNT : 2021GRALV010. tel-03331649 HAL Id: tel-03331649 https://tel.archives-ouvertes.fr/tel-03331649 Submitted on 2 Sep 2021 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 obtenir le grade de DOCTEUR DE L’UNIVERSITE GRENOBLE ALPES préparée dans le cadre d’une cotutelle entre la Communauté Université Grenoble Alpes et l’Université de Genève Spécialités: Chimie Biologie Arrêté ministériel : le 6 janvier 2005 – 25 mai 2016 Présentée par François Bonnardel Thèse dirigée par la Dr. Anne Imberty codirigée par la Dr/Prof. Frédérique Lisacek préparée au sein du laboratoire CERMAV, CNRS et du Computer Science Department, UNIGE et de l’équipe PIG, SIB Dans les Écoles Doctorales EDCSV et UNIGE Etude bioinformatique des lectines: nouvelle classification et prédiction dans les génomes Thèse soutenue publiquement le 8 Février 2021, devant le jury composé de : Dr. Alexandre de Brevern UMR S1134, Inserm, Université Paris Diderot, Paris, France, Rapporteur Dr. -
Rice False Smut [Ustilaginoidea Virens (Cooke) Takah.] in Paraguay
ISSN (E): 2349 – 1183 ISSN (P): 2349 – 9265 3(3): 704–705, 2016 DOI: 10.22271/tpr.2016. v3.i3. 093 Short communication Rice false smut [Ustilaginoidea virens (Cooke) Takah.] in Paraguay Lidia Quintana1*, Susana Gutiérrez2, Marco Maidana1 and Karina Morinigo1 1Facultad de Ciencias Agropecuarias y Forestales, Universidad Nacional de Itapúa, Encarnación, Paraguay 2 Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Corrientes, Argentina *Corresponding Author: [email protected] [Accepted: 28 December 2016] [Cite as: Quintana L, Gutiérrez S, Maidana M & Morinigo K (2016) Rice false smut [Ustilaginoidea virens (Cooke) Takah.] in Paraguay. Tropical Plant Research 3(3): 704–705] False smut of rice, caused by Ustilaginoidea virens (Cooke) Takah., is a common disease in rice panicles. Disease was first reported in India (1878) and was considered as a secondary disease due to their sporadic occurrence (Ladhalakshmi et al. 2012). In the 2014–2015 growing season disease survey was conducted in different rice producting areas of the country. Rice plants of IRGA 424 cultivar were observed, whose panicles had grains replaced by globose yellowish green masses of spores. These symptoms were visible after crop flowering, when the fungus transforms individual grains of the panicle into globose green-yellow mass that subsequently acquire greyish-black color. In the national bibliography no history published about this disease was found, thus the objective of this study was to determine the etiology of this new disease in Paraguay. One hundred and twenty panicles taken from fields with symptoms and signs of false smut were collected in the districts of General Delgado, General Artigas and Coronel Bogado (Itapúa Department), districts of Santa Maria, San Juan Bautista and San Juan de Ñeembucú (Misiones Department). -
Reduction of Pectinesterase Activity in a Commercial Enzyme Preparation
Journal of the Science of Food and Agriculture J Sci Food Agric 85:1613–1621 (2005) DOI: 10.1002/jsfa.2154 Reduction of pectinesterase activity in a commercial enzyme preparation by pulsed electric fields: comparison of inactivation kinetic models Joaquın´ Giner, Pascal Grouberman, Vicente Gimeno and Olga Martın´ ∗ Department of Food Technology, University of Lleida, CeRTA-UTPV, ETSEA, Avda Alcalde Rovira Roure 191, 25198-Lleida, Spain Abstract: The inactivation of pectinesterase (PE) in a commercial enzyme preparation (CEP) under high intensity pulsed electric fields (HIPEF) was studied. After desalting and water dilution of the raw CEP, samples were exposed to exponentially decay waveform pulses for up to 463 µs at electric field intensities ranging from 19 to 38 kV cm−1. Pulses were applied in monopolar mode. Experimental data were fitted to a first-order kinetic model as well as to models based on Fermi, Hulsheger¨ or Weibull equations to describe PE inactivation kinetics. Characteristic parameters for each model were calculated. Relationships between some of the parameters and process variables were obtained. The Weibull model yielded the best accuracy factor. The relationship between residual PE and input of electrical energy density was found to be that of exponential decay. 2005 Society of Chemical Industry Keywords: pulsed electric fields; kinetics; pectinesterase; model; inactivation INTRODUCTION It has become customary to use CEPs in fruit and Pectinesterase (PE; EC 3.1.1.11) is a pectic enzyme vegetable juice technology. Depending -
Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis. -
Pseudodidymellaceae Fam. Nov.: Phylogenetic Affiliations Of
available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 87: 187–206 (2017). Pseudodidymellaceae fam. nov.: Phylogenetic affiliations of mycopappus-like genera in Dothideomycetes A. Hashimoto1,2, M. Matsumura1,3, K. Hirayama4, R. Fujimoto1, and K. Tanaka1,3* 1Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan; 2Research Fellow of the Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan; 3The United Graduate School of Agricultural Sciences, Iwate University, 18–8 Ueda 3 chome, Morioka, 020-8550, Japan; 4Apple Experiment Station, Aomori Prefectural Agriculture and Forestry Research Centre, 24 Fukutami, Botandaira, Kuroishi, Aomori, 036-0332, Japan *Correspondence: K. Tanaka, [email protected] Abstract: The familial placement of four genera, Mycodidymella, Petrakia, Pseudodidymella, and Xenostigmina, was taxonomically revised based on morphological observations and phylogenetic analyses of nuclear rDNA SSU, LSU, tef1, and rpb2 sequences. ITS sequences were also provided as barcode markers. A total of 130 sequences were newly obtained from 28 isolates which are phylogenetically related to Melanommataceae (Pleosporales, Dothideomycetes) and its relatives. Phylo- genetic analyses and morphological observation of sexual and asexual morphs led to the conclusion that Melanommataceae should be restricted to its type genus Melanomma, which is characterised by ascomata composed of a well-developed, carbonaceous peridium, and an aposphaeria-like coelomycetous asexual morph. Although Mycodidymella, Petrakia, Pseudodidymella, and Xenostigmina are phylogenetically related to Melanommataceae, these genera are characterised by epi- phyllous, lenticular ascomata with well-developed basal stroma in their sexual morphs, and mycopappus-like propagules in their asexual morphs, which are clearly different from those of Melanomma. -
Corn Smuts S
A Pacific Northwest Extension Publication Oregon State University • University of Idaho • Washington State University PNW 647 • July 2013 Corn Smuts S. K. Mohan, P. B. Hamm, G. H. Clough, and L. J. du Toit orn smuts are widely distributed throughout the world. The incidence of corn smuts in the Pacific Northwest (PNW) varies Cby location and is usually low. Nonetheless, these diseases occasionally cause significant economic losses when susceptible cultivars are grown under conditions favorable for disease development. Smut diseases of corn are, in general, more destructive to sweet corn than to field corn. The term smut is derived from the powdery, dark brown to black, soot-like mass of spores produced in galls. These galls can form on various plant parts. Three types of smut infect corn—common smut, caused by Ustilago maydis (= Ustilago zeae); head smut, caused by Sphacelotheca reiliana; and false smut, caused by Ustilaginoidea virens. False smut is not a concern in the PNW, so this publication deals University S. Krishna by State Mohan,Photo © Oregon only with common and head smuts. Figure 1. Common smut galls on an ear of sweet corn. Each gall represents a single kernel infected by the common Common smut smut fungus. Common smut is caused by the fungal pathogen U. maydis and is also known as boil smut or blister smut (Figure 1). Common smut occurs throughout PNW corn production areas, although it is less common in western Oregon and western Washington than east of the Cascade Mountains. Infection in commercial plantings may result in considerable damage and yield loss in some older sweet corn cultivars, but yield loss in some of the newer, less susceptible cultivars is rarely significant. -
GANNABAN-THESIS-2019.Pdf
Identification of novel sources of variation for the improvement of cold germination ability and early seedling vigor in upland cotton (Gossypium hirsutum L.) by Ritchel Bueno Gannaban, B.S. A Thesis In Plant and Soil Science Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCES Approved Dr. Rosalyn B. Angeles-Shim Chair of Committee Dr. Benildo G. de los Reyes Dr. Brendan R. Kelly Dr. Endang Septiningsih Mark Sheridan Dean of the Graduate School August, 2019 Copyright 2019, Ritchel Bueno Gannaban Texas Tech University, Ritchel Bueno Gannaban, August 2019 ACKNOWLEDGMENTS It is my pleasure to acknowledge everyone whose efforts and contributions led me to the completion of this research study. Without the support and encouragement, I would not have been able to complete this very important chapter of my life’s journey. I would like to thank my thesis advisor, Dr. Rosalyn B. Angeles-Shim of the Department of Plant and Soil Science at Texas Tech University. Dr. Shim provided the opportunity for me to pursue my graduate studies. With her guidance, I managed to survive the grueling life of a graduate student. Dr. Shim’s office was always open whenever I had a question about my research or writing. She consistently allowed this paper to be my own work, but steered me in the right direction whenever she thought I needed it. Not only she is a very considerate adviser but also a confidant who never fails to see the potential in every person. It is truly an honor to work under a great mentor. -
Ascomycota, Leotiomycetes): a New Bambusicolous Fungal Species from North-East India
Taiwania 62(3): 261-264, 2017 DOI: 10.6165/tai.2017.62.261 Gelatinomyces conus sp. nov. (Ascomycota, Leotiomycetes): a new bambusicolous fungal species from North-East India Vipin PARKASH* Rain Forest Research Institute, Soil Microbiology Research Lab., AT Road, Sotai, Post Box No. 136, Jorhat-785001, Assam, India. *Corresponding author's email: [email protected] (Manuscript received 21 July 2016; accepted 14 June 2017; online published 17 July 2017) ABSTRACT: This study represents a newly discovered and described macro-fungal species under family Leotiomycetes (Ascomycota) named as Gelatinomyces conus sp. nov. The fungal species was collected from decayed bamboo material (leaves, culms and branches) during the survey in Upper Assam, India. It looks like a pine-cone with gelatinous ascostroma. The asci are thin-walled and arise in scattered discoid apothecia which are aggregated and clustered to form round gelatinous structure on decayed bamboo material. The study also brings the first record of fungal species from north east region of India. A taxonomic description, illustrations and isolation and culture of Gelatinomyces conus sp. nov. are provided in this study. KEY WORDS: Apothecium, Bambusicolous fungus, Gelatinous ascostroma, India, New fungal species. INTRODUCTION mounted in the DPX fixative (a mixture of distyrene (a polystyrene), a plasticizer (tricresyl phosphate), and Bamboo is like a life line in north-east India. In xylene), on the slides. Spore dimensions were obtained India, north-east states harbours bamboo in the form of under BIOXL (Labovision trinocular microscope) and homestead stands, bamboo groves (public/ private the basidiospores were microphotographed (Gogoi & domain) and natural bamboo brakes. But the knowledge Parkash 2015). -
Genbank Is a Reliable Resource for 21St Century Biodiversity Research
GenBank is a reliable resource for 21st century biodiversity research Matthieu Leraya, Nancy Knowltonb,1, Shian-Lei Hoc, Bryan N. Nguyenb,d,e, and Ryuji J. Machidac,1 aSmithsonian Tropical Research Institute, Smithsonian Institution, Panama City, 0843-03092, Republic of Panama; bNational Museum of Natural History, Smithsonian Institution, Washington, DC 20560; cBiodiversity Research Centre, Academia Sinica, 115-29 Taipei, Taiwan; dDepartment of Biological Sciences, The George Washington University, Washington, DC 20052; and eComputational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052 Contributed by Nancy Knowlton, September 15, 2019 (sent for review July 10, 2019; reviewed by Ann Bucklin and Simon Creer) Traditional methods of characterizing biodiversity are increasingly (13), the largest repository of genetic data for biodiversity (14, 15). being supplemented and replaced by approaches based on DNA In many cases, no vouchers are available to independently con- sequencing alone. These approaches commonly involve extraction firm identification, because the organisms are tiny, very difficult and high-throughput sequencing of bulk samples from biologically or impossible to identify, or lacking entirely (in the case of eDNA). complex communities or samples of environmental DNA (eDNA). In While concerns have been raised about biases and inaccuracies in such cases, vouchers for individual organisms are rarely obtained, often laboratory and analytical methods used in metabarcoding -
Genbank Dennis A
Published online 28 November 2016 Nucleic Acids Research, 2017, Vol. 45, Database issue D37–D42 doi: 10.1093/nar/gkw1070 GenBank Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell and Eric W. Sayers* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA Received September 15, 2016; Revised October 19, 2016; Editorial Decision October 24, 2016; Accepted November 07, 2016 ABSTRACT data from sequencing centers. The U.S. Patent and Trade- ® mark Office also contributes sequences from issued patents. GenBank (www.ncbi.nlm.nih.gov/genbank/)isa GenBank participates with the EMBL-EBI European Nu- comprehensive database that contains publicly avail- cleotide Archive (ENA) (2) and the DNA Data Bank of able nucleotide sequences for 370 000 formally de- Japan (DDBJ) (3) as a partner in the International Nu- Downloaded from scribed species. These sequences are obtained pri- cleotide Sequence Database Collaboration (INSDC) (4). marily through submissions from individual labora- The INSDC partners exchange data daily to ensure that tories and batch submissions from large-scale se- a uniform and comprehensive collection of sequence infor- quencing projects, including whole genome shotgun mation is available worldwide. NCBI makes GenBank data (WGS) and environmental sampling projects. Most available at no cost over the Internet, through FTP and a submissions are made using the web-based BankIt wide range of Web-based retrieval and analysis services (5). http://nar.oxfordjournals.org/ or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt.