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The Evolution of Secondary Metabolism Regulation and Pathways in the Aspergillus Genus
THE EVOLUTION OF SECONDARY METABOLISM REGULATION AND PATHWAYS IN THE ASPERGILLUS GENUS By Abigail Lind Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Informatics August 11, 2017 Nashville, Tennessee Approved: Antonis Rokas, Ph.D. Tony Capra, Ph.D. Patrick Abbot, Ph.D. Louise Rollins-Smith, Ph.D. Qi Liu, Ph.D. ACKNOWLEDGEMENTS Many people helped and encouraged me during my years working towards this dissertation. First, I want to thank my advisor, Antonis Rokas, for his support for the past five years. His consistent optimism encouraged me to overcome obstacles, and his scientific insight helped me place my work in a broader scientific context. My committee members, Patrick Abbot, Tony Capra, Louise Rollins-Smith, and Qi Liu have also provided support and encouragement. I have been lucky to work with great people in the Rokas lab who helped me develop ideas, suggested new approaches to problems, and provided constant support. In particular, I want to thank Jen Wisecaver for her mentorship, brilliant suggestions on how to visualize and present my work, and for always being available to talk about science. I also want to thank Xiaofan Zhou for always providing a new perspective on solving a problem. Much of my research at Vanderbilt was only possible with the help of great collaborators. I have had the privilege of working with many great labs, and I want to thank Ana Calvo, Nancy Keller, Gustavo Goldman, Fernando Rodrigues, and members of all of their labs for making the research in my dissertation possible. -
Identification and Nomenclature of the Genus Penicillium
Downloaded from orbit.dtu.dk on: Dec 20, 2017 Identification and nomenclature of the genus Penicillium Visagie, C.M.; Houbraken, J.; Frisvad, Jens Christian; Hong, S. B.; Klaassen, C.H.W.; Perrone, G.; Seifert, K.A.; Varga, J.; Yaguchi, T.; Samson, R.A. Published in: Studies in Mycology Link to article, DOI: 10.1016/j.simyco.2014.09.001 Publication date: 2014 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Visagie, C. M., Houbraken, J., Frisvad, J. C., Hong, S. B., Klaassen, C. H. W., Perrone, G., ... Samson, R. A. (2014). Identification and nomenclature of the genus Penicillium. Studies in Mycology, 78, 343-371. DOI: 10.1016/j.simyco.2014.09.001 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 78: 343–371. Identification and nomenclature of the genus Penicillium C.M. -
Characterisation of Fungal Contamination Sources for Use in Quality Management of Cheese Production Farms in Korea
Open Access Asian-Australas J Anim Sci Vol. 33, No. 6:1002-1011 June 2020 https://doi.org/10.5713/ajas.19.0553 pISSN 1011-2367 eISSN 1976-5517 Characterisation of fungal contamination sources for use in quality management of cheese production farms in Korea Sujatha Kandasamy1,a, Won Seo Park1,a, Jayeon Yoo1, Jeonghee Yun1, Han Byul Kang1, Kuk-Hwan Seol1, Mi-Hwa Oh1, and Jun Sang Ham1,* * Corresponding Author: Jun Sang Ham Objective: This study was conducted to determine the composition and diversity of the fungal Tel: +82-63-238-7366, Fax: +82-63-238-7397, E-mail: [email protected] flora at various control points in cheese ripening rooms of 10 dairy farms from six different provinces in the Republic of Korea. 1 Animal Products Research and Development Methods: Floor, wall, cheese board, room air, cheese rind and core were sampled from cheese Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea ripening rooms of ten different dairy farms. The molds were enumerated using YM petrifilm, while isolation was done on yeast extract glucose chloramphenicol agar plates. Morphologically a Both the authors contributed equally to this work. distinct isolates were identified using sequencing of internal transcribed spacer region. ORCID Results: The fungal counts in 8 out of 10 dairy farms were out of acceptable range, as per Sujatha Kandasamy hazard analysis critical control point regulation. A total of 986 fungal isolates identified https://orcid.org/0000-0003-1460-449X and assigned to the phyla Ascomycota (14 genera) and Basidiomycota (3 genera). Of these Won Seo Park https://orcid.org/0000-0003-2229-3169 Penicillium, Aspergillus, and Cladosporium were the most diverse and predominant. -
Identification and Nomenclature of the Genus Penicillium
available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 78: 343–371. Identification and nomenclature of the genus Penicillium C.M. Visagie1, J. Houbraken1*, J.C. Frisvad2*, S.-B. Hong3, C.H.W. Klaassen4, G. Perrone5, K.A. Seifert6, J. Varga7, T. Yaguchi8, and R.A. Samson1 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands; 2Department of Systems Biology, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; 3Korean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, Korea; 4Medical Microbiology & Infectious Diseases, C70 Canisius Wilhelmina Hospital, 532 SZ Nijmegen, The Netherlands; 5Institute of Sciences of Food Production, National Research Council, Via Amendola 122/O, 70126 Bari, Italy; 6Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada; 7Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Közep fasor 52, Hungary; 8Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan *Correspondence: J. Houbraken, [email protected]; J.C. Frisvad, [email protected] Abstract: Penicillium is a diverse genus occurring worldwide and its species play important roles as decomposers of organic materials and cause destructive rots in the food industry where they produce a wide range of mycotoxins. Other species are considered enzyme factories or are common indoor air allergens. Although DNA sequences are essential for robust identification of Penicillium species, there is currently no comprehensive, verified reference database for the genus. To coincide with the move to one fungus one name in the International Code of Nomenclature for algae, fungi and plants, the generic concept of Penicillium was re-defined to accommodate species from other genera, such as Chromocleista, Eladia, Eupenicillium, Torulomyces and Thysanophora, which together comprise a large monophyletic clade. -
EFFECTS of BOTANICALS and BIOCONTROL AGENTS on GROWTH and AFLATOXIN PRODUCTION by Aspergillus Flavus INFECTING MAIZE in SOME PARTS of NIGERIA
EFFECTS OF BOTANICALS AND BIOCONTROL AGENTS ON GROWTH AND AFLATOXIN PRODUCTION BY Aspergillus flavus INFECTING MAIZE IN SOME PARTS OF NIGERIA BY OKECHI, OGECHUKWU CALISTA PG/Ph.D./09/54408 DEPARTMENT OF MEDICAL LABORATORY SCIENCES FACULTY OF HEALTH SCIENCES AND TECHNOLOGY COLLEGE OF MEDICINE UNIVERSITY OF NIGERIA ENUGU CAMPUS OCTOBER, 2014 TITLE PAGE EFFECTS OF BOTANICALS AND BIOCONTROL AGENTS ON GROWTH AND AFLATOXIN PRODUCTION BY Aspergillus flavus INFECTING MAIZE IN SOME PARTS OF NIGERIA BY OKECHI, OGECHUKWU CALISTA PG/Ph.D./09/54408 A THESIS SUBMITTED TO THE DEPARTMENT OF MEDICAL LABORATORY SCIENCES, FACULTY OF HEALTH SCIENCES AND TECHNOLOGY, IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE AWARD OF THE DEGREE OF DOCTOR OF PHILOSOPHY (Ph.D.) IN MEDICAL LABORATORY SCIENCES (MEDICAL MIROBIOLOGY), COLLEGE OF MEDICINE, UNIVERSITY OF NIGERIA ENUGU CAMPUS SUPERVISOR: PROFESSOR N.F. ONYEMELUKWE OCTOBER, 2014 i DEPARTMENT OF MEDICAL LABORATORY SCIENCES COLLEGE OF MEDICINE UNIVERSITY OF NIGERIA Telegrams NIGERSITY, ENUGU ENUGU CAMPUS HEAD OF DEPARTMENT NIGERIA OUR REF:……………………UN/CM/MLS/B2 Tel. YOUR REF: ……………… DATE: …………… CERTIFICATION Mr / Mrs / Miss OKECHI OGECHUKWU CALISTA a Ph.D student of the Department of Medical Laboratory Sciences, College of Medicine University of Nigeria, Enugu Campus, majoring in MEDICAL MICROBIOLOGY has satisfactorily completed the requirement for the research work. The results embodied in the work have not been submitted in part or full to any Diploma or Degree of this in any other University. Supervisor’s Name: PROF N .F. ONYEMELUKWE Signature: _____________________________________ ii DEDICATION To Almighty God and my loving mother Mrs. Caroline Nwamaka Okechi. iii ACKNOWLEDGEMENTS My profound gratitude goes to Almighty God for making this study a reality. -
Lists of Names in Aspergillus and Teleomorphs As Proposed by Pitt and Taylor, Mycologia, 106: 1051-1062, 2014 (Doi: 10.3852/14-0
Lists of names in Aspergillus and teleomorphs as proposed by Pitt and Taylor, Mycologia, 106: 1051-1062, 2014 (doi: 10.3852/14-060), based on retypification of Aspergillus with A. niger as type species John I. Pitt and John W. Taylor, CSIRO Food and Nutrition, North Ryde, NSW 2113, Australia and Dept of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA Preamble The lists below set out the nomenclature of Aspergillus and its teleomorphs as they would become on acceptance of a proposal published by Pitt and Taylor (2014) to change the type species of Aspergillus from A. glaucus to A. niger. The central points of the proposal by Pitt and Taylor (2014) are that retypification of Aspergillus on A. niger will make the classification of fungi with Aspergillus anamorphs: i) reflect the great phenotypic diversity in sexual morphology, physiology and ecology of the clades whose species have Aspergillus anamorphs; ii) respect the phylogenetic relationship of these clades to each other and to Penicillium; and iii) preserve the name Aspergillus for the clade that contains the greatest number of economically important species. Specifically, of the 11 teleomorph genera associated with Aspergillus anamorphs, the proposal of Pitt and Taylor (2014) maintains the three major teleomorph genera – Eurotium, Neosartorya and Emericella – together with Chaetosartorya, Hemicarpenteles, Sclerocleista and Warcupiella. Aspergillus is maintained for the important species used industrially and for manufacture of fermented foods, together with all species producing major mycotoxins. The teleomorph genera Fennellia, Petromyces, Neocarpenteles and Neopetromyces are synonymised with Aspergillus. The lists below are based on the List of “Names in Current Use” developed by Pitt and Samson (1993) and those listed in MycoBank (www.MycoBank.org), plus extensive scrutiny of papers publishing new species of Aspergillus and associated teleomorph genera as collected in Index of Fungi (1992-2104). -
IDENTIFICATION and COMPARISION of FUNGI from DIFFERENT DEPTHS of ANCIENT GLACIAL ICE Angira Patel a Thesis Submitted to the Grad
IDENTIFICATION AND COMPARISION OF FUNGI FROM DIFFERENT DEPTHS OF ANCIENT GLACIAL ICE Angira Patel A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the Requirements for the degree of MASTER OF SCIENCE MAY 2006 Committee: Dr. Scott Rogers, Advisor Dr. Stan Smith Dr. Dawn Hentges ii ABSTRACT Dr. Scott Rogers, Advisor Glacial ice serves as a unique preservation matrix for contemporary and ancient microorganisms. The main objective of this study was to evaluate and test the existence of the fungi encased in ancient glacial ice of Antarctica and Greenland. PCR (polymerase chain reaction) amplification was used to isolate the DNA followed by DNA sequencing to obtain the DNA sequences of the ancient microorganisms. Most of the sequences obtained from ancient microbes were similar to the contemporary fungi. Few fungi cultured were approximately 10,000 years old. Microorganisms isolated from ancient glacial ice have undergone repeated phases of evolutionary changes, such as irradiation, freezing and thawing, and in the process they have been archiving various biogenic materials over the period of time. These microorganisms entrapped in glacial ice provide valuable information about the evolutionary processes, as well as the rich biodiversity during ancient times. Hence, various species of microorganisms may appear to be extinct, but factually they might be dormant, entrapped in ice for millions of years and are capable to reappear amidst suitable conditions. The results of this study can be used in future to relate the biological, biogeochemical and genetic composition to a unique and well characterized geologic history of the fungi entrapped in ancient glacial ice. -
A Brief Review of Bioactive Metabolites Derived from Deep-Sea Fungi
Mar. Drugs 2015, 13, 4594-4616; doi:10.3390/md13084594 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Review A Brief Review of Bioactive Metabolites Derived from Deep-Sea Fungi Yan-Ting Wang, Ya-Rong Xue and Chang-Hong Liu * State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University; 163 Xianlin Avenue, Nanjing 210023, Jiangsu, China; E-Mails: [email protected] (Y.-T.W.); [email protected] (Y.-R.X.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel./Fax: +86-25-8968-5469. Academic Editor: Johannes F. Imhoff Received: 2 June 2015 / Accepted: 14 July 2015 / Published: 23 July 2015 Abstract: Deep-sea fungi, the fungi that inhabit the sea and the sediment at depths of over 1000 m below the surface, have become an important source of industrial, agricultural, and nutraceutical compounds based on their diversities in both structure and function. Since the first study of deep-sea fungi in the Atlantic Ocean at a depth of 4450 m was conducted approximately 50 years ago, hundreds of isolates of deep-sea fungi have been reported based on culture-dependent methods. To date more than 180 bioactive secondary metabolites derived from deep-sea fungi have been documented in the literature. These include compounds with anticancer, antimicrobial, antifungal, antiprotozoal, and antiviral activities. In this review, we summarize the structures and bioactivities of these metabolites to provide help for novel drug development. Keywords: deep-sea fungi; bioactive compounds; anticancer; antimicrobial; antiviral; antifungal 1. Introduction Fungi are well known for their vast diversity of secondary metabolites, which include many life-saving drugs and highly toxic mycotoxins [1]. -
Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium 2 Molds on Cheese 3 4 Ina Bodinaku1, Jason Shaffer1, Allison B
bioRxiv preprint doi: https://doi.org/10.1101/647172; this version posted May 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Rapid phenotypic and metabolomic domestication of wild Penicillium 2 molds on cheese 3 4 Ina Bodinaku1, Jason Shaffer1, Allison B. Connors2, Jacob L. Steenwyk3, Erik Kastman1, Antonis 5 Rokas3, Albert Robbat2,4, and Benjamin Wolfe1,4,* 6 7 1Tufts University, Department of Biology, Medford, MA, USA 8 2Tufts University, Department of Chemistry, Medford, MA, USA 9 3Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA 10 4Tufts University Sensory and Science Center, Medford, MA, USA 11 *Correspondence: [email protected] 12 13 14 ABSTRACT Fermented foods provide novel ecological opportunities for natural populations of 15 microbes to evolve through successive recolonization of resource-rich substrates. Comparative 16 genomic data have reconstructed the evolutionary histories of microbes adapted to food 17 environments, but experimental studies directly demonstrating the process of domestication are 18 lacking for most fermented food microbes. Here we show that during the repeated colonization 19 of cheese, phenotypic and metabolomic traits of wild Penicillium molds rapidly change to 20 produce mutants with properties similar to industrial cultures used to make Camembert and 21 other bloomy rind cheeses. Over a period of just a few weeks, populations of wild Penicillium 22 strains serially passaged on cheese resulted in the reduction or complete loss of pigment, 23 spore, and mycotoxin production. Mutants also had a striking change in volatile metabolite 24 production, shifting from production of earthy or musty volatile compounds (e.g. -
Phylogeny of Penicillium and the Segregation of Trichocomaceae Into Three Families
available online at www.studiesinmycology.org StudieS in Mycology 70: 1–51. 2011. doi:10.3114/sim.2011.70.01 Phylogeny of Penicillium and the segregation of Trichocomaceae into three families J. Houbraken1,2 and R.A. Samson1 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 2Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. *Correspondence: Jos Houbraken, [email protected] Abstract: Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit. -
Diversity and Control of Spoilage Fungi in Dairy Products: an Update
microorganisms Review Diversity and Control of Spoilage Fungi in Dairy Products: An Update Lucille Garnier 1,2 ID , Florence Valence 2 and Jérôme Mounier 1,* 1 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM EA3882), Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France; [email protected] 2 Science et Technologie du Lait et de l’Œuf (STLO), AgroCampus Ouest, INRA, 35000 Rennes, France; fl[email protected] * Correspondence: [email protected]; Tel.: +33-(0)2-90-91-51-00; Fax: +33-(0)2-90-91-51-01 Received: 10 July 2017; Accepted: 25 July 2017; Published: 28 July 2017 Abstract: Fungi are common contaminants of dairy products, which provide a favorable niche for their growth. They are responsible for visible or non-visible defects, such as off-odor and -flavor, and lead to significant food waste and losses as well as important economic losses. Control of fungal spoilage is a major concern for industrials and scientists that are looking for efficient solutions to prevent and/or limit fungal spoilage in dairy products. Several traditional methods also called traditional hurdle technologies are implemented and combined to prevent and control such contaminations. Prevention methods include good manufacturing and hygiene practices, air filtration, and decontamination systems, while control methods include inactivation treatments, temperature control, and modified atmosphere packaging. However, despite technology advances in existing preservation methods, fungal spoilage is still an issue for dairy manufacturers and in recent years, new (bio) preservation technologies are being developed such as the use of bioprotective cultures. This review summarizes our current knowledge on the diversity of spoilage fungi in dairy products and the traditional and (potentially) new hurdle technologies to control their occurrence in dairy foods. -
Diversity of Yeast and Mold Species from a Variety of Cheese Types Nabaraj Banjara University of Nebraska-Lincoln, [email protected]
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in Food Science and Food Science and Technology Department Technology 2-2015 Diversity of yeast and mold species from a variety of cheese types Nabaraj Banjara University of Nebraska-Lincoln, [email protected] Mallory J. Suhr University of Nebraska-Lincoln, [email protected] Heather E. Hallen-Adams University of Nebraska-Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/foodsciefacpub Part of the Food Microbiology Commons, and the Other Ecology and Evolutionary Biology Commons Banjara, Nabaraj; Suhr, Mallory J.; and Hallen-Adams, Heather E., "Diversity of yeast and mold species from a variety of cheese types" (2015). Faculty Publications in Food Science and Technology. 140. http://digitalcommons.unl.edu/foodsciefacpub/140 This Article is brought to you for free and open access by the Food Science and Technology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in Food Science and Technology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Current Microbiology (2015); doi: 10.1007/s00284-015-0790-1 Copyright © 2015 Springer Science+Business Media New York. Used by permission. Submitted December 23, 2014; accepted January 8, 2015; published online February 19, 2015. digitalcommons.unl.edu Diversity of Yeast and Mold Species from a Variety of Cheese Types Nabaraj Banjara, Mallory J. Suhr, and Heather E. Hallen-Adams Department of Food Science and Technology, University of Nebraska–Lincoln, 143 Filley Hall, Lincoln, NE 68583-0919, USA Corresponding author — Heather E.