International Union Of Microbiological Societies Research Articles

A scientist and a world-class personality: Nikolai Petrovich Elinov (1928–2017)

The essay is dedicated to Nikolai Petrovich Elinov, an eminent scientist with a global reputation, who has made a substantial contribution to the development of medical microbiology, mycology, and biotechnology in the Russian Federation. N. P. Elinov is a professor, Doctor of Biological Sciences, Honored Scientist of the RSFSR, and rector of the Leningrad Chemical-Pharmaceutical Institute. He is an active member of the St. Petersburg Engineering Academy and the New York Academy of Sciences, author of 10 textbooks, 8 handbooks, 10 monographs, over 400 articles in domestic and foreign journals, and holds 70 patents for inventions. Professor N. P. Elinov is widely recognized in the scientific community for his work in areas such as biology of aposporous yeast, chemistry and biotechnology of microbial polysaccharides, and others. He has established a school of students and followers, including 50 candidates and 9 Doctors of Science. Under his guidance, the microbiology department laid the foundations for engineering and microbiological training of specialists. As the rector of LCFI, Nikolai Petrovich contributed to the organization of the country’s only faculty for training biotechnology engineers, leading the university to top positions in preparing specialists for the pharmaceutical industry. In 1968, Nikolai Petrovich became a member of the International Commission on Yeast Organisms of the International Union of Microbiological Societies. His name was included in the book “2000 Outstanding Scientists of the Late 20th Century” (1998) by the Cambridge International Biographical Center (UK), where he was recognized as a specialist in microbiology and biotechnology. This essay, based on archival materials, publications, articles, and colleagues’ memories, reveals the key milestones in the life and scientific achievements of Nikolai Petrovich Elinov.

Recent trend, biases and limitations of cultivation-based diversity studies of microbes.

The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.

Microbial Taxonomy Run Amok.

DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. We exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.

A machine-compiled microbial supertree from figure-mining thousands of papers

Background There is a huge diversity of microbial taxa, the majority of which have yet to be fully characterized or described. Plant, animal and fungal taxa are formally named and described in numerous vehicles. For prokaryotes, by constrast, all new validly described taxa appear in just one repository: the International Journal of Systematics and Evolutionary Microbiology (IJSEM). This is the official journal of record for bacterial names of the International Committee on Systematics of Prokaryotes (ICSP) of the International Union of Microbiological Societies (IUMS). It also covers the systematics of yeasts. This makes IJSEM an excellent candidate against which to test systems for the automated and semi-automated synthesis of published phylogenies. New information In this paper we apply computer vision techniques to automatically convert phylogenetic tree figure images from IJSEM back into re-usable, computable, phylogenetic data in the form of Newick strings and NEXML. Furthermore, we go on to use the extracted phylogenetic data to compute a formal phylogenetic MRP supertree synthesis, and we compare this to previous hypotheses of taxon relationships given by NCBI’s standard taxonomy tree. This is the world’s first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Additionally we reflect on how recent changes to UK copyright law have enabled this project to go ahead without requiring permission from copyright holders, and the related challenges and limitations of doing research on copyright-restricted material.

Strained fermented milks – A review of existing legislative provisions, survey of nutritional labelling of commercial products in selected markets and terminology of products in some selected countries

A survey of the information contained in the labels of 109 commercial concentrated fermented milks from the Eastern Mediterranean, Australasia, the United Kingdom, Ireland, the United States of America and Canada plus Skyr (from Iceland), Ymer (from Denmark) and Chakka (from India) was carried out in late 2012 and early 2013. There were substantial differences in composition. The carbohydrate, fat and protein contents ranged between 1–12, 0–20 and 3.3–11 g/100 g, respectively. Considering the compositional data of the product and existing legislative provisions, a typical strained product should have a protein content of ≥8 g/100 and ~5 g/100 g of carbohydrates, and it would be appropriate to name such products as ‘strained yoghurt’, ‘Greek strained yoghurt’ and/or ‘Labneh’. A higher content of carbohydrate would suggest that the product was made using the product formulation method (i.e. without straining the fermentate), or the milk base had been fortified with skimmed milk before straining the fermentate to enhance the yield of the product, and such products should be known, for example, as ‘Greek‐style yoghurt’. It was also observed in some of the samples that the nomenclature of the starter cultures did not conform to recommendations of the International Union of Microbiological Societies (IUMS). Manufacturers could address such issues to minimise consumer confusion.

Recently agreed changes to the International Code of Virus Classification and Nomenclature

The International Committee on Taxonomy of Viruses (ICTV; http://www.ictvonline.org/) is a committee of Virology Division of the International Union of Microbiological Societies, and its operation is governed by Statutes agreed with Virology Division. The classification and nomenclature of viruses is then subject to rules formalized into a Code (required by Statute 8.1). The need for a review of the Statutes and Code became clear during editorial work involved in production of the Ninth ICTV Report [1]. Changes to these documents require the approval of the ICTV Executive Committee (EC) and the full ICTV membership. Changes to the Statutes also require the agreement of Virology Division. The changes described in this article were discussed and agreed by the ICTV EC over a period of more than two years. Notification of a ballot was sent via email on 14 January 2013 to the 165 members of ICTV, namely the ICTV EC Members, Life Members, ICTV Subcommittee Members and ICTV National Representatives. Members were then requested to vote on whether or not to ratify the proposals (voting closed on 14 February 2013). The return rate of votes was approximately 41%, and all proposed changes were accepted, mostly unanimously. The only significant exception was the proposed change to the species definition in Rule 3.21 (Rule 3.20 in the latest version of the code) which was approved by 45:21 with two abstentions. In this article, we present the new version of the Code, highlighted in bold to show those parts that have recently been changed. Those changes are then explained in the sections that follow. It should be noted that some rules were deleted and that some renumbering of sections has therefore taken place. In recent years, the Code has been published with some explanatory Comments from the EC, and the opportunity has been taken to revise and update these where necessary. The changes to the Statutes are the subject of a separate article [2].

Recently agreed changes to the Statutes of the International Committee on Taxonomy of Viruses

The International Committee on Taxonomy of Viruses (ICTV; http://www.ictvonline.org/) is a committee of Virology Division of the International Union of Microbiological Societies, and its operation is governed by Statutes agreed with Virology Division. The classification and nomenclature of viruses is then subject to rules formalized into a Code (required by Statute 8.1). The need for a review of the Statutes and Code became clear during editorial work involved in production of the Ninth ICTV Report [1]. Changes to these documents require the approval of the ICTV Executive Committee (EC) and the full ICTV membership. Changes to the Statutes also require the agreement of Virology Division. The changes to the Statutes described in this article were discussed and agreed by the ICTV EC over a period of more than two years. Many of these changes are relatively minor adaptations and clarifications. Notification of a ballot was sent via email on 14 January 2013 to the 165 members of ICTV, namely the ICTV EC Members, Life Members, ICTV Subcommittee Members and ICTV National Representatives. Members were then requested to vote on whether or not to ratify the proposals (voting closed on 14 February 2013). The return rate of votes was approximately 41 %, and all proposed changes were accepted unanimously. The proposed changes to the Statutes were then submitted to Virology Division and were approved unanimously by the Advisory Board and Executive Committee on 19 April 2013. In this article, we present the new version of the Statutes, highlighted in bold to show those parts that have recently been changed. Those changes are then explained in the sections that follow. The changes to the Code are the subject of a separate article [2].

アメリカのバイオテクノロジーの父は日本人だった

アメリカのバイオテクノロジーの父は日本人だった

World Federation for Culture Collections: professionals underpinning microbial systematics

The World Federation for Culture Collections (WFCC) is a multidisciplinary commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and networking between the collections and their users, to organise workshops and conferences, publications and newsletters and work to ensure the long-term perpetuation of important collections.

Report from the 40th meeting of the Executive Committee of the International Committee of Taxonomy of Viruses

The Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) held its 40th meeting at the Istanbul Convention and Exhibition Centre in Istanbul, Turkey, from August 7 to 9, 2008. This was just prior to the XIV International Congress of Virology (ICV), part of the joint meeting organized by the International Union of Microbiological Societies (IUMS), also in Istanbul, Turkey, from August 11 to 15, 2008. Most of the EC meeting was concerned with the discussion of taxonomic proposals. This communication reports the principal items of business discussed at the meeting.

Modulation of the Structure, Catalytic Activity, and Fidelity of African Swine Fever Virus DNA Polymerase X by a Reversible Disulfide Switch

African swine fever virus polymerase X (pol X) is the smallest DNA polymerase known (174 amino acids), and its tertiary structure resembles the C-terminal half of prototypical X-family pol beta, which includes a catalytic dNTP-binding site (palm domain) and a finger domain. This structural similarity and the presence of viral genes coding for other base excision repair proteins suggest that pol X functions in a manner similar to pol beta, but inconsistencies concerning pol X catalysis have been reported. We examined the structural and functional properties of two forms of pol X using spectroscopic and kinetic analysis. Using (1)H-(15)N correlated NMR, we unambiguously demonstrated the slow interconversion of pol X between a reduced (pol X(red)) and an oxidized form (pol X(ox)), confirmed by mass spectrometry. Steady-state kinetic analysis revealed that pol X(ox), with a disulfide bond between Cys-81 and Cys-86, has approximately 10-fold lower fidelity than pol X(red) during dNTP insertion opposite a template G. The disulfide linkage is located between two beta-strands in the palm domain, near the putative dNTP-binding site. Structural alignment of pol X with a pol beta ternary structure suggests that the disulfide switch may modulate fidelity by altering the ability of the palm domain to align and stabilize the primer terminus and catalytic metal ion for deprotonation of the 3'-OH group and subsequent phosphoryl transfer. Thus, DNA polymerase fidelity is altered by the redox state of the enzyme and its related conformational changes.

Alcoholic fermentation: beverages to biofuel

The history of yeast association with human society is synonymous with the production of alcoholic beverages such as wine and beer, and the scientific discovery by Louis Pasteur, some 150 years ago, that yeasts such as Saccharomyces cerevisiae metabolize sugars into ethanol. Today, the production of alcoholic beverages is a massive, globalized industry that exploits ongoing advances in knowledge about the ecology, biochemistry, physiology and molecular biology of yeasts. Recent concerns about the sustainability of world energy derived from fossil fuels and the associated impacts of climate change have focused attention on ethanol as an alternative or additional energy source, and its production by yeasts as a biofuel. With this background, the International Commission on Yeasts hosted the 26th International Specialized Symposium on Yeasts (ISSY26) with the theme –‘From alcoholic beverages to bioethanol for transportation: a new challenge for fermenting yeast.’ The International Commission on Yeasts is a commission within the Mycology Division of the International Union of Microbiological Societies (IUMS, http://www.iums.org) that hosts general congresses on yeasts every four years and specialized symposia on yeasts every other year. ISSY26 was held at Sorrento, Italy, June 3–7, 2007. This thematic edition of FEMS Yeast Research brings together a selection of 20 articles comprising MiniReviews and research papers that …

The Eleventh International Congress of Mycology of the International Union of Microbiological Societies, San Francisco, California, 23–28 July 2005

The International Union of Microbiological Societies has three divisions – Bacteriology and Applied Microbiology, Mycology and Virology – which come together every 3 years for the organization of their international congresses. In 2005, the American Society for Microbiology hosted these congresses in San Francisco. Yeasts fall within the Division of Mycology and this report covers the numerous contributions on yeasts to the Mycology Congress. Overall, about 3000 registrants attended the combined Congresses, with about 275 delegates focussing on Mycology. The Mycology program was organized into plenary, symposium and poster sessions under the themes of Development, Evolution, Ecology, Medical Mycology and Industrial Mycology. Contributions on yeasts were represented throughout these themes. The application of genomics was prominent in most presentations and has emerged as a fundamental tool to study and understand yeast evolution, phylogeny, ecological adaptation, physiology, structural development, mechanisms of pathogenesis and epidemiology. Under the impact of genomic analyses, the traditional research boundaries between yeasts and filamentous fungi are beginning to blur, and an increasing number of fungal biologists are now working in …

Biological Information Standards

The revolutions caused by advanced computing power, advanced informatics and the Internet have changed the way scientific data are stored, located and disseminated. Today almost every scientist uses the Internet to share data, sometimes just with a close colleague, other times through large-scale databases. The volume, complexity and heterogeneity of biological data make data sharing a daunting task. Standards are clearly required to allow smooth and coherent data sharing. Biological informatics already has established some standards for sharing data, from nomenclature to exchange protocols. In this paper we will give a brief introduction of those data standards. Library and information science has a long tradition of developing standards for sharing bibliographic data. Traditionally libraries have used technology to facilitate cooperation and collaboration in the creation of catalogue records for bibliographic materials. Library and information science has developed a set of well-established standards for sharing data, such as Anglo-American cataloguing rules, MARC format, Dublin core, and Z39.50. Resulting expertise from this experience could help to further improve the standards for biological data. Natural history museums are the major holding agency for biodiversity data. Specimen data in the museums are often maintained in a form of catalogs similar to bibliographic catalogues in the libraries. Although the nature of the books in a library and specimens in the museum differ, the techniques for managing bibliographic data and specimen data are similar. The biological science community has conducted research into adopting standards developed by information scientists. For example, the Consortium for the Computer Interchange of Museum Information (CIMI) published the "CIMI's Guide to Best Practice: The Dublin Core" as the guide for use of the Dublin Core for sharing data among museum collections. We can expect that information scientists, who have developed the standards for sharing bibliographic data, surely could play an important role in sharing biological information. Stanley Blum (see For Further Reading) roughly categorizes biological data standards into three types: vocabulary or authority standards, which specify sets of values to make the data in different systems directly comparable; semantic standards, which specify the meanings of data elements or structures; and data exchange standards, which specify both syntactic and semantic components of a data stream enabling data to be shared between systems. A vocabulary standard specifies a set of values that are mutually understood among a group of people. That is, it specifies the valid values of an attribute. Most vocabulary standards also include supplementary information, such as an abbreviation, code or definition for each term or value in the set. Examples of vocabulary standards may include lists of scientific names, author names and abbreviations. Vocabulary standards enable users of two or more independently developed information systems to apply the values uniformly as descriptors of related data objects. If the values are applied consistently, the participating databases can inter-operate at the value level, making the data in different systems directly comparable. An example is the Integrated Taxonomic Information System (ITIS). ITIS is a database of North American species names and their hierarchical classification, which has been developed by an international partnership of agencies and taxonomic specialists. For each scientific name, ITIS includes the authority (author and date), taxonomic rank, associated synonyms and vernacular names where available, a unique taxonomic serial number, data source information (publications, experts,etc.) and data quality indicators. An even more ambitious project is Species 2000, established by the International Union of Biological Sciences (IUBS), in cooperation with the Committee on Data for Science and Technology (CODATA) and the International Union of Microbiological Societies (IUMS) in September 1994. Species 2000 has the objective of enumerating all known species of organisms on Earth by forming a federation of interoperable species databases, including ITIS. Thus, Species 2000 will deliver a standard set of data for every known species. A semantic data standard specifies definitions, context and assembly rules that enable combinations of simple data values (character strings, numbers, etc.) to convey information (meaningful messages) between people or information systems. It specifies the meanings of data elements or more complex data structures. Such a standard can be expressed as a data dictionary, a conceptual schema or a natural language description of data structure and integrity rules. Darwin Core is an example of semantic standard and one of a series of tools developed for the Species Analyst (a research project developing standards and software tools for access to the world's natural history collection and observation databases). It is a profile describing the minimum set of rules for search and retrieval of natural history collections and observation databases. Other examples of semantic data standards include Access to Biological Collections Data (ABCD) and Structure of Descriptive Data(SDD), being developed by subgroups of the Taxonomic Databases Working Group (TDWG). The Darwin Core forms a subset of ABCD standard. ABCD Task Group is developing an XML schema as a data interchange standard for item-level data. An item may be a specimen, culture, living organism or observation of an organism. The schema provides a comprehensive basic structure and is consequently quite large and highly structured. It will be used as the standard format in which the results of a distributed query will bereturned. It is to be used as a result-schema, that is, for data returned from collection databases as the result of a request. A non-hierarchical access schema with a reduced number of elements (such as the Darwin Core) will be used for these data requests. The current draft of the profile, labeled version 1.04, can be found at the schema subgroup's website at www.bgbm.org/TDWG/CODATA/Schema/default.htm. ABCD structures the interchange of information about the holdings of museums or observations. It does not, however, address the issue of descriptions of what is being held or observed. DELTA and SDD are designed to handle the morphological and other descriptive information about a species. One more example is the Ecological Metadata Language (EML), a metadata standard developed to represent ecological rather than taxonomic data. The purpose of EML is to provide the ecological community with an extensible and flexible metadata standard for use in data analysis and archiving. This will support automated machine processing, searching and retrieval. EML is implemented as a series of XML document types that can be used in a modular and extensible manner. Each EML module is designed to describe one logical part of the total metadata that should be included with any ecological data set. A data exchange standard typically includes both semantic and syntactic components. The semantic component provides the meanings for a data structure, which saves users from having to negotiate the semantics with every exchange event. The syntactic component specifies the data structure itself, as well as how it should be encoded in a data stream or file. Any exchange minimally involves two software systems — the source and target. Export and import routines are required at either endof the exchange to create and read the data file. The most commonly supported file formats, such as fixed-length and delimited, have their limitations. A tremendous amount of effort is now being invested in developing XML related standards, and integrating this markup language into network-based interoperability tools. The Herbarium Information Standards and Protocols for Interchange of Data (HISPID) is a standard format for the interchange of electronic herbarium specimen information. Published in 1993, HISPID is concerned primarily with data interchange standards. The interchange of taxonomic, nomenclature, bibliographic, rare and endangered plant conservation, and other related information is not dealt with in this standard, unless it specifically refers to a particular accession. Another example requiring attention is Z39.50, a computer protocol that defines a standard way for two computers to communicate for the purpose of information retrieval. Z39.50 is an ANSI standard and has also been adopted as an ISO standard (ISO23950). In practice, Z39.50 supports information retrieval in a distributed client and server environment where a computer operating as a client submits a search request (i.e., a query) to another computer acting as an information server. Software on the server performs a search on one or more databases and creates a result set of records that meets the criteria of the search request. The server returns records from the result set to the client for processing. The power of Z39.50 is that it separates the user interface on the client side from the information servers, search engines and databases. Z39.50 provides a consistent view of information from a wide variety of sources, and it offers client implementers the capability to integrate information from a range of databases and servers. The biological science community has adopted the Z39.50 standard. For example, the Consortium for the Computer Interchange of Museum Information (CIMI) has implemented the Z39.50 specifications to support the search and retrieval of museum information among multiple museums. The Z39.50 Biology Implementers Group (ZBIG) developed a Z39.50 profile that provides a common language for data exchange by sending a single query to multiple biological collections. The Distributed Generic Info Retrieval (DiGIR) is a commonly accepted protocol for exchanging biological data. DiGIR provides the infrastructure for performing distributed information retrieval. The purpose of DiGIR is to provide a single point of access todistributed information resources, so that location and technical characteristics of native resource are transparent to users. As a client/server protocol, DiGIR uses HTTP as the transport mechanism and XML for encoding messages sent between client and server. It was originally developed to replace the Z39.50 protocol used in the Species Analyst project, but is also designed to work with any type of information, not just natural history collections. A major contributor to DiGIR is the Mammal Networked Information System (MaNIS) project (http://elib.cs.berkeley.edu/manis/). Although data sharing has been adopted in areas such as biodiversity and genomics, the issue remains controversial in neuroscience. There are negative reactions to sharing neuroscience data, such as primary data is too complex for anyone other than the producer of the data to understand or someone else might find something new from the data that the producer worked hard to collect. Neuroscientists are working on these sociological issues of sharing data now. However, there is a significant and growing need among neuroscientists to exchange experimental data. Several efforts have been developed to facilitate the sharing of primary data in the neuroscience community. In 2000, considerable debate emerged over the new policy of the Journal of Cognitive Neuroscience, which required that the primary data of papers published in the journal be made freely available. A new database has also been established specifically for the storage and sharing of functional magnetic resonance imaging (fMRI) data from cognitive studies. To share data effectively, it will be necessary to create sharing rules and guidelines. The involvement of the neuroscience and computer science community is essential to creatingthese new rules for data sharing. As a component of the Human Brain Project, Gardner proposed the Common Data Model (CDM) as a framework for federation of a broad spectrum of disparate neuroscience information resources. However, universal data sharing has not been fully adopted in the field of neuroscience, and there are no well-established and commonly accepted standards for sharing neuroscience data. Although the complexity and heterogeneity of biological data make the establishment of widespread collaboration a daunting task, the advantages of sharing data would be enormous. With more and more information scientists joining the bioinformatics field, bringing in the expertise and experiences of developing standards for sharing bibliographic data,the biological community will obtain the huge benefit of sharing data through well-established data standards. Chulin Meng is a doctoral student in the Graduate School of Library and Information Science at the University of Illinois, Urbana-Champaign, 501 E. Daniel St., Champaign, IL, 61820. He may be reached at 217-333-6298 or by email at cmeng@uiuc.edu.

Viruses in and out

A report on the twelfth Congress of Virology, part of 'The world of microbes', the joint meeting of the three divisions of the International Union of Microbiological Societies, Paris, France, 27 July to 1 August 2002

Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network.

The emergence of disease caused by penicillin-resistant and multidrug-resistant pneumococci has become a global concern, necessitating the identification of the epidemiological spread of such strains. The Pneumococcal Molecular Epidemiology Network was established in 1997 under the auspices of the International Union of Microbiological Societies with the aim of characterizing, standardizing, naming, and classifying antimicrobial agent-resistant pneumococcal clones. Here we describe the nomenclature for 16 pneumococcal clones that have contributed to the increase in antimicrobial resistance worldwide. Guidelines for the recognition of these clones using molecular typing procedures (pulsed-field gel electrophoresis, BOX-PCR, and multilocus sequence typing) are presented, as are the penicillin-binding profiles and macrolide resistance determinants for the 16 clones. This network can serve as a prototype for the collaboration of scientists in identifying clones of important human pathogens and as a model for the development of other networks.

The Tenth International Symposium on Yeasts (ISY 2000). "The rising power of yeasts in science and industry".

The Tenth International Symposium on Yeasts was held at Papendal, Arnhem, The Netherlands, during 27 August–1 September 2000. It was organized by Hans van Dijken (chair), Lex Scheffers (secretary), Pieter de Geus, Wendell Iverson and Ria Komen-Zimmerman under the auspices of The Netherlands Foundation for Biotechnology and the Delft University of Technology, on behalf of the International Commission for Yeasts (ICY). The ICY is affiliated with the International Union of Microbiological Societies (IUMS) through its Mycology Division, and was established in 1966. Its mission is to promote international interest and collaboration on yeasts through the organisation of two series of symposia. The first of the series are the International Symposia on Yeasts (ISY) which are held every four years and focus on all aspects of yeast biology and technology (e. g. ISY 2000). The second series, the International Specialized Symposia on Yeasts (ISSY) are held every year between the ISY and focus on more specific topics. So far, the ICY has commissioned the organization of 10 ISY and 20 ISSY, which have been held in a range of countries. This Tenth International Symposium on Yeasts attracted some 400 registrants from 40 countries. The scientific program was introduced by 12 plenary lectures that provided the foundations for several thematic sessions, and covered the broad spectrum of interest in yeast research. In all, 107 oral presentations and 165 poster displays were delivered during the 41/2 days of meeting. Some highlights of the program are presented in the following sections. Functional genomic analysis . Stephen Oliver started the scientific program with a plenary paper that described a systematic analytical approach, through EUROFAN, to determine the function of the 6000 open reading frames in Saccharomyces cerevisiae . This was followed by presentations that described the genomics of regulatory networks, transporters, cell wall chitin production, …

The current state of plant virus taxonomy

Virus taxonomy can be defined as the arranging of viruses into related clusters, identification of the extent of relatedness within and among these clusters, and the naming of the clusters (= taxa). The first internationally organized initiative for the naming and classification of animal, plant and microbial viruses was the formation of the International Committee on Nomenclature of Viruses in 1966. This was renamed the International Committee on Taxonomy of Viruses (ICTV) in 1973 and has since produced seven reports reviewing the state of virus taxonomy, the latest of which was published recently (Van Regenmortel et al., 2000). This brief review describes the current classification of plant viruses, outlines the principles used in virus classification and their application, and highlights the taxa created since the previous ICTV Report (Murphy et al., 1995) was published. Most plant viruses are classified in 649 species, most of which are classified among 73 genera. Forty-nine genera are classified among 15 families; the remaining 24 genera have not been assigned to a family. Some species are recognized as members of a family but have not been assigned to a particular genus; 15 other recognized distinct species of uncertain taxonomic status, designated Unassigned Species, have yet to be assigned to a genus or family. The current classification is shown in Table 1, which also shows the classification of viroids (7 genera in 2 families). As in the 7th ICTV Report (van Regenmortel et al., 2000), the families and genera are arranged according to their genome types (ssDNA, dsRNA, etc.), although this grouping has no taxonomic status. A complete listing of plant virus and viroid species then recognized, together with their recommended abbreviations, has been published in Fauquet and Mayo (1999). The main guiding principles in devising a taxonomy for viruses have been discussed in Mayo and Pringle (1998). They are: stability—that is that once decided, names and relationships should remain unaltered for as long as possible, thereby facilitating reference to older literature. Unlike other biological taxonomies, that for viruses has no Rule of Priority. That this system has functioned well is possibly due to the relatively few virus species (currently 1550 of all types) that have been described. utility—that is, the scheme of taxonomic relationships should be found to be useful by the wider virology community. To this end, ICTV decisions are taken in consultation with, and usually at the prompting of, study groups of interested virologists. Utility is usually the result of a prior demand for taxonomic order. It can be assessed by the compliance of working virologists. acceptability—that is, working virologists should be happy to use the names and taxonomic relationships listed. All decisions are susceptible to modification by succeeding taxonomic proposals. Unacceptable names and taxa are eliminated in this way. flexibility—that is that the taxonomy is amenable to revision and reassessment in the light of new discoveries. Newly recognized viruses are constantly being described, as are novel details in the genetic structures of known viruses. A useful taxonomy and nomenclature must therefore adapt to new information. The ICTV is a committee of the Virology Division of the International Union of Microbiological Societies (IUMS), which represents the interests of member microbiological societies. ICTV comprises national members nominated by countries with microbiological societies affiliated to IUMS, life members elected by ICTV, and the elected members of the Executive Committee (EC). Decisions of ICTV are made at plenary sessions of the International Virology Congresses (convened every 3 years) and by postal voting. Statutes define the constitution of ICTV, its mode of operation and how it is constituted. The current version of the Statutes is published in the 7th ICTV Report (Van Regenmortel et al., 2000). The ICTV is advised by its EC, which consists of elected officials among whom are the chairs of subcommittees that represent the major fields of virology. The Plant Virus Subcommittee has at present 21 study groups, each of which is concerned with a particular taxon or group of taxa. The groups make proposals for changes to taxonomy within their fields of interest to accommodate new information as it emerges. Proposals approved by the subcommittees are considered by the EC and, if approved, are presented to the ICTV for ratification. Proposals from outside the ICTV structure are normally referred to the appropriate study group for discussion, or failing this, to the appropriate subcommittee. The Executive Committee of the ICTV has developed an International Code of Nomenclature based on ad hoc rules (Mayo and Horzinek, 1998; Van Regenmortel et al., 2000). These present the modus operandi of the ICTV and are the justification for the decisions of the executive committee and its subcommittees. Many of the rules contained in the code are self-evident. Others, however, have been devised in response to pressures from the virology community for guidance, or even pleas for consistency, in decision-making. Some issues that have provoked comment recently are: The rules state that a new name should be distinctive (Rule 3.14), easy to remember (Rule 3.12), be free of association with any individual’s name (Rule 3.11), and avoid absurdity or offence in any language (Rule 3.19). Also, names should not convey particular meaning such that some members of the taxon would seem not to belong in it (Rule 3.18). Unlike the names of species in all other biological disciplines, those of virus species are not latinized. Thus species names have no gender. The names of genera must end in ‘-virus’ and the names of families must end in ‘-viridae’. Because taxa have been named in the past under less well developed rules, some in the current list have names that are in contravention of current practice. However, in the interests of the stability of nomenclature, few have been altered. All taxon names (including those of species) are written in italic script and have a capital initial letter for the first name. However, in vernacular usage the name is not used formally and italic script is not necessary. Thus, the potyvirus Tobacco etch virus is classified in genus Potyvirus and family Potyviridae. Collective names such as ‘potyviruses’ and ‘nepoviruses’ are never italicised. How the ICTV decides that particular virus isolates belong to one or another species, or are strains within a single species, has been a contentious issue (Van Regenmortel et al., 1997). The basis for decisions is the definition of a virus species that has been accepted by ICTV. It is: ‘A virus species is a polythetic class of viruses that contitutes a replicating lineage and occupies a particular ecological niche’ (Van Regenmortel, 1990). The current ICTV Report (Van Regenmortel et al., 2000) lists the criteria used to differentiate distinct species from virus strains. It is important to emphasize that the criteria used for demarcating species in different families can, and sometimes do, differ. This is both because families can be intrinsically different and because the criteria used are determined by virologists in different study groups. In Table 1, the taxa that were not in the previous ICTV Report (Murphy et al., 1995) are marked in bold text. The most striking novelties are that retrotransposons found in plants are now classified in two genera in two families (Pseudoviridae and Metaviridae) and that viroids have been classified in seven genera distributed among two families. The latest report also contains three new plant virus families (Luteoviridae, Caulimoviridae and Closteroviridae), 26 new genera and three renamed genera in family Geminiviridae (Mastrevirus, Curtovirus and Begomovirus). M.A.M. and A.A.B. are, respectively, Secretary of the ICTV Executive Committee and Chair of the Plant Virus Subcommittee; M.A.M. is supported by funding from the Scottish Executive Rural Affairs Department, and A.A.B. by Horticulture Research International.

Address by the representative of the “International Union of Microbiological Societies”, IUMS, and the “International Committee on Food Microbiology”, ICFMH, to the “World Conference on Science” (WCS), Budapest, Hungary, 26 June–1 July 1999.

Address by the representative of the “International Union of Microbiological Societies”, IUMS, and the “International Committee on Food Microbiology”, ICFMH, to the “World Conference on Science” (WCS), Budapest, Hungary, 26 June–1 July 1999.

Quality control of culture media — perspectives and problems

The Working Party on Culture Media (WPCM) of the International Union of Microbiological Societies (IUMS) has promoted and facilitated the development of methods for quality control of culture media used for the detection and enumeration of food-borne microorganisms since the early 1980s. While progress has been made in establishing protocols to test for productivity and selectivity of media, problems associated with the influence of food constituents and background microflora, as well as the presence of sublethally injured cells in test foods, are yet to be fully addressed before optimum methods for assessing the quality of media can be defined. However, for various reasons, the development of standardised procedures which account for the influence of food constituents or state of debilitation of target microorganisms may not be practical or even desirable.