Dedicated to the ecology and evolutionary biology of the parasites of unicellular organisms (UOPs)
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Bacteriophage Ecology Group (BEG) News | |
Dedicated to the ecology and evolutionary biology of the parasites of unicellular organisms (UOPs) |
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| © Stephen T. Abedon (editor) | ||
| contents | BEG News (009) | top of page | ||
| © Phage et al. | July 1, 2001 issue (volume 9) |
| 1. | editorial | this page |
| 2. | new BEG members | this page |
| 3. | new links | this page |
| 4. | new features | this page |
| 5. | upcoming meetings | this page |
| 6. | jobs | this page |
| 7. | submissions (a.k.a., stuff to read) | this page |
| 8. | letters | this page |
| 9. | phage image | this page |
| 10. | new publications (abstracts) | this page |
| 11. | acknowledgements | this page |
| 12. | Bacteriophage Ecology Group | elsewhere |
| 13. | comments | mail to |
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Editorials should be written on subjects relevant to The Bacteriophage Ecology Group as an organization, to BEG News (either the concept or a given issue of BEG News), or the science of Bacteriophage Ecology. While my assumption is that I will be writing the bulk of these editorials, I wish to encourage as many people as possible to seek to relieve me of this duty, as often as possible. Additionally, I welcome suggestions of topics that may be addressed. Please address all correspondences to abedon.1@osu.edu or to "Editorials," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all submissions as Microsoft Word documents, if possible (I'll let you know if I have trouble converting other document formats), and in English.
Naming BacteriophagesThe first bacteriophage known to science was the Bacteriophagum intestinale described by Félix d'Hérelle (3), an enterobacterial phage or a mixture of phages that was considered by d'Hérelle as a single virus with many races. In 1961 Eisenstark published the first list of phages, which included 111 phages with tailed, cubic or filamentous morphology (4). A second phage list, published by Fraenkel-Conrat in 1974, included 411 bacterial viruses and the dimensions and physicochemical properties of many of them (5). Unfortunately, phage names with the Greek letter f were reported without this letter. At present, over 5000 bacteriophages have been studied by electron microscopy and can be attributed to 11 virus families. During 80 years, phage names have been constructed in the absence of any system and usually reflect little more than their author's imagination (or lack thereof). Phage nomenclature is therefore in a primitive and confusing state. Phage names may:
As a result, (i) phage names do not reflect basic phage properties, (ii) synonyms and homonyms abound, and (iii) some designations are unduely complicated and a printer's nightmare. Certain synonyms of enterobacterial phages are even willful creations of investigators who published one and the same virus up to six times under different designations. Further ambiguities are created by the identity of some Roman letters and numerals (I, V), or are the product of odd printer conventions (witness, for the latter, the ambiguous numeral subscript status of the original T phages of Escherichia coli B; 2). However, one notes that quite numerous phage names have been constructed from host names and therefore reflect host ranges, and that names of temperate phages often comprise two elements, one for the phage and another for the host strain. Eighty years after the discovery of phages, it it clearly too late to construct a nomenclature system that reflects basic phage properties such as nucleic acid or particle shape. The most that can be done is to limit the amount of synonyms and homonyms. The practice of constructing phage names from host names should be continued as it gives at least a clue to the phage. We suggest the following:
For reference, see our new web site, Bacteriophage Names 2000, which presents these names alphanumerically, by phage family, and by host genera. We have also compiled a "List of Phage Names" that we present below. References
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The BEG members list can be found at www.phage.org/beg_members.htm as well as on the BEG home page. As we add new members, these individuals will be introduced in this section. Note that, in fact, there are two ways of "joining" BEG. One, the "traditional" way, is to have your name listed on the web page and on the list server. The second, the "non-traditional" way, is to have your name only listed on the list server. The latter I refer to as "non-members" on that list. Members, e.g., individuals listed on the BEG home page, should be limited to individuals who are actively involved in science and who can serve as a phage ecology resource to interested individuals. If you have an interest in phage ecology but no real expertise in the area, then you should join as a non-member. To join as a member, please contact BEG using the following link: abedon.1@osu.edu. Include:
Note that it is preferable that you include the full reference, including the abstract, if the reference is not already present in the BEG bibliography. Responsibility of members includes keeping the information listed on the BEG members list up to date including supplying on a reasonably timely basis the full references of your new phage ecology publications. Reprints can also be sent to The Bacteriophage Ecology Group, care of Stephen Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. To join BEG as a non-member, please contact BEG using the following link: abedon.1@osu.edu and minimally include your name and e-mail address.
- your name
- your e-mail address
- your snail-mail address
- the URL of your home page (if you have one)
- a statement of whether or not you are the principal investigator
- a statement of your research interests (or phage ecology interests)
- a list of your phage ecology references, if any
| name (home page links) |
status | address | |
|---|---|---|---|
| Christina Burch | --- | cburch @princeton.edu |
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540 |
| interests: | I have used the bacteriophage phi-6 as a model system to examine whether conceptual frameworks such as Fisher's geometric model of adaptation and Wright's adaptive landscape accurately predict the genetics of adaptation. (contents | BEG members | top of page) | ||
| Sylvain Moineau | PI | Sylvain.Moineau @bcm.ulaval.ca |
Professeur agrégé / Associate Professor, Department of Biochemistry and Microbiology, Faculté des sciences et de genie, Université Laval, Québec, Canada, G1K 7P4 |
| interests: | My research group focuses on phages of Lactococcus lactis and Streptococcus thermophilus. These dairy phages are investigated from several aspects such as classification, control, detection, ecology, evolution, genomic and proteomic. (contents | BEG members | top of page) | ||
| David Prangishvili | PI | david.prangishvili @biologie.uni-r.de |
Universität Regensburg, Lehrstuhl für Mikrobiologie, Univesitätsstrasse 31, 93053 Regensberg GERMANY |
| interests: | Molecular biology of extremely thermophilic Archaea including genomics and the evolution of their viruses. (contents | BEG members | top of page) | ||
| Jan Rybniker | --- | jrybnike @smail.uni-koeln.de |
Institut für medizinische Mikrobiologie, Immunologie und Hygiene; University of Cologne |
| interests: | Mycobacteriophages as vectors (always interested in more vectors); general interest in phages - esp. mycobacteriophages (environmental isolation). (contents | BEG members | top of page) | ||
| Steve Tucker | --- | s.tucker @mailbox.gu.edu.au |
19 Avocado Cres., Bli Bli, Griffith University, Queensland, Australia 4560 |
| interests: | Potential of phages to influence the number and species composition of bacterioplankton in aquatic ecosystems. (contents | BEG members | top of page) | ||
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Links relevant to The Bacteriophage Ecology Group fall into a number of categories (e.g., see Bacteriophage Ecology Links at www.phage.org/beg_links.htm). Listed below are new links found on that page. If you know of a link that should be included on this page, or the whereabouts of a now-dead link, please let me know.
Have you ever wondered how I find new links? Well, as part of my apparently ongoing effort to avoid actually doing a new search for new links, I will tell you my little secrets. Note that these are useful for all sorts of on-line efforts such as finding images for lectures or for seminars. There is no time saver quite like borrowing an image rather than drawing one from scratch.
(Just remember to properly cite all images stolen. I usually do this by linking the image to its source page, though beware that the image may very well have been posted where you found it in violation of copyright. Also, make sure you ask permission before including online images in offline publications and theses.)
So we'll start with images. The hard (but still useful) way to find images is to open your favorite browser, do some sort of key word search, and then manually look for images. A shortcut is to do an altavista (www.altavista.com) image search. This requires that you seek out the "images" link on the altavista homepage (or, alternatively, just click here).
Want to find the image of a phage? Just type "phage" (without the quotation marks) into the altavista image search engine. This will result in the display of a variety of phage or phage-related images. By clicking the associated URL you can visit the page the phage image is found on and then download the image to your own computer by right-mouse clicking on the image and then saving it.
(beware, by the way, that it isn't altogether uncommon for authors to misspell "page" as "phage" or, blasphemy, for the suffix phage to be used to describe all sorts of things that have less to do with bacteria, e.g., "macrophage", etc. Note, for example, the following image:
which is found at the following URL: http://www.bayarea.net/~phage/peeve.htm.)
More interested in text than images? It is no secret that my favorite search engine is supplied by the people at google (www.google.com). This isn't just because a search for "phage" or "bacteriophage" has this site as its number one hit. It is, instead, because google simply works better than other search engines (even yahoo agrees: see: http://google.yahoo.com/bin/query?p=bacteriophage&hc=0&hs=0).
If you are looking for pages addressing, for example, phage ecology, you could try a phage ecology google search. That will yield over 3,000 hits. You can narrow this significantly by placing phage ecology in quotes in your google search: "phage ecology". Now there are "just" 77 web pages listed.
What now? Well, this is the painful part. Now one must walk through each page to confirm that the page really does deal with issues of phage ecology and, otherwise, is reasonably relevant to a phage ecologist. Then, for the sake of links-page maintenance, it is necessary to make sure that the page is not already listed (and, for that matter, it is also necessary to make sure that the links already listed still work... Yuck!).
Want another short cut? Go to the google advanced search page. Now we can get fancy. Want to find all the world's (known) web sites or pages with a link to BEG? Go down to "Page-Specific Search" and do a search under "Links" for www.phage.org. Press the "Search" button and google will display over 300 links presumably phage-ecology related links (see: link:www.phage.org).
Anyway, enough excuses. It's going to be a long, hot summer and with any luck (and sufficient motivation) by the next issue of BEG News I will have updated the BEG links library with new links.
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In this section I highlight new or updated features of the BEG site. If you have any ideas of how either the BEG site or BEG News might be improved, please let me know.
Bacteriophage Names 2000:Hans Ackermann has assembled a list of 5000+ phage names (organized with my help). Check it out!
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The BEG Meetings link will continue. Reminders of upcoming meetings will be placed in this section of BEG News. If you know of any meetings that might be of interest to BEG members, or would like to recap a meeting that you've attended, then please send this information for posting to abedon.1@osu.edu or to "BEG Meetings," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906.
Microbial Population Biology Gordon ConferenceThis meeting will be held from July 29 through August 3, 2001. The web page for this meeting can be found at http://www.grc.uri.edu/programs/1999/micropop.htm. OK, there will only be one seminar specifically covering phages (by John Yin), but presumably there will be lots of related stuff (e.g., two sessions are titled "Viral Evolution"). Here are some pictures of Western Mass and Williams college:
Evergreen International Phage MeetingThere is still time (before July 1) to get in your abstract for this Summer's phage meeting, to be held August 8-13, 2001. The web page for this meeting can be found at http://www.evergreen.edu/user/T4/2001Meet.html. As always, this will be the meeting that brings together phage people with the widest possible array of interests - from the ecological to the molecular - in a setting of rain forest spender in the city that Time Magazine dubbed the "Hippest town in the West".
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Looking for job? Looking to fill a position? Please send advertisement and information to abedon.1@osu.edu or to "Jobs", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all information as text (e.g., as an e-mail) or as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats), and in English. I will update this section as I receive material, regardless of what date this issue of BEG News goes live.
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Submissions are non-editorial items describing or highlighting some aspect of bacteriophage ecology including news pieces, historical pieces, reviews, and write-ups of research. Peer review of submissions is possible and a desire for peer review should be indicated. Send all submissions to abedon.1@osu.edu or to "Submissions", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all submissions as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats), and in English.
