Wikipedia:Wiki Ed/University of Toronto/HMB436H Medical and Veterinary Mycology (Fall 2015)/overview

  Course name Medical and Veterinary Mycology   Institution University of Toronto   Instructor <dd style="margin: 0; padding: 5px 0 10px 0; font-size: 16px; border-bottom: 1px solid #ADADAD; clear: both">Medmyco</dd> </dl> <dl style="padding-bottom: 10px"> <dt style="font-size: 12px; font-weight: normal; margin: 0; padding: 0">Subject</dt> <dd style="margin: 0; padding: 5px 0 10px 0; font-size: 16px; border-bottom: 1px solid #ADADAD; clear: both">Mycology</dd> </dl> <dl style="padding-bottom: 10px"> <dt style="font-size: 12px; font-weight: normal; margin: 0; padding: 0">Course dates</dt> <dd style="margin: 0; padding: 5px 0 10px 0; font-size: 16px; border-bottom: 1px solid #ADADAD; clear: both">2015-09-01 – 2015-12-31</dd> </dl> <dl style="padding-bottom: 10px"> <dt style="font-size: 12px; font-weight: normal; margin: 0; padding: 0">Approximate number of student editors</dt> <dd style="margin: 0; padding: 5px 0 10px 0; font-size: 16px; clear: both">14-20</dd> </dl>

This lecture-based course will familiarize students with fungi of public health importance, particularly those that cause disease in humans and other animals. The course will focus on the clinical presentation, pathophysiology, and treatment of fungal infections, as well as the ecology, physiology and evolutionary biology of the agents responsible. The course will also address other ways in which fungi influence human and animal health. Click here to go to the course website. Mycology is that branch of biology that deals with the study of fungi. Medical mycology, in turn, is the study of fungi that cause disease. Generally speaking, there are relatively few fungi that are capable of causing human disease. By contrast, there are many bacteria and viruses able to infect people or cause them to become ill through other mechanisms. Even though their numbers are few, the fungal agents of human illness are uniquely problematic. This is partly due to the fact that fungi are more closely related to animals than other common disease-causing microbes. This closer relationship means that the drugs intended to disrupt fungal metabolic processes often have pronounced toxicity to humans. Fungal diseases are also interesting because their importance has grown with medical advancements. For example, fungal diseases tend to show up increasingly as complications of other diseases that compromise the immune system, like HIV/AIDS and diabetes, or as a result of treatments that cause immunosuppression, such as those used to treat cancer or to prevent rejection following organ transplantation. Fungi are the seventh most important agents of infection-related death in the United States resulting in nearly double the number of deaths as tuberculosis (see ). If all this sounds interesting, then this course is for you.
 * Course overview
 * Why medical mycology?

When I have taught this course in the past, I have included a written assignment where students each prepare a fully-referenced "biography" of a particular fungus, something along the lines of the popular blog, Fungus-of-the-Month, developed by my friend and colleague Professor Tom Volk at University of Wisconsin, La Crosse. These short articles are fun to read and fun to write, and I was always impressed with what my students produced, but I felt that more could be done with it. Here's where Wikipedia comes in. Although there are a whole bunch of very good Wikipedia articles on fungi (e.g., User:Sasata/Reviewed_content lists some of the best), there are really a lot of fungi! And many of the better-known, really important species are not represented. This is our chance to change that. For this year's class assignment, I'm going to have each student prepare a Wikipedia article on a different species of fungus that is important in human or animal health. Remember that many biomedically important fungi are also important for other reasons (e.g., some may be plant pathogens, some may be used for industrial applications, and some just might have interesting stories associated with them). Your assignment is not limited to discussing solely the biomedical aspects of your fungus - I expect your assignment to be comprehensive!
 * The assignment

This assignment will be fun but it won't be easy. Because Wikipedia is a real online encyclopedia, there are a number of rules you will need to learn and follow, particularly about how to write the article, the tone you must use, the critical importance of backing up each fact you present with an appropriate citation, and a number of other issues that you will learn as you work through the assignment and we discuss your work in class. The assignment overall is worth 30% of your grade, and it is broken-up into 5 parts. The first 4 parts each count for 5%, and these are the assignments described below in Weeks 1, 2, 4 and 7. These are due by midnight EDT on September 18, 25, October 16, and October 30, 2015, respectively. The actual text of your article is due on November 13, 2015 and will count for 15% of your grade. It is important that you keep to these deadlines, and I will be checking your progress online. Late assignments will not be considered. For those of you needing assistance with this project you progress, I will hold an office hour each week following class. We will also discuss in class some of the other resources that are available to you. This is a serious and difficult exercise, but it is also intended to be fun and to give back to the community. Hopefully it will inspire you to continue contributing to Wikipedia and help you learn about medical mycology at the same time!

Lastly, I cannot overemphasize the need to READ ALL OF THE INSTRUCTIONS BELOW AND FOLLOW THEM. I will deduct marks, many in some cases, if your assignments do not comply with my instructions. Don't say I didn't warn you.

([ Click to return to your main course page and continue.])

Week 1 - September 16, 2015: Wikipedia essentials

 * In class
 * Overview of the course
 * How will Wikipedia be used in the course?


 * Assignment (due Friday September 18, 2015) (worth 5% of your grade)
 * Create an account (if you do not already have one), make edits in a sandbox, and learn the basic rules of Wikipedia. Feel free to read the WP:Username policy if you need help selecting an appropriate handle.
 * Enroll in the course on the Wiki Education page by clicking the "Enroll" button at the top, and entering the enrollment token you were provided.
 * Once you have a Wikipedia user account, please email me your user name (james.scott@utoronto.ca) - I need to know this in order to mark your assignments.

Week 2 - September 23, 2015: Editing basics

 * In class
 * Basics of editing
 * Anatomy of Wikipedia articles, what makes a good article, how to distinguish between good and bad articles
 * Tips on finding the best articles to work on your assignments and to contribute to your classmates' assignments.
 * I will provide you with the enrollment token you will need to register for the course by clicking on the Enroll button at the top of this page.
 * Handouts: Using talk pages, Evaluating Wikipedia article quality, Wikimarkup cheatsheet


 * Assignment (due Friday September 25, 2015) (worth 5% of your grade)
 * Complete the online training for students online student orientation.
 * Create a user page, and sign up on the list of students on the course page. Once I receive your Wikipedia username, I will list it beside one of the fungi included in the topics list under "Week 3", below.
 * Practice editing and communicating on Wikipedia, introduce yourself to your classmates' by leaving a message for them on their Talk Pages (hint: scroll to the bottom of this page where the enrolled students are listed, if you are not visible in this list it means you have not enrolled).
 * Read several of the following Wikipedia articles: Apophysomyces variabilis, Aspergillus ochraceus, Aspergillus versicolor, Blastomyces dermatitidis, Chrysosporium keratinophilum, Malassezia pachydermatis, Microsporum audouinii, Paecilomyces variotii, Microsporum gypseum, Paracoccidioides brasiliensis, Scedosporium prolificans. These are examples of what I consider to be excellent articles on mycological topics, and could serve as models for the format, tone and citation requirements for your article. There are also a number of excellent Wikipedia articles macrofungi, mostly in the phylum Basidiomycota -- check out some of the contributions of User:Sasata.


 * Milestone:
 * All students have Wikipedia user accounts and will be assigned a topic on the course page. All students will also have competed the online training for students (and I will check that you have done it).

Week 3 - September 30, 2015: Citing sources and obeying copyright

 * In class
 * We will briefly discuss referencing on Wikipedia and Wikipedia’s copyright policy.
 * I will hand out a topic to each of you that will be the subject of your assignment.
 * Handouts: How to get help
 * Provisional list of topics (I will assign each student with a topic - you don't get to chose)

I hope you have gathered by now that writing an encyclopedia entry is quite different from writing a term paper in many ways, one of which is the need to select references carefully to support facts. And although many references may support the same fact, some references are much more suitable than others given the situation.

As you may have already suspected, all sources are not equal. Some are objective and neutral, based on evidence and analysis; others are subjective and biased, based on opinion and spin. Although this distinction may seem straightforward, it is not always easy to distinguish between the two types of sources. For the purposes of writing an encyclopedia entry on a species of fungus, the very best sort of information is kind that comes from secondary and tertiary sources, based on research findings that were published in peer-reviewed primary sources. Ultimately if you need to use a primary reference to support a fact because there are no alternatives, go ahead and use it, but because of the particular sensitivity of health-related topics, you should only cite secondary sources when it comes to issues related to treatment. For more information I encourage you to read the articles on Identifying reliable sources, Identifying primary and secondary sources for biology articles and the handout on the right dealing with editing medicine topics.
 * Selecting the right references

Below are a some excellent online mycology resources you can access to help you with your project. Several of these links require that you access them from a computer accessing the internet through the University of Toronto.
 * Resources


 * MycoBank - this is an online database that connects you with the most current names of fungi and it provides extensive additional references for many in addition to photographs (so you know what they look like - but remember, you cannot use these photographs in your assignment).


 * University of Alberta Microfungus Collection and Herbarium - This is the world's largest culture collection of biomedically important fungi, and it is located in Canada. The online database contains very detailed records of isolations of fungi from humans and animals, and provides links to the papers where they are documented.


 * Centraalbureau voor Schimmelcultures - this is a very large culture collection of fungi located in The Netherlands. Their website contains a number of searchable databases that provide information on strains of many different species contained in their collection. Lots of these are medically important. The records also provide links to papers where many different aspects of the particular species are described. There are also links to a large number of peer-reviewed publications in the journal Studies in Mycology.


 * Web of Science - This database will help you to locate peer-reviewed papers, including review articles, where you can learn about your fungus. You can access it through the University of Toronto domain through this link, or you can log on through the University of Toronto Library Portal for access. You can search your fungus using its current (and former!) species names in the Topic field. This search will return large numbers of papers (hopefully) which you will need to sort through to find the important ones. Clicking on a paper hyperlink will let you read the abstract, and in many cases, it should provide you a direct link to the full-text paper (again as long as you are logged on through through the university's domain or through the library portal).


 * PubMed is another article search engine which is very useful in searching the biomedical literature. you can access it by following this link. It is not as comprehensive as Web of Knowledge because it is focused mainly on biomedically important topics. But a number of articles can be accessed through PubMed which are absent (or at least hard to find) on Web of Knowledge. PubMed will only provide you links to the full-text of papers that are Open Access.


 * Index Fungorum - This is a search engine similar to MycoBank. Although it is not as comprehensive in some areas, Index Fungorum is still very useful to help you figure out what names your fungus might have had in the past.


 * CMI Descriptions of Pathogenic Fungi and Bacteria – Although many of these profiles are dated (and the names are old), there is still a great deal of useful information in this growing archive. I encourage you to search your fungus (and all of its various historical names) here to see if you find anything worthwhile. Browsing several of these profiles will also give you a clearer idea of how you should approach the writing tone of your article. As long as you are attached to the internet through the University of Toronto backbone, you can follow this link to the CABI portal - CMI Descriptions of Pathogenic Fungi and Bacteria.

There are a number of great books on medical mycology in the Gerstein Library in the stacks under the call number range in RC117. Also, you may find some worthwhile reference books in the general mycology section at QK603. Besides Gerstein, the Noranda Library at the Earth Sciences Centre has lots of mycology books too. A few that I think are particularly useful for this exercise include:


 * Barron G.L. 1968. The genera of Hyphomycetes from soil. Baltimore, MD: Williams and Wilkins. 364 pp. This book is a great guide to some of the common genera of moulds in soil. It does not break down the genera by species, but it does provide great ecological commentary on a number of interesting species. A number of the names used in this book are old, so in order to find your fungus in the book, you may need to search it under one of the older synonyms. Despite the older naming systems, the information continues to be excellent. Embed this reference:


 * Domsch K.H., Gams W., Anderson T.H. 1980. Compendium of soil fungi. Vol. 1. London, UK: Academic Press. 859 pp. This is a two volume set of books that deals with soil-borne fungi, as the name suggests. The first volume is arranged alphabetically by genus, and the second slimmer volume contains all of the bibliographical references. Whereas Professor Barron's book (described above) only deals with asexual soil fungi, this book also includes a bunch of fungi that occur commonly as sexual forms. Like Professor Barron's book, many of the names are old, and it may be challenging in some cases to track your fungus down in this book. Nevertheless, once you find it, the book contains a wealth of information about habitat, physiology and other aspects of fungal biology. In many cases, the most common species in each genus are discussed separately, which is useful, and often identification keys are provided. Embed this reference:


 * Farr D.F., Bill G.F., Chamuris G.P., Rossman A.Y. 1989. Fungi on plants and plant products in the United States, 2nd Edition. St. Paul: APS Press. This large and comprehensive volume includes lists of plant species (economically important and otherwise) on which various species fungi are known to grow. It is arranged in two parts, the first by plant family within which plant taxa are arranged by genus and species, followed by a list of fungal species known to inhabit them. The second part of the book is arranged alphabetically by fungal genus, and for each species of fungus it provides an exhaustive list of plants on which that species has been found to occur. This is a great reference for host preferences of plant-associated fungi. Embed this reference:


 * Howard D.H. 2007. Pathogenic fungi in humans and animals, 2nd ed. New York, NY: Marcel Dekker. 800 pp. This is an excellent reference for up-to-date naming, particularly of opportunistic pathogens. Although it does not include a great deal of habitat information, there is better coverage of the range of human diseases associated with fungi that you can find in typical mycological reference books. Genera like Acremonium, Aspergillus, Fusarium, Scopulariopsis and Sporothrix as well as the pathogenic yeasts and mucormycota are well covered. Embed this reference:


 * Kane J., Summerbell R.C., Sigler J., Krajden S, Land G. 1997. Laboratory handbook of dermatophytes: a clinical guide and laboratory handbook of dermatophytes and other filamentous fungi from skin, hair, and nails. Belmont, CA: Star Pub. This excellent guide provides an overview of dermatophyte fungi (the genera Trichophyton, Microsporum and Epidermophyton), as well as taxa that look resemble them (notably the genera Chrysosporium, Geomyces, Myceliophthora, Sporotrichum and some others). Embed this reference:


 * Kirk P.M. et al. (eds) 2011. Ainsworth & Bisby's Dictionary of the Fungi, 10th ed. Wallingford, UK: CABI International. This is a fungal "encyclopedia" that defines terms & concepts, provides overviews of different taxa and lists important references. Although this book will not give you much specific information on individual fungal species, it provides a wealth of places you can go to find detailed information on different genera and the species they contain. It also includes some useful facts on genera, such as the number of species that are currently recognized. The book also defines terms used in mycology, so if you encounter a word that you don't know, this is a good place to learn what it means. Embed this reference:


 * Kwon-Chung K.J., Bennett J.E. 1992. Medical mycology. Philadelphia, PA: Lea & Febinger. This is a very good general reference book on medical mycology with excellent coverage of the true human pathogenic fungi and the medically important yeasts in the genera Candida and Cryptococcus. Embed this reference:


 * Onions, A.H.S.; Allsopp, D.; Eggins, H.O.W. 1981. Smith's introduction to industrial mycology (7th ed.). London, UK: Arnold. Although the taxonomy in this book is quite dated, it remains an excellent guide to fungi that are used or encountered in industry including food processing. The front part of the book is alphabetically arranged by genus, and includes good coverage of the common air- and food contaminant fungi such as the genera Aspergillus, Cladosporium, Paecilomyces, Penicillium and Scopulariopsis. The back part of the book includes coverage of laboratory techniques for manipulating and storing fungi along with some information on fungal physiology, growth conditions and toxins. Embed this reference:


 * Rippon J.W. 1988. Medical mycology, 3rd ed. Philadelphia: WB Saunders. 797 pp. As the title suggests, this is a book that talks about clinical mycology. It contains descriptions of diseases that are cause by fungi as well as discussion of the species responsible for causing these diseases. Although the book is rather old, the information it contains (apart from the taxonomy) is still excellent. It is a particularly good reference for the "true" fungal pathogens in the genera Blastomyces, Coccidioides and Histoplasma in addition to a bunch of other opportunistic agents that cause mycetomas, cutaneous infections, etc. Embed this reference:


 * Pitt J.I, Hocking A.D. 1999. Fungi and food spoilage, 2nd Edition. Gaithersburg: Aspen Publishing. 593 pp. This is an excellent guide to the fungi encountered in food spoilage, including many hyphyomycetes, a number of ascomycetes and some zygomycetes. It gives tidy, comprehensive descriptions of important genera and species, including photographs, line drawings and taxonomic keys. Embed this reference:


 * Samson R.A., Hoekstra E.S., Frisvad J.C. 2004. Introduction to food- and airborne fungi, 7th ed. Baarn, The Netherlands: Centraalbureau voor Schimmelcultures, Institute of the Royal Netherlands Academy of Arts and Sciences. This great book deals with fungi that spoil foods and occur in indoor environments. There is a great deal of overlap between these fungi and the species that are occasionally implicated in opportunistic infections, and the taxonomy included is quite up-to-date. The book is a particularly good reference for members of the genera: Alternaria, Aspergillus, Cladosporium, Paecilomyces, Penicillium, Scopulariopsis, and many others. Embed this reference:


 * Watanabe T. 2011. Pictorial atlas of soil and seed fungi, 3rd ed. Boca Raton, FL: CRC Press. This book provides identification keys and habitat descriptions for a large number of soil fungi including many that are opportunistic pathogens. Although it is not as comprehensive as The Compendium of Soil Fungi, Dr. Watanabe's book includes a number of the more obscure taxa that are not commonly included in these sorts of reference guides. The second edition will work if that's you can find. Embed this reference:

Week 4 - October 7, 2015: Develop an annotated bibliography and point-form article outline

 * Assignment (due Friday October 16, 2015) (worth 5% of your grade)
 * If an article on your fungus already exists, copy its source code and paste it into your sandbox page below the sandbox template at the top  ← Do not delete this from the top of your sandbox page
 * Compile a bibliography of relevant references in your sandbox, linking each reference to the point-formed facts you plan to use that reference to support. I expect at least 20-30 "facts" (hopefully more) supported by at least 10 references. As you paste references into your "References" section, try to keep them arranged in alphabetical order (see the code below). Wikipedia will render them in the order that they were cited, but if you need to go back and use a reference you have already cited in another place, if they are arranged alphabetically it will be easier to make sure you don't have duplicates. You're annotated bibliography might look something like the example below (except I expect it to be much more comprehensive). If you have lots of points, you may find it easier to arrange them under headings like Growth and morphology, Physiology, Habitat and ecology, etc.
 * When using taxonomic ("scientific") names, capitalize and italicize the genus: Penicillium, Trichophyton. Italicize but do not capitalize taxonomic ranks at the level of species and below: Penicillium digitatum, Trichophyton tonsurans; no exception is made for proper names forming part of scientific names. The formal names of higher taxa (order, family, etc.) are capitalized in Latin (Ascomycota, Zygomycota) but not in their English equivalents (ascomycetes, zygomycetes); they are not italicized in either form. The first time the name of a species is used, the genus name should be spelled out completely, Trichophyton tonsurans; but in subsequent uses, the name of the genus can be abbreviated to the first letter, T. tonsurans. You should be aware that there are two exceptions to this. The first is when you the name starts a sentence, and the second is if you are discussing multiple different species whose genus names begin with the same letter. In both cases the genus name needs to be spelled out completely.
 * When you cite references, do not use so-called in-line citing, instead use the style outlined in the example below where the references are consolidated in alphabetical order in a References section, and the short-name is used to call the reference shen it is invoked in the text. Place references at the end of the sentence immediately following punctuation (i.e., no space), or within the sentence where you require multiple references supporting different points. In all cases, references should be places immediately to the right of text or punctuation with no space. Multiple references should not be separated by punctuation or spaces.

{{markup|title=
 * ==Fungus name==

Growth and morphology

 * fast-growing, yellow colonies
 * conidia 1-celled, rough-walled

Physiology

 * nutrition, uses fructose, sorbitol and sucrose

Habitat and ecology

 * reported from dermatophytosis-like infection, heart valve infection
 * resistant to amphotericin B
 * etc, etc.

Week 5 - October 14, 2015: Expand your article in your Wikipedia sandbox

 * Homework
 * Do not edit the article in the main space.
 * Write a 3–4 paragraph draft of your article in full sentences including citations on your Wikipedia sandbox.
 * Make a Taxobox for your species using the template below and paste it in at the top of your sandbox right below the code line, replacing the temporary names (e.g., "Division_name") with the correct taxonomy based on the record on MycoBank or Index Fungorum:


 * Milestone
 * All students have started editing draft articles in their Wikipedia sandboxes.
 * Once you have created your Taxobox I will start looking for an image you can use. Please do not upload one yourself or "harvest" one from the web. You can only use images that have proper copyright clearance otherwise they will be deleted.

Week 6 - October 21, 2015: Helping your peers

 * Assignment (due Friday October 30, 2015) (worth 5% of your grade)
 * Review and comment on the draft articles of at least 2–3 your classmates (last week's homework). Provide comments and constructive criticism to help them polish their articles and fix any major issues. Do not just say "Nice job! That looks great!!". You can suggest additional or better references, ways that they can organize the headings and subheadings of their articles to improve the flow, other articles on Wikipedia that they could look at that might help them to build their article, essays on Wikipedia they could read that might help them to overcome issues they might be having, etc. The more, the better.
 * If your peers have had difficulties carrying out the homework assignments from week 4 and 5, this is your opportunity to help them.
 * Leave your comments on their user talk page, do not edit their sandbox.
 * Continue to work on your article and integrate the comments you receive.


 * Milestone
 * All articles have been reviewed by others. All students have reviewed articles by their several of their classmates.

Week 7 - October 28, 2015: Your midterm exam is this week

 * Homework
 * Continue to work on your article

Week 8 - November 4, 2015: Polishing your article

 * Homework
 * Continue research on your article.
 * Take a look at several of the articles of your peers and comment on them.

Week 9 - November 16, 2015: Final due date

 * Assignment (due Monday November 16, 2015) (worth 15% of your grade)
 * Leave your article in your sandbox and I will grade it there. If there are revisions to your article date-stamped after the due date, I will grade the last revision prior to midnight on the due date.
 * Frequently asked questions:
 * 1. What do I need to hand in?
 * I plan to grade your assignment based on what is in your sandbox at midnight on the due date. All marking will be done from your Wikipedia sandbox based on the last revision prior to the due date.


 * 2. What happens to my article after the due date?
 * Once I have taken a look at it, I'll follow-up with you about any questions I have. In most cases I'll also do some light editing. After this, either of us can go through the process of submitting it (I'm happy to do it if you feel the lack of a pending grade causes you to lose interest). You've all done quite good work, and I fully intend to make sure it all gets into the main encyclopedia.


 * 3. Do I need to "submit" my article in Wikipedia by clicking ?


 * No. Whatever you do, don't click submit your draft for review!. If you do, chances are it will wind up with an editor unfamiliar with the Education Program who will decline it. It is much better if I have a chance to go through your article first to make sure there are no major errors and that it's adequately written before it gets submitted to the editors. Once I have examined your article, I will do one of the following things myself (or instruct you on how to perform them):


 * a. If an article on your fungus already exists (and about half of your fungi already have stubs), the article can be migrated to the main space by clicking  in your sandbox, copy everything below the   tag, then go to the article stub in the main space, click   there, delete the content and paste in yours and make a note in your edit summary that your edit was a major revision to a stub as part of a WP:Education project, and sign it.


 * b. If your fungus does not already have a stub in the main space, one will need to be created. In this case it is essential that the name of the fungus is spelled correctly during the article creation. If a spelling error is made at the creation stage, it is difficult to resolve. I would prefer to do this myself if this is the route that is needed.


 * 4. I still want a photograph but you haven't given me one.
 * That means that I don't have one, at least not right now. That won't affect your grade. But I do plan to try to grow some of these species and obtain photographs in the next several weeks at which time I will attach them to your article.


 * Milestone
 * Students have finished all their work on Wikipedia that will be considered for grading.

Grading
Wikipedia contributions will be graded as follows:


 * 5% each (x4): Participation grade for early Wikipedia exercises (weeks 1, 2, 4, and 7, due September 18, 25, October 16, and October 30, 2015)
 * 15%: Quality of main Wikipedia contributions due November 13, 2015