Wikipedia:Wiki Ed/University of Toronto/HMB436H Medical and Veterinary Mycology (Fall)
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- Course name
- HMB436H Medical and Veterinary Mycology
- Institution
- University of Toronto
- Instructor
- James Scott
- Wikipedia Expert
- Ian (Wiki Ed)
- Subject
- Mycology
- Course dates
- 2016-09-14 00:00:00 UTC – 2017-01-20 23:59:59 UTC
- Approximate number of student editors
- 30
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.
Why medical mycology?
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 PMID 11486286). If all this sounds interesting, then this course is for you.
The assignment
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 "Fungus of the Month" 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, 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!
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 count for 1 %, 10 % and 9 %, and these are the assignments described below in Weeks 1, 5 and 7. These are due by midnight EDT on September 16, October 14 and October 28, 2016, respectively. The actual text of your article is due at the end of Week 9 on November 11, 2016 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 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.
Timeline
Week 1
- Course meetings
-
- Wednesday, 14 September 2016
- In class - In class
- Overview of the course
- How will Wikipedia be used in the course?
Make note now of your assignment due dates and plan accordingly. I will grade the last version of your work in your sandbox date-stamped prior to midnight EDT on the due date:
- Assignment #1: Wikipedia enrolment and training - due Sept 16, 2016 (3 %)
- Assignment #2: Article outline - due Oct 14, 2016 (10 %)
- Assignment #3: Three peer reviews - due Oct 28, 2016 (6 %)
- Assignment #4: Final article - due Nov 11, 2016 (16%)
- Assignment - Assignment #1 – Wikipedia basics
- 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 Wikipedia Username Policy if you need help selecting an appropriate handle.
- Enroll in the course on the Wiki Education –?� I will provide instructions on how to do this in class.
- 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
- Course meetings
-
- Wednesday, 21 September 2016
- In class - 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.
- Handouts: Using talk pages, Evaluating Wikipedia article quality, Wikimarkup cheatsheet
- On your own
Practice editing and communicating on Wikipedia, introduce yourself to your classmates' by leaving a message for them on their Talk Pages. You can link to the talk pages of the other students enrolled in the course by clicking on the Students tab above.
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.
Week 3
- Course meetings
-
- Wednesday, 28 September 2016
- In class
- We will briefly discuss referencing on Wikipedia and Wikipedia’s copyright policy.
- I will assign each student with a species from the list below - you don't get to chose. I've assembled a list of "noteworthy" fungi that don't have adequate representation on Wikipedia. Not all of the species are human pathogens; some are important animal pathogens or plant pathogens while others are important because of biochemicals they produce.
- We will discuss references and I will provide some suggested online and book references in the list below (along with the code you need to embed the references in your Wikipedia article).
- Handouts: How to get help
Selecting the right references
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 Editing medicine topics.
- Assignment - Assignment #2 – Article outline
Once I assign you a species to work on, you should begin to assemble the outline of your article. Your outline will include all of the facts you intend to use in your final article and the relevant references that support those facts. You will be assembling your article drafts in your sandbox using the code template I will provide next week. In the meantime, you can begin to collect your ideas.
- Acrophialophora fusispora
- Amauroascus kuehnii
- Arthrobotrys oligospora
- Aspergillus candidus
- Aspergillus clavatus
- Aspergillus glaucus
- Basidiobolus ranarum
- Bjerkandera adusta
- Chaetomium perlucidum
- Chlamydosauromyces punctatus
- Cladophialophora carrionii
- Conidiobolus coronatus
- Cunninghamella echinulata
- Dactylellina haptotyla
- Fonsecaea compacta
- Harposporium anguillulae
- Madurella mycetomatis
- Nannizziopsis guarroi
- Neoscytalidium dimidiatum
- Nigrospora sphaerica
- Ophidiomyces ophidiicola
- Passalora fulva
- Penicillium spinulosum
- Penicillium verrucosum
- Petriella setifera
- Phialophora verrucosa
- Pleurophoma pleurospora
- Pleurostomophora richardsiae
- Rhinocladiella mackenziei
- Sagenomella keratitidis
- Tetraploa aristata
- Thermomyces lanuginosus
- Zasmidium cellare
- Online resources
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.
- MycoBank 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).
- UAMH Centre for Global Microfungal Biodiversity is the largest culture collection of biomedically important fungi in the western hemisphere, and it is located here at the University of Toronto. 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 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 will need to use your UTORID to access it unless you use a campus computer. 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.
- PubMed is another article search engine which is very useful in searching the biomedical literature. 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.
- Books
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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=barron1968>Barron, George L. (1968). The genera of Hyphomycetes from soil. Baltimore, MD: Williams & Wilkins. ISBN 9780882750040.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=domsch1980>Domsch, K.H.; Gams, Walter; Andersen, Traute-Heidi (1980). Compendium of soil fungi (2nd ed.). London, UK: Academic Press. ISBN 9780122204029.</ref>
- Farr D.F., Bills 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=farr1989>Farr, David F.; Bills, Gerald F.; Chamuris, George P.; Rossman, Amy Y. (1989). Fungi on plants and plant products in the United States (2nd ed.). St. Paul, Minn.: APS Press. p. 1252. ISBN 0890540993.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=howard2007>Howard, Dexter H. (2007). Pathogenic fungi in humans and animals (2nd ed.). New York, NY: Dekker. ISBN 0824706838.</ref>
- 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). You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=kane1997>Kane, Julius; Summerbell, Richard C.; Sigler, Lynne; Krajden, Sigmund; Land, Geoffrey (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. ISBN 978-0898631579.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=kirk2011>Kirk, P.M.; Cannon, Paul F.; Minter, David W.; Stalpers, J. A. (2011). Dictionary of the fungi (10th ed.). Wallingford: CABI Pub. / CSIRO. ISBN 1845939336.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=kwon-chung1992>Kwon-Chung, K.J; Bennett, J.E. (1992). Medical mycology. Philadelphia: Lea & Febiger. ISBN 0812114639.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=onions1981>Onions, A.H.S.; Allsopp, D.; Eggins, H.O.W. (1981). Smith's introduction to industrial mycology (7th ed.). London, UK: Arnold. ISBN 0-7131-2811-9.</ref>
- 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 caused 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=rippon1988>Rippon, John Willard (1988). Medical mycology: the pathogenic fungi and the pathogenic actinomycetes (3rd ed.). Philadelphia, PA: Saunders. ISBN 0721624448.</ref>
- 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 hyphomycetes, a number of ascomycetes and some zygomycetes. It gives tidy, comprehensive descriptions of important genera and species, including photographs, line drawings and taxonomic keys. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=pitt1999>Pitt, J.I.; Hocking, A.D. (1999). Fungi and food spoilage (2nd ed.). Gaithersburg, Md.: Aspen Publications. ISBN 0834213060.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=samson1981>Samson, Robert A.; Hoekstra, Ellen S.; Frisvad, Jens C. (2004). Introduction to food- and airborne fungi (7th ed.). Washington, DC: ASM Press. ISBN 9070351528.</ref>
- 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. You can use this reference by adding the following code to the list in your reflist template located at the bottom of your article:
<ref name=watanabe2009>Watanabe, Tsuneo (2009). Pictorial atlas of soil and seed fungi: morphologies of cultured fungi and key to species (3rd ed.). Boca Raton, Fla.: CRC. ISBN 1439804192.</ref>
Week 4
- Course meetings
-
- Wednesday, 5 October 2016
- Coding your article
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
{{tlx|User sandbox|YourName}} ← 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 History, Taxonomy, Growth and morphology, Physiology, Habitat and ecology, etc. Note that only the first letter of the heading is capitalized.
When using scientific names, capitalize and italicize the genus: e.g., Penicillium, Trichophyton''. Italicize but do not capitalize taxonomic ranks at the level of species and below: e.g., 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, e.g., Ascomycota, Zygomycota, but not in their English equivalents e.g., ascomycetes, zygomycetes; neither of these forms are italicized. The first time the name of a species is used, the genus name should be spelled out completely, e.g., Trichophyton tonsurans; but in subsequent uses, the name of the genus can be abbreviated to the first letter, e.g., T. tonsurans. You should be aware that there are two exceptions to this: 1) when you the name starts a sentence, and 2) 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 placed immediately to the right of text or punctuation with no space. Multiple references should not be separated by punctuation or spaces.
Copy the following code to your sandbox below the {{User sandbox|YourName}} template. Once you get everything functioning, you can start to replace the text with your own material and expand it accordingly.
{{Taxobox
| regnum = Fungi
| divisio = Division_name
| subdivisio = Subdivision_name
| classis = Class_name
| ordo = Order_name
| genus = Genus_name
| species = Genus_first_letter. species_name
| binomial = Genus species
| binomial_authority = publication_authority_name (date)
| synonyms = *First_synonym <small>authority_name (date)</small>
*Second_synonym <small>authority_name (date)</small>
*Third_synonym <small>authority_name (date)</small>
}}
==History==
*discovered in Switzerland in 1897<ref name=onions1981 />
==Taxonomy==
*originally considered a species of Penicillium<ref name=onions1981 />
*later thought to be a member of the genus Thysanophora<ref name=barron1968 />
==Growth and morphology==
*fast-growing,<ref name=barron1968 /> yellow colonies<ref name=onions1981 />
*conidia 1-celled,<ref name=howard2007 /> rough-walled<ref name=barron1968 />
==Physiology==
*uses fructose,<ref name=domsch1980 /> sorbitol<ref name=barron1968 /> and sucrose<ref name=domsch1980 />
*maximum growth temperature 38 °C<ref name=rippon1988 />
==Habitat and ecology==
*reported from dermatophytosis-like infection,<ref name=rippon1988 /> heart valve infection<ref name=kwon-chung1992 />
*resistant to amphotericin B<ref name=kane1997 />
*etc, etc.
==References==
Week 5
- Course meetings
-
- Wednesday, 12 October 2016
- Working on your article
Spend your time this week finalizing the outline of your article which is due at the end of this week. If you have questions as you work, please address these during the tutorial. If you have urgent questions, please post them to the course talk page and I will answer them there. Before you post a question, please look to make sure that your question has not already been answered! A few things to keep in mind as you complete the draft of your article:
- Work only in your sandbox, do not work on your article in the Wikipedia mainspace.
- Do not add images to your article draft. You can only use images that abide the Wikipedia Image Use Policy, otherwise they will be removed by other editors. Ultimately you may be able to locate one or more suitable images on Wikimedia Commons or possibly I can provide some. Either way I am not grading your outline based on how pretty it is. I will be grading it based on the text content. Bear this in mind.
Week 6
- Course meetings
-
- Wednesday, 19 October 2016
- Assignment - Assignment #3 – Helping your peers
If your peers have had difficulties on their article outline, this is your opportunity to help. Review and comment on three (3) draft articles written by your classmates (i.e., last week's assignment). Provide comments and constructive criticism to help them polish their articles and fix any major issues.
Spend a bit of time getting to know their fungus. Then 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 advice you provide to your peers, the better your grade in this part of the assignment will be. As you go about this exercise, please keep the following in mind:
- Do not just say "Nice job! That looks great!!". I expect you to provide meaningful feedback.
- 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.
Week 7
- Course meetings
-
- Wednesday, 26 October 2016
- Assignment - Assignment #4 – Final article
Starting this week you will begin to convert your article outline into a proper article. This means converting all of the facts you have assembled into flowing sentences. It may be appealing to use portions of sentences verbatim from the sources you used to find your facts. Do not do this because it is plagiarism (even if you cite it!). It is important that you put everything into your own words. This is not as daunting as it seems, and the training module linked below will help you to understand how to do this if you are having difficulty.
A few things to keep in mind as you go about this exercise:
- Continue to work in your sandbox only, do not work on your article in the Wikipedia mainspace. This prevents well-meaning editors from reverting your edits until your work is complete.
- Compare your work against that of your peers. This will help you to make sure that you have not missed essential components of your article. It may also give you ideas that you can incorporate to improve your final article. If you need to add additional references, that's OK.
- Re-read a few "good" articles on microfungi. This will help you to make sure that your tone and language are appropriate.
- As you write your text, make sure that the style and tone are consistent with the standards of Wikipedia. This link describes the criteria I will be using to grade your assignment: Wikipedia: Writing better articles.
Week 8
- Course meetings
-
- Wednesday, 2 November 2016
- Formatting your article
As you continue to work on your final article, below are a few points of guidance on formatting according to wikipedia conventions. If you follow these guidelines, I guarantee it will improve your final mark on the assignment.
- Only the first letter of a heading is capitalized.
e.g., ==Growth and morphology==
- The placement of citations is after punctuation with no space.
e.g., Conidia brown.[1] Conidiophores rough,[2][3] with prominent brown spots.[4]
- There is a non-breaking space ( ) between a number and its corresponding units.
e.g., 20 °C
- Make sure all of your references are consolidated at the end of your article enclosed in the reflist template rather than not inserted in-line.
- The word "fungi" is plural. So a sentence that starts "This fungi is important because..." might cause me to have a stroke when I read it. The singular is "fungus".
- Stay on topic. Your article is about your fungus, not other fungi or all fungi. Avoid including information of a general nature and focus instead on what is important or interesting about your fungus.
- Don't clutter your article with superfluous wiki links. You should only link a term the first time you use it. When you do insert a link, make sure it is specific and not a link to a disambiguation page.
Lastly, I want you to consider carefully the tone and style of your article by comparing the following passages before- and after editing of the article on Scedosporium prolificans. This comparison may also provide you with some ideas of how to spice up your facts with additional details you be able to draw from your references.
Before
History
Hennebert and Desai discovered this fungi as new in 1974 but they called it Lomentospora prolificans instead.[4] They thought it was related to the Beauveria species.[4] Malloch and Salkin came around in 1984 and found the same thing but they didn't know that Hennebert and Desai already found it so they called it Scedosporium inflatum because of the cell that makes its conidia that swells up.[9] They suspected that it was related to microascaceae fungi and maybe Pseudallescheria even though it didn't make the right kind of spore at the time.[9] Later in 1991 Guého and De Hoog looked at both species and figured out it should be called Scedosporium prolificans. That name is correct as far as DNA sequencing is concerned but even as recent as 4 years ago people were still calling it Scedosporium inflatum in papers which is wrong.[10]
After
History
The genus Lomentospora was erected by G. Hennebert and B.G. Desai in 1974 to accommodate a culture obtained from greenhouse soil originating from a forest in Belgium.[4] The fungus, which they named Lomentospora prolificans, was thought incorrectly to be related to the genus Beauveria - a group of insect-pathogenic soil fungi affiliated with the Order Hypocreales.[4][7] The genus name "Lomentospora" referred to the shape of the apex of the spore-bearing cell, which the authors interpreted to be a rachis resembling a bean pod of the sort constricted at each seed. The species epithet "prolificans" derived from the prolific nature of the mold's sporulation. The fungus was later independently described as Scedosporium inflatum by Malloch and Salkin in 1984 from a bone biopsy of the foot of a boy who had stepped on a nail.[a][9] The species epithet "inflatum" referred to the characteristically swollen base of the spore-bearing cell which they recognized correctly to be an annelide. Malloch and Salkin did not observe a sexual state, however they recognized the fungus to be associated with the family Microascaceae, and suspected it to be allied with the genus Pseudallescheria.[9] In 1991, Guého and De Hoog re-examined a set of cultures of Scedosporium-like fungi from clinical cases by careful morphological examination and the evaluation of DNA-DNA reassociation complementarity. Along with two strains from their own work, they found the cultures of Hennebert & Desai and Malloch & Salkin to constitute a single species which they confirmed to belong in the genus Scedosporium.[5] Lomentospora prolificans was then transferred to Scedosporium as S. prolificans, and Scedosporium inflatum became a synonym. This synonymy has since been confirmed by phylogenetic analysis of the nuclear ribosomal internal transcribed spacer regions.[10] Despite this change, and even as recently as 2012, the name Scedosporium inflatum has continued to appear in the medical literature.[11][12]
Week 9
- Course meetings
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- Wednesday, 9 November 2016
- Final thoughts
**Your finished article is due Friday November 11, 2016**
- 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 Submit your draft for review!?
No, 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 Edit source in your sandbox, copy everything below the <!-- EDIT BELOW THIS LINE --> tag, then go to the article stub in the main space, click Edit source 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 Ian (Wiki Ed) (talk) 20:33, 26 January 2017 (UTC).
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. Remember that I'm grading the content and form of your article, not how pretty it looks. 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.