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Instructions for research paper   1)There should be a title page – or at least minimally there should be a paper title, your name and the course name should be on it at the top of the first page of the research paper.  Following the title, your name, etc., there should be an introduction section (approximately a paragraph or two), the main body of your paper and then a conclusion section (at least a paragraph or two). The paper should be approximately 4-5 pages in length, not including the title page or bibliography.  This will be described further a little later on in this document.                                                                                                          2) Make sure there is a bibliography section (i.e. list of references a.k.a. works cited) at the end and there should really be more than 4 to 5 references that are peer-reviewed references (or at least highly valid sites like the government’s CDC site or the UN’s WHO site) (NOT including your text book and lab manual).  Wikipedia as a reference for text of this paper is NOT acceptable.  If using a website from an organization such as the WHO, you need to provide specific URL (website) information for the particular page or subsection you looked at and technically you are also supposed to provide the date when you accessed the site.  Do not just say that you used a “CDC” or WHO” site (and 2 WHO sites [or 2 CDC sites as a 2nd example] do not count as 2 independent sites because the first site could be a “home page” directing you to the other site – even 2 content-related WHO sites coming from the same home page will not count [or CDC sites as a 2nd example]).  At least one of your references should be a review article on the subject from a peer-reviewed journal such as Emerging Infectious Diseases or a research article from a journal such as Journal of Bacteriology.  Read the entire article – do not just use the abstract. Copies of your references should be turned in with the final version of the paper as above^ (or at least the most useful pages from your references so I can verify the use of its content.) a)How to format your references: (In reality, there are several different styles regarding creation of a bibliography.  Many of you had exposure to APA and / or MLA style. The style I am providing below is what many scientists use: CBE / CSE, which share many similarities with APA and MLA.  It is all right with me if you want to continue using APA or MLA style, because the same basic information is included regardless of style (the differences are in the organization of that information).  I am mostly concerned with you [the student] demonstrating to me that you know how to do citations properly and know how to generate an appropriate bibliography / reference section / work cited list.) i)An example of an appropriate reference from the internet website would be:  United States Department of Health and Human Services Centers for Disease Control and Prevention. Updated on Jan. 9, 2008. Shiga toxin-producing Escherichia coli (STEC) 2005 Case Definition. National Notifiable Disease Surveillance System.  Available at http://www.cdc.gov/ncphi/disss/nndss/nndsshis.htm , accessed 3/28/08. (= Ref. 1).   ii) You may also be using journal articles and a sample reference would look like Trachman, J.D., Yasmin, M. 2004.Thermo-osmoregulation of heat labile enterotoxin expression by Escherichia coli. Current Microbiology 49:353-60.  (= Ref. 2) iii) NY Times articles, etc. may also be used.  An example of this way this type of article would be referenced: Murphy K. Concern Mounts as Bacteria Resistant to Antibiotics Disperse Widely.  NY Times, published Aug. 22, 2006. (= Ref. 3) iv)Also, you should be using your textbook and the textbook should also be referenced (as many of you were doing for your lab reports and other writing assignments).  One way to reference your textbook would be: Tortora, G.J., Funke, B.R., Case, C.L. 2007. Microbiology: An Introduction (Ed. 9). Pearson: Benjamin Cummings, San Francisco, CA. (= Ref. 4) IMPORTANT: For this project, do NOT use sites like WIKIPEDIA for the text content of this paper  or for the poster. b) Example of how to carry out citations in a text: E. coli, in many cases, is completely harmless and is commonly found as a commensal of the GI tract (Tortora et al., 2007); however, as we know from reading the NY Times articles on enterohemorrhagic E. coli (EHEC) (Murphy, 2006) as well as what the professor described about her published research on enterotoxigenic E. coli  (Trachman and Yasmin, 2004) sometimes infection of the GI tract by certain strains of E. coli can lead to disease in human beings.  Many of these organisms pick up traits characteristic of more virulent microorganisms that often cause disease in the GI tract, such as EHEC picking up virulence factors from shigella species that cause dysentery (http://www.cdc.gov/EPO/dphsi/casedef/shiga_current.htm). Alternatively: E. coli, in many cases, is completely harmless and is commonly found as a commensal of the GI tract (4); however, as we know from reading the NY Times articles on enterohemorrhagic E. coli (EHEC) (3) as well as what the professor described about her published research on enterotoxigenic E. coli  (2) sometimes infection of the GI tract by certain strains of E. coli can lead to disease in human beings.  Many of these organisms pick up traits characteristic of more virulent microorganisms that often cause disease in the GI tract, such as EHEC picking up virulence factors from shigella species that cause dysentery (1). c)When you turn in your paper, you need to submit photocopies of your reference material (or at least key pages from each reference) (with the exceptions of: textbook & lab manual). These documents should be in a section labeled APPENDIX I. 3) Wherever you cite other individuals’ words or ideas or information that is NOT common knowledge, there should be a citation.  A citation is an indication that these thoughts, words, information, etc. are someone else’s – these can be done as endnotes rather than footnotes.  The citations can be numbered i.e. 1, 2, etc. with the complete information at the end in a bibliography (work cited) section correlating to the numbers used in the text. 4) However, a lot of the text of this assignment should really be your own words – you should be paraphrasing – this means that much of the text should not be someone else’s exact words.  However, regardless, wherever there is an exact quote or a paraphrase containing information that is NOT your own (and most of what you are writing about, is NOT gong to be common knowledge), there needs to be a citation.  If you are using an exact quote, the words should be enclosed in quotation marks, i.e. “The exact quotation should be in quotation marks as is occurring with this sentence.” 5) This paper should not consist of “piecing” together long passages of other people’s texts nor should it be minor little rearrangements of these other people’s texts, or minor little rewording of these other people’s texts.  There should be a logical flow to the information you are providing in your chosen words.   6)  This is not to say that you can not use someone else’s ideas (or information gathered from  them) at all.  However, the other person’s words/ ideas do need to be cited properly.  In academic circles, it is perfectly acceptable to use someone else’s ideas or information from their work as long as it is attributed to the original owner of the ideas or information.  Furthermore, by performing a thorough search of the “literature” and properly attributing the ideas or information, it makes the writer look more learned and “diligent” in carrying out the assigned task. 7)Another example of where you should be inserting your own thoughts is at the end of the paper. What are your thoughts? What do you feel you learned by writing the paper?  8) You may choose to write a slightly lengthier paper.  If you decide to go beyond the 4 to 5 page minimum, among the items that could be included would be a small introductions with some more thoughts in your own words.   9)Some other brief reminders about the paper:   a) The length is a minimum of 4 complete to 5 pages and the type should be double-spaced.  If your paper is 4 complete pages, your bibliography section should be on the 5th page. If your paper is 5 pages long, then the bibliography section can still be on the 5th page. The paper length of 4 to 5 pages does not include figures, tables, etc.  If you include this type of information, refer to it in your text and include it in an appendix at the end of the document.  These may be some of the figures, tables, etc. used in your poster presentation.  These will be in APPENDIX 2.   b) You should be using text in the range of 10 to 12 font size. c)There should be the standard 1 inch margins on the left, right, top and bottom borders. Note: Your paper is being judged on content as well as your ability to demonstrate information  literacy.   A)You need to use appropriate resources and they should be properly documented (see above). B)You need to properly cite in the text of your paper (to give attribution to the authors who provided with the content of your paper).  Instructions are provided above.  Use MLA, APA or style provided in this document.  The information is similar but maybe arranged differently. C)You need to have a “proper” bibliography / references list / work cited list.  The references should be correctly referenced (format to some extent is less important than content – use MLA, APA or the style given to you in this handout (the information expectations are similar, but information is arranged slightly differently). D)The content needs to be accurate and you need to attempt to put some of the information in your own words (i.e. paraphrase). I will reward you for the attempt if done with some degree of accuracy. Put quotation marks around exact quotes.  Plagiarism is not acceptable. E)Make some attempt at using academic English.  Please go to the Writing Center for help if you feel the need. Also submission of a rough draft a week or so before it is due would be a wise move so you can get feedback from me. F)Go to the library workshops for help regarding finding resources, regarding plagiarism, etc. if you need a refresher. Many of you have taken these workshops for your English classes. Some instructions/ guidelines for writing about a specific microorganism on a specific microorganism regarding global climate change 1)In the introduction, write a discussion as to why your chosen microorganism is associated with the problem of global warming/ global climate change..  What is the microorganism’s host range?  Is it restricted to humans?  Is it transmitted directly or indirectly – or both? Does it require a vehicle or vector for transmission?  Does it have a preferred portal of entry i.e. does it matter how it enters the human body with respect to its ability to cause infection or disease?  What is the microorganism’s reservoir?  Can it be found as a commensal of the human being?  Is it part of the normal human flora?  Can there be carriers?  Is the microorganism only found in certain parts of the world? Certain climates? Certain types of local environments? 2) In the main body of the paper, there are several subsections to be considered (which might overlap in content to a certain extent with the introduction).   a) Type of Microorganism:  What kind of microorganism is it?  Is it bacterial, viral, fungal.  You should discuss your organism somewhat.  If it is viral, fungal, etc. you may have to do a little extra reading in one of the non-assigned chapters like Chap. 13 on viruses and Chap. 12 on Fungi, Protozoa, etc.  Also, Chap. 21-26 on specific diseases and microorganisms may contain useful information. b) Epidemiology:  How is this organism transmitted to human beings?  Is this related to points discussed above?  Where is this microorganism normally found in the environment – the microorganism might even be typically associated with human beings but we did not necessarily know about it until recently?   Has human behavior or environmental conditions changed to cause this microorganism to now cause human disease?  Has the microorganism evolved (changed at the genetic level) to become more pathogenic or more easily transmissible to humans, etc.?  Is the microorganism considered to be contagious (communicable)?  c) Disease and virulence factors:  What kind of disease(s) is this organism associated with in human beings? What is known about its virulence factors?  Is there anything particularly interesting in the way the microorganism interacts with the human immune system (this point relates to the virulence of the microorganism)?  Does the organism cause acute /chronic/ subacute/ latent infections?  Are the infections sporadic in the human population or is there potential for the microorganism to cause epidemics or even pandemics?  Does the microorganism cause disease in the human being as a primary infection or does it cause problems because it sets the stage for secondary infections? d) Detection/diagnosis: Is this organism easy to diagnose / detect in humans? In their natural environment? How easy is the microorganism to grow in the laboratory? Study in the laboratory?  Why or why not? e)Treatment: If disease by the microorganism is treated, describe how?  Can we use antibiotics or other drugs?   Why or why not?  Are there problems with drug resistance? f)Prevention: If disease by the organism is preventable, describe how?  Here we are referring to several considerations:   a) Is there a vaccine available?  Is it widely used?  Are there problems with the vaccine or with making it widely available?   b) If the vaccine is not used widely, explain why?  If there are other problems with the vaccine explain (there may even be societal issues involved).   g)Breaking the chain of transmission: Are there other options with disease prevention by this organism?  How about breaking the chain of transmission?  This might require thinking about disinfection, etc. or changing human / animal behavior / pesticide use / other environmental considerations.  3)Conclusion: Provide a summary statement regarding your infectious disease agent regarding its association with global warming. Please focus on your microorganism in its particular context.  In some cases it may be particular strains or serovars  Note: Lists are provided in a separate document.