Medical Microbiology & Techniques

Lab Report for Gram Negative Rod Unknown Identification – Outline and Guidelines

Lab report format/sections

Format/Submission (4)

• All text and images (in the report) must be computer-generated.
• DO NOT include a title page.

 

• All main-text fonts should be 12-pt font and in Arial, Times New Roman, or Calibri.

 

• Pages should be numbered.

 

• Include a unique and descriptive title.

 

• Include (1) your name; (2) course code/title; (3) GA names.

 

Introduction (4)

As with any introduction, begin on a general level, moving to more specific information.

• Discuss the importance of unknown identification in medical microbiology.

 

• You’ll may need to cite a peer-reviewed source here. For citations/references, you can use the style of the Canadian Journal of Microbiology

 

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(http://www.nrcresearchpress.com/page/cjm/authors#guide - it’s a pretty simple style), Cite (author, year), not by number.

 

• Last paragraph in introduction should talk about the purpose of this experiment.

 o  What will you be doing (i.e., what approach) to identify your unknown?

 

• Around 350 words/ ½ page (single-spaced) maximum.

 

 

Materials & Methods (4)

 

 

• A folder with pictures of all possible test results will be provided to you (unknown 57). Not all the tests provided are needed for the identification.

 

• Write short paragraph briefly describing how each of the necessary test is done. You can reference these tests and report the findings in the results section.

 

o This is not a protocol! It is enough to say that “a smear from the culture was Gram stained,” without going into each of the steps of a Gram stain.

 

• You should not be discussing the rationale for the tests in this section.

 

• Look at the materials and methods section of a journal to see the style of writing in this section.

 

• In many cases, it’s best to divide up your M/M and give each one of your techniques a header of its own; it looks much easier and organized this way.

 

 

Results (8) [+ Figures & Tables (8)]

• This should be at about 2-3 pages (single-spaced), 3 max.

 

• The results section is where you inform the reader of what you did, and what results you obtained. Walk the reader through the experimental process. i.e., what workflow must be followed? Why is a certain test done? What was the result according to the pictures you received (unknown 57)? How does this inform the next experiment? etc.

 

• Include a description of the results you observed, but do your best not to interpret the results. o E.g., It is perfectly acceptable to say “the slant changed to a blue color, indicating that the

 

bacteria can utilize citrate”. Do not, however, go on to discuss the implications of the bacterium being citrate-positive here.

 

• Within the results text, you must include reference to all of your figures and tables.

 

• Always describe what type of data you are referring to. E.g., As opposed to simply stating,

 

“Figure 1 shows that the bacterium is citrate positive.”, the better way to make reference to

 

figures would be, “A colour change in the citrate tubes incubated for 24 hours (Figure 1) indicate that the bacterium is citrate positive.”

• You are required to include in this section:

 

• Figure 1: Flow-chart/dichotomous key for unknown determination – we should be able to use to chart to get to all 10 of the unknowns, not just yours.

• Table 1: List of results – include all of the tests that you consider necessary and all of the

 

corresponding results, whether or not they were conclusive or consistent with your expected results.

• • The identification of the unknown based on the tests you selected.

 

• Be sure to include figure legends, below the figure, including a unique and descriptive title, as well as a description of the figure. (Note – the figure legend is NOT the same as a “graph

 

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legend”.) We should be able to figure out what’s happening in the figure based on this legend (but an analysis of the results shown should not be included here).

 

• Be sure to include table legends, above the table, including a unique and descriptive title. If there are any footnotes that need to be made, include those at the bottom of the table.

 

Discussion (Topics do not have to be addressed in this order) (8)

• Expect this section to be around ½ or ¾ page (single-spaced), 1 page maximum.

 

• This is where you tie together concepts you brought up in the introduction, with the new data generated in the course of the experiments. In this section, you will briefly reiterate the results (not at the same level of detail as in Results) and interpret these results.

 

• What is your conclusion (identification of your bacterium), based on the results you obtained?

 

• Provide some background information about your microbe, especially with respect to medical microbiology. Some information may include (but not limited to):

 

o Where are these bacteria found (i.e., in nature or in living organisms)? o How are these bacteria relevant in medical microbiology?

 

o  Other interesting/surprising information.

• Note formatting of scientific names:

 

• At first mention, genus name is always capitalized and italicized; species name is lowercase and italicized.

• E.g., Citrobacter freundii

• For subsequent mentions, use first initial of genus, in capital, and spell out species name.

• E.g., C. freundii

 

• Note the use of capitals/lowercase letters, the period, the space, and italics. Watch for auto-correct errors.

 

References (6)

 

• You must include (and cite) at least 1 relevant, scholarly article. (These should be peer-reviewed scientific articles from a reputable source.)

 

• Follow the in-text citation and reference style of Canadian Journal of Microbiology OR Council of Science Editors (CSE)/Council of Biology Editors (CBE). See guidelines later in this document.

 

• This section also includes correct citations in the rest of the report.

 

Other Documents to Include – Scan as PDF or images (.png, .jpg only – convert from HEIC if that is your phone’s default)

• Expected results table and flowchart (Worksheet).

 

Notes:

 

• The mark you receive on this report is based on the quality of the report and your judgment and reasoning skills. Marks for successful (or unsuccessful) identification of your unknown are awarded as one mark (1/45).

 

• Be careful with how you use references. Paraphrase, cite, and include your sources in the References section. Failure to properly cite sources will constitute academic dishonesty and may result in further disciplinary action. This includes taking sentences and thoughts, word-for-word, even if they are cited. When paraphrasing, ensure that you give appropriate credit (immediately after the statement using the information from that source).

 

 

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Guidelines for referencing:

 

Referencing in the body of your text:

 

Statements based on fact must be cited in the text of your paper immediately (i.e., not at the end of a string of sentences based on the article). Each reference you use must be cited using the surnames of the authors, and the year. Examples below are in the format of the Canadian Journal of Microbiology.

E.g.,:

 

Observations of nodule morphology at the microscopic level have been made, and are useful in identifying the characteristics of a functional nodule (Newcomb 1976).

 

Swamynathan and Singh (1995) studied purine mutants and suggested that S. meliloti pur^- mutants are unable to produce functional nodules because of pleiotropic changes on the cell surface of the bacteria.

 

If there are more than two authors, the citation should provide the name of the first author followed by et al. and the date. E.g.,:

 

Mutants were able to curl root hairs and promote cortical cell division, but did not produce infection threads (VandenBosch et al. 1985).

 

Buendia-Claveria et al. (2003) reported that a purine mutant of Sinorhizobium fredii HH103 produced ineffective nodules on some hosts, was unable to nodulate others, and also demonstrated changes in surface polysaccharides.

 

If you are writing a series of connected sentences in a paragraph based on one source, you only need to cite that source after the first statement.

 

Do NOT use numbered citations.

 

References section:

 

Full reference citations should be included in your References section. (Examples below are in the format of the Canadian Journal of Microbiology – see online guides to APA format for references.) There are tools (reference managers) that can be helpful (though not infallible – check for errors.). List sources alphabetically by the last name of the first author.

 

When citing a paper in a scientific journal, use this format: author, initials, date, title, journal, volume number, pages. E.g.

 

Koonin, E.V., Mushegian, A.R., Galperin, M.Y., and Walker, D.R. 1997. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25: 619–637.

 

When citing a book written by one or more authors (rather than a book with chapters by different authors) use this format: author, initials, date, title, (edition), publisher, location. E.g.,

 

de Kruif, P. 1996. Microbe hunters. Harcourt Brace and Company, San Diego, CA.

 

When citing a chapter from a book (where there is an editor), use this format: author, initials, date, title, editor, location, publisher, pages. E.g.,

 

Yost, C.K., and Hynes, M.F. 2000. Rhizobial motility and chemotaxis: molecular biology and ecological

role. In Prokaryotic Nitrogen Fixation: A Model System for the Analysis of a Biological Process.

Edited by E. W. Triplett. Wymondham, UK: Horizon Scientific Press. pp. 237-250.

 

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If you use different chapters in such a book (i.e., where chapters may have different authors), each chapter should be listed separately:

 

O'Brian, M.R. 2000. Heme biosynthesis and function in the Rhizobium-legume symbiosis. In Prokaryotic Nitrogen Fixation: A Model System for the Analysis of a Biological Process. Edited by E. W. Triplett. Wymondham, UK: Horizon Scientific Press, pp. 509-528.

 

Yost, C.K., and Hynes, M.F. 2000. Rhizobial motility and chemotaxis: molecular biology and ecological

 

role. In Prokaryotic Nitrogen Fixation: A Model System for the Analysis of a Biological Process.

Edited by E. W. Triplett. Wymondham, UK: Horizon Scientific Press. pp. 237-250.

 

If you are using an interview (or other communication) with a reputable scientific authority for the basis of a statement, you can cite that person in your references as personal communication. E.g.,

 

Hynes, M.F. 2016. (University of Calgary.) Personal communication.

 

In most cases, websites (including Wikipedia) are NOT acceptable reference sources. In a few cases, government or educational institutions may provide online information that can be cited as reference sources. (You may also need to refer to mass media articles published online, if you use them.)

 

If you are citing a website, use the following style:

 

Parrish, T. 2011. Eleventh case of Legionnaires' disease diagnosed. Pittsburgh Tribune Review, 16 September 2011 [online]. Available from http://www.pittsburghlive.com/x/pittsburghtrib/news/pittsburgh/s_757049.html#ixzz1YiGCECI [Accessed 19 Oct. 2011]

 

“Common knowledge” does not need to be cited. Textbooks for courses are NOT usually appropriate reference sources – you may use a textbook to gather information, but if it does not appear to be common knowledge, you should seek the original scientific publications that actually report the fact(s) described. If you are not sure whether something is common knowledge, please ask!

 

Help for paraphrasing, referencing and reference lists (and avoiding plagiarism):

 

Your write-up should be written in your own words and sources should be cited. This involves more than changing a few words and citing the source, as you are still using someone else’s intellectual work. Avoid including original phrases (or, of course, entire sentences) from your sources – if you do, they must be within quotation marks to clearly indicate that they are not your own words. (Such direct citations are rare in science, though – it’s expected that in nearly all cases, you’ll find a way to paraphrase the information.) Even following the order of particular sentences (that you may have reworded) in a paragraph from a source can be unacceptable, if you are presenting the same information – this is sometimes called “unacceptable paraphrasing”, and can be regarded as plagiarism. Plagiarism is representing someone else's ideas, writing or other intellectual property as your own, and is a serious academic offense.

 

Paraphrasing is the process of putting someone else’s ideas into your own words (without actually copying from the original). University students are expected to paraphrase appropriately in their writing. Be aware that paraphrasing someone else’s work, even if you list it as a reference, is considered plagiarism unless properly acknowledged in the text. Proper acknowledgement means that you indicate that you are paraphrasing. For example, you might write: “Brown and Desai (2000) reported, …” The source must also be listed in the References. It takes some practice to learn how to effectively paraphrase, but this is a necessary skill in scientific writing.

 

 

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Plagiarism:

 

Many people are unaware of what constitutes plagiarism. Consider the following sentences, taken directly from page 67 of: Gunawardena, AHLAN, Greenwood, JS, and Dengler, NG. 2003. Programmed cell death remodels lace plant leaf shape during development. The Plant Cell 16: 60-73.

 

"Therefore, a combination of electrophoresis of isolated DNA and the TUNEL assay were used to identify lace plant nuclei that were undergoing DNA fragmentation. Nuclei became TUNEL positive soon after tonoplast rupture and persisted until the very late stages of PCD in the sites of perforation formation. DNA laddering was not observed at any stage of perforation formation. Rather, extensive smearing, indicating DNA fragments form a continuous size range, was observed after electrophoresis of DNA from tissues with TUNEL-positive nuclei." (Gunawardena et al. 2003)

 

Now look at the following examples that represent possible ways someone might try to discuss that information:

 

Example 1:

 

Both electrophoresis of isolated DNA and the TUNEL assay were used in identifying lace plant nuclei that were undergoing DNA fragmentation (Gunawardena et al, 2003). Nuclei became TUNEL positive shortly after tonoplast rupture and persisted until the very late stages of PCD in the sites of perforation formation. Laddering of DNA was not observed at any stage of perforation formation. Instead, extensive smearing, indicating DNA fragments form a continuous size range, was observed after DNA electrophoresis from tissues with TUNEL-positive nuclei.

 

• This is plagiarism, even though the source is cited. Changing a word or two in each sentence is not acceptable - you must be able to extract the key points and put them in your own words, phrases, logical order, etc.

 

Example 2:

 

The researchers used electrophoresis of isolated DNA and an assay (TUNEL) to identify nuclei from plant cells where DNA fragmentation was taking place. "Nuclei became TUNEL positive soon after tonoplast rupture and persisted until the very late stages of PCD in the sites of perforation formation. DNA laddering was not observed at any stage of perforation formation." (Gunawardena et al, 2003). Smearing indicated that DNA fragments form a continuous size range as shown in TUNEL-positive nuclei DNA electrophoresis.

 

• The overall wording and structure of the paragraph are still too similar to the original. Direct quotes are rarely used in scientific writing, although inclusion of the reference and use of quotes does avoid plagiarism for this component of the text.

 

Example 3:

 

In their studies of lace plant cells undergoing PCD, Gunawardena et al. (2003) studied one of the hallmarks of this process: fragmentation of nuclear DNA. The TUNEL assay detects nuclei containing fragmented DNA, and nuclei in early to late phases of PCD were identified as positive via this assay. Electrophoresis revealed that the DNA fragments from nucleic acid isolated from such nuclei varied widely in size, unlike the distinct multimeric fragments generally observed in animal cells undergoing apoptosis.

 

 

The examples above are somewhat artificial, but should give you an idea of what plagiarism involves. It takes some practise to learn how to effectively paraphrase, but this is a necessary skill in scientific writing.