Record the data of "BLAST"
Guidelines
For full points your report MUST meet the following criteria:
All reports should be typed and single spaced, with an extra space between paragraphs.
Avoid personal pronouns (I, we) – and do NOT USE THEM AT ALL in Methods or Results (there is some leniency in the Intro and Discussion but if possible avoid it there too). Don’t say, “I used a mortar and pestle to mash up some avocado with distilled water.” Instead say, “The avocado was mashed with some distilled water using a mortar and pestle.”
Each section should have a header (Introduction, Materials, Methods, etc). Pages should be numbered at the bottom of the page.
There should be no spelling errors. Grammar should be correct. Scientific names should be written in proper format, ie. Genus species or G. species.
Title Page: Your title should be a single sentence. EXAMPLE: “Identification of An Unknown Bacterium”. Below that include your name and the number of your unknown.
Introduction: State the purpose of your study in a few sentences and in VERY general terms (ie no details, no procedures, no results) state how the study was conducted. Then give examples of how this type of study is important i.e., why is the ability to identify unknown bacteria important?
Materials and Methods: This section should contain a detailed description of how each test was performed so someone else can perform the same experiments and obtain the same results.
Do not mention dates and you should not feel you must describe techniques in chronological order; use any order that makes sense.
Use a separate paragraph for each method – you can group things together if it makes sense to do so but your choices must be sensible.
Briefly mention what the test was trying to determine but do NOT describe the results, do NOT describe the hypothetical results and do NOT write in present or future tense. –
Example of correct wording “In order to determine if it was completely cooked, a potato was smashed with a hammer”
An example of what NOT to do. “Next smash a potato with a hammer; if it smashes easily then this is a positive result indicating the potato is done but if the potato is immediately flattened this is a negative result indicating the potato needs further cooking time”.
Do mention each step, temperature, length of time or amount of reagent.
Do not mention that you used aseptic technique as this is assumed.
Similarly you don’t have to go into detail about basic techniques – eg. how to prepare a smear, inoculate media, do a pure culture streak, etc – stating that you performed these techniques is sufficient. However, DO give times, temperature and amounts of reagents eg. For incubations or staining.
Although it may feel natural to say what result was obtained after you describe the procedure, do NOT state the results here. Results should be placed in the results section (not the Materials and methods section). This section should be written in your own words, not directly copied from the lab manual.
Results:
This has two EASY parts.
ONE. In a single paragraph, describe the physical characteristics of your unknown. This should include both the growth characteristics in different types of media (see culture characteristics lab), as well as features visible on a slide (morphology, arrangement, and Gram staining characteristics). Also include any information you have obtained regarding any other physical characteristics (ie endospores, etc.)
TWO. Make a table that clearly and concisely shows the results for each of the tests done on your unknown. Columns are: test, date, observations, (optional: positive/negative).
Discussion:
First make a flow chart showing your process of elimination from numbered tube to best candidate.
Next write a series of logical and chronological paragraphs explaining your flow chart. “For unknown 67, the Gram stain revealed it was a Gram positive rod, which eliminated all Gram negatives and the Gram positive cocci. The glucose test was negative, indicating this organism cannot ferment glucose; this eliminated four potential groups including a,b,c, and d. Then briefly list the series of tests that narrowed it down to the group x.
Following that discuss each test that ruled out any bacteria and describe that decision point. How many were ruled out. What did this test reveal about your unknown (metabolically). Do NOT reiterate results or observations unless you are explaining how/why a test was difficult to interpret.
E.g. this would be a poorly written sentence “Then I did a catalase test and it was positive.” A better statement would be “A positive catalase test indicated that the organism has the enzyme catalase which converts H2O2, one of the toxic byproducts of oxygen metabolism, to the more harmless products of H2O and O2.” Your statement of the significance of each test must be written in your own words. “This eliminated 27 species leaving 35 contenders”
Once you get to a smaller number of candidates (less than 20 let’s say) then you can start mentioning them specifically. Eg. The negative urease test ruled out species x, y, z and w, leaving 8 candidates remaining.”
AGAIN: this part of the discussion shows how you eliminated all possible groups and decided on your specific answer. This means you should start with the Gram stain and proceed with each of the subsequent tests that narrowed it down to the specific organism.
Once you have determined the identify of your unknown bacterium, then make a new paragraph to discuss your sequencing results – do you feel they helped, confirmed, contradicted or were useless? Don't worry about including the methods in your methods section and don't worry about going into much detail. What will you do with the results is more important– in other words you have a final opportunity to use the sequence data to change your ID if you feel that is more reliable AS LONG AS you defend your choice with compelling data.
Now that you have an ID, you should read about the group it belongs to in Bergey’s Manual, your text, at the CDC, WHO and any other reputable source. You can use the internet, but stick with sites that end in .edu or .gov and please note that while it can be a useful starting point, you cannot use Wikipedia – or ANY wiki, not even Microbewiki - as a source for a formal lab report. Likewise do not rely on the content on educational websites written for a class – such as microbiology 300 at the University of Utah. This is not peer reviewed! Depending on your species, this may mean discussion of the family, genus, or species of your bacterium. The defining characteristics of the group in general and your species in particular should be included, as should their significance to humans and common habitats. Information should be cited.
Also in your discussion, you should point out any discrepancies between expected results and actual results. Indicate possible sources of error and any alterations you would make in a subsequent study.
The discussion should be at least one page and cannot exceed three pages. Be sure you consult at least 2 sources to provide specific information about your organism and you should provide at least 3⁄4 of a page about the organism based on the researchyou’ve done.
