Microbiology Journal of Cellular Biochemistry
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Microbiology Journal of Cellular Biochemistry
STAPH LAB REPORTS
Microbiology 311L – Fall 2017
first draft due in lab 7 & 9 November
final copy due Monday 20 November
You and your lab partner are producing and handing in a JOINT lab report for the Staph lab. You either both swim or you both sink. The format and grading scheme are described below. Realistically, you’re probably looking at 7-10 pages – maybe more.
Remember that you’re telling a story to a reader: what you did, why you did it and what you found. You’re telling the story in a way so that readers can interpret your data, come to their own conclusions, and if they want, have enough information to try and reproduce your experiments.
Please DO NOT INCLUDE the mixed Gram (+) and Gram (-) culture from the lab exercise or the PDFs of the DNA sequencing chromatograms.
TITLE and AUTHORS
- do this on a separate page – each of the other sections don’t have to start on separate pages
- come up with a descriptive title telling the reader what you did in your project
- list the names of the people who did the work – you decide on the order of the names
- Abstract: none needed for this report
INTRODUCTION
- Write some background of what is known about the Staphylococci which live on / infect humans and exist otherwise in the environment. This doesn’t need to be an exhaustive list with what they all are or do. Which ones are the big players in our normal flora / normal environment and which ones cause some of the major problems?
- Talk briefly about the idea of multi-test media and about 16S rRNA sequencing for identifying bacteria. Google 16S and you’ll hit some good information.
- Typically the last paragraph of an introduction says something like “In the present study, we attempted to…..” or “The goals of these studies were to…..” and then something like “In our studies, we found that…..”
MATERIALS AND METHODS
- Divide this section up into subheadings for each of your major techniques. Information you want to have in here includes:
– how/where you collected samples and how you plated them
– how you did Gram staining or tests like coagulase (reference these – not to my labs but to real publications!)
– which sample was inoculated into the Staph strip and how you finished the tests for the strip
– which sample was put into the PCR, how you set up the PCR reactions and how were they cycled
– how you cleaned up your DNA with the spin columns
– how you did a gel (here’s how to say it – modify it a bit for your report but this is the idea: 12 ml of each purified PCR reaction was mixed with 3 ml of 5x sample loading buffer and then run in a 1% agarose gel containing 1 mg/ml ethidium bromide in 1x Tris-borate-EDTA buffer (TBE). DNA size markers (whatever we actually use) were run as standards. The gel was run at 125V in 1x TBE for approximately 45 minutes. PCR products were visualized and photographed on a UV transilluminator). “Hyperladder” is the brand name of a particular set of DNA gel size markers. We don’t use it so please just refer to them as markers
– how DNA sequence analysis was done (see lab 8)
– you can include a flow chart if it will help to explain things (call it a Figure)
– all the info for tests and molecular stuff is in your labs!
FIGURES / TABLES
- Make your figures and tables FIRST. They will be the basis for writing the rest of your paper.
- You could include any pictures (plates / Staph strips); a table of Staph strip results; a screen shot of your DNA sequence analysis; further sequence analysis (% identity etc)
- Keep the figures simple. Massive tables of numbers are a pretty sure way to loose the attention of a reader. You can use color to some extent, but remember that most journals are still in paper format and are published in black and white.
- If you show tables, make sure to provide column and row headings.
- Make sure to have a figure legend for each figure / table. Give a brief description of what the reader is seeing for each and briefly tell what was done. You can embed them in the text right next to the figure or you can put the figures and their legends in a separate section of the document.
RESULTS
- Walk the reader through your figures and make sure to refer to the figure/table numbers as you go. Assume they really don’t know much about what you did and use the results to tell them about it – think about some freshman bio major reading this, not Dr.O.
- Stick to the facts in this section but don’t interpret the findings here. That’s the purpose of your discussion. Lead the reader from one figure to the next in some logical order with some transitions between the figures in your text.
- If you didn’t get a PCR product from which to obtain DNA sequence, still show your gel (markers with sizes indicated) and just state what you were trying to do but that you didn’t get a product and so no DNA sequence is available.
DISCUSSION
- This is where you can discuss your interpretations of your results. Were your results in line with what is known at Staphylococci in general and about the particular ones you identified? Were your unknowns one that your would expect to find in the source (nose, throat, cell phone etc) you got them from? If not, why not???
- Here’s a good place to talk about some reasons why you might not have gotten a PCR product but what information you could have gotten from it (ie how does 16S rRNA sequence allow you to determine genus/species?)
- Often, the first paragraph describes again what you were trying to do and an overview of what you found.
REFERENCES / LITERATURE CITED
- You need to have at least 5 references IN ADDITION TO the textbook.
- ONLY 2 WEBSITES CAN BE CITED as sources!
- WIKI is NOT an acceptable reference for a lab report. It is, however, a good place to get started for some basic information. Google Scholar and PubMed are great places to look for real published information.
- Each scientific journal can have its own format for references. Let’s all use this one from the Journal of Cellular Biochemistry for citations from journals:
Owen TA, Aronow M, Shalhoub V, Barone LM, Wilming L, Tassinari MS, Kennedy MB, Pockwinse S, Lian JB, Stein GS. 1990. Progressive development of the rat osteoblast phenotype in vitro: reciprocal relationships in expression of genes associated with osteoblast proliferation and differentiation during formation of the bone extracellular matrix. J Cell Physiol 143:420-430.
or this one for citations from books:
Owen, T. A., J. Holthuis, V. Shalhoub, E. Markose, M. Aronow, J. B. Lian, and G. S. Stein. 1990. Evidence for a functional relationship between proliferation and initiation of osteoblast phenotype development. in Calcium Regulation and Bone Metabolism. D. V. Cohn, F. H. Glorieux, and T. J. Martin, eds. Elsvier, Amsterdam, the Netherlands. pp. 371-376.
GRADING
- This report is worth 20% of your lab grade (ie 10% of course grade) — 7% of your lab grade for the first draft — 13% of your lab grade for the final version
- Total points (100 possible) will be determined as follows for EACH version: (see the separate grading sheet for a more detailed break down of points)
Possible Points
Appropriate title, names 10
Introduction 20
Materials and Methods 20
Figures and Results 20
Discussion 20
References (number, validity, format) 10
PRACTICAL STUFF
- I’m not counting pages, but am looking for you to do a nice job telling your story.
- Please double space and use 11 or 12 point font. I’m old…….
- TAKE THE TIME TO PROOFREAD!!! In this age of spell and grammar check, there’s absolutely not excuse for typos and sentences that aren’t sentences. I will dock you points for this stuff!
- If there are journal articles you find in PubMed that you would like to use as sources but our library doesn’t have access to them, please send me the PubMed ID number (PMID) and I’ll try to get you the pdf file.
Micro 311L – Staph Lab format Fall 2017 Page 4
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