Homework answers / question archive / Lab Practical-1 and Research Assignment and Report Fall 2021 - BIO 3302L Instructions and Guidelines You will be assigned a culture tube containing 1 type of bacteria

Lab Practical-1 and Research Assignment and Report Fall 2021 - BIO 3302L Instructions and Guidelines You will be assigned a culture tube containing 1 type of bacteria

Biology

Share With

---

Lab Practical-1 and Research Assignment and Report

Fall 2021 - BIO 3302L

Instructions and Guidelines

You will be assigned a culture tube containing 1 type of bacteria. You will also receive a set of pictures of different lab tests that were performed on this organism (these pictures are your data).  From this data you must deduce which of 10 bacteria is your unknown.

 

You will then write a lab report which will focus primarily on the RESULTS and DISSCUSSION sections.   

 

Your report must contain the following: 

 

Cover page – Your name, your instructor’s name, your section number, and the title of your project

 

Introduction – VERY BRIEFLY – state the objectives of your investigation and LIST THE 10 different bacteria from which your unknown is drawn – you could mention that 5 are gram positive and 5 gram negative and indicate these.  DO NOT PROVIDE A GENERAL DISCUSSION ABOUT BACTERIOLOGY.

 

 

Materials and Methods –BRIEFLY state that gram staining was performed and then list the different types of media (and their abbreviations) that were inoculated and incubated 48 hours, 37 °C. Blood Agar (BA), Mannitol Salt Agar (MSA), MacConkey Agar (Mac), and Phenylethyl Alcohol (PEA). DO NOT PROVIDE ANY DETAILS OR PROTOCOLS ON HOW these were prepared – it is enough to state that the plates were prepared using standard protocols.

 

Results – written text about your results should be contained EXCLUSIVELY in the figure legends (captions) that go along with your data figures and your table.

 

• Insert into your report all data pictures provided to you – and add a figure number and legend (caption) to go with each – see instructions in the links below. NOTE: A figure legend is a concisely written bit of text that enables the reader to fully understand the content of the figure without having to refer to the main text. It should have a title, some methods (e.g. stain or test performed), result description, and if you want, you may add a conclusion based on the result (e.g. Figure 1. Gram Stain of unknown bacteria. Shows predominately pink clusters of short rods. From this result it can be inferred that the unknown is gram negative and must be one of these five bacteria: …..”)

 

Guide for making figure legends:https://blog.bioturing.com/2018/05/10/how-to-craft-a-figure-legend-for-scientific-papers/

Guide for making table and figure legends: http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWtablefigs.html

 

• Provide a table (Table 1.) of bacteria and their characteristics that was provided to you by your instructor to which you have added to the UNKNOWN column the characteristics of your unknown (as observed in your data pictures).  This chart should then be HIGHLIGHTED or COLORED in some way to emphasize characteristics shared by your unknown and the other candidate bacteria (either the 5 gram positives or the 5 gram negatives – but not both groups)

 

• Add a Legend to table-1 e.g. Table-1. Comparison of the characteristics of an unknown bacteria to the characteristics of 10 different candidate bacteria. Bacterial characteristic information was obtained primarily from Bergey’s Manual and from observations of bacteria cultured in the Citytech microbiology lab.  NOTE: unlike figure legends, table legends go above the table.

 

NOTE – figure legends are typically found below or to the side of a picture, while table legends are above the table: http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWtablefigs.html

 

 

 

 

 

 

 

Discussion/Conclusions (this is often a single section with discussion and conclusions combined)

 

• This section MUST START OR END (first or last sentence) WITH A STATEMENT LIKE THIS:

The results obtained from available evidence indicate that the unknown bacteria is (most likely / or) probably STATE THE FULL NAME OF THE BACTERIAL species.  If you put this at the end – you could make it a separate Conclusions section (with 1-2 sentences), and the preceding section would just be Discussion.

 

• Add a flow chart that illustrates how different pieces of evidence allowed you to eliminate various candidates and arrive at your conclusion.  NOTE: you could also have done this in the results section by adding to each of your figure legends a bit of text at the end that tells how the data in the picture allowed you to eliminate different candidates - e.g. see the example legend for Figure-1. above)

 

• After the flow chart you could discuss: problems were encountered, ambiguous / anomalous results in data pictures, or ambiguity in the interpretation of results due to the fact that some tests are VARIABLE for different strains of a particular bacterial species used in our microbiology lab. If there were problems, tell what tests could be repeated to help resolve your difficulties in interpreting results.

 

• In a final section of your Discussion, report some general information about your (identified) organism (e.g. its pathogenicity; its normal habitat; unusual characteristics; effects on humans, good or bad; virulence, etc).  You should cite at least 4 sources here and have proper in-text citations provided (see below). I would recommend starting with a search of Bergey’s Manual (https://www.biodiversitylibrary.org/item/41848#page/7/mode/1up ) – I suggest searching this online version for your particular bacteria (use the “Search Inside” tab on the top right).  When you cite the information that you find – take the weblink from the page(s) where you find your information and put them into a citation formatter (e.g. the CitationMachine or Zoterobib) and it will give you a properly formatted citation that includes a link to the page where the info was found (if you choose APA formatting).

 

Other sources of information should come from the scientific literature – e.g. by searching the Pubmed Central (PMC) online database: https://www.ncbi.nlm.nih.gov/pmc/ .

 

-----------------------------------------------------------------------------------------------------------------------------------------------

 

Use of In-Text Citations and Final List of References/Citations (Bibliography)

 

Besides assessing microbiology skills and knowledge, this exercise will also assess your ability to use relevant resource material to complete a research project. Therefore, you must include some researched information that is properly cited (within the text of your report) and in a citation/reference list at the end of your report.  

 

Areas where you may include researched information include the materials and methods section (to site protocols used) and in your discussion. Important sources such as scientific journals (e.g. anything found in a Pubmed database), Bergey’s Manual, medical text books, encyclopedias or other reliable sources must be used in preparation of the paper. Your text book should not be used as a source of information. There must be a minimum of four (4) references (for your entire report) including at least two primary sources.

In your final reference list, clearly indicate below each reference if it is a primary source or a secondary source (write this in parentheses below each reference).

 

Your final paper will be assessed for how well you build a case that your unknown is a particularbacteria, and also on the general reporting criteria listed below:

 

1. Your ability to understand and address the research objectives of this project.  
2. Your use of information (from the literature, web, and the table provided by your instructor) to effectively to accomplish this specific purpose.
3. Your ability to present information in a clear and meaningful way.
4. Your ability to identify credible and relevant sources
5. Your ability to cite sources properly (in APA or some other style). You must use in-text citations and have a final reference list.
6. Your ability to incorporate ideas of others in an ethical manner; summarizing, paraphrasing and quoting are correct and appropriate (and not plagiarized).

 

Sources should be properly cited using American Psychological Association formatting (APA6 or APA7 is a good choice – choose one and be consistent with all in-text citations and final references). 

 

Citations typically contain the following (not necessarily in this order)

• the title of the paper (or chapter if citing a book),
• the name of the journal (or book)
• editors if a book is cited
• volume number
• complete pagination (first and last page of the work cited)
• year of publication

 

 

Primary and Secondary Sources for Science

In the Sciences, primary sources are documents that provide full description of the original research. For example, a primary source would be a journal article where scientists describe their research on the human immune system. A secondary source would be an article commenting or analyzing the scientists' research on the human immune system

	Primary Source	Secondary Source
DEFINITIONS	Original materials that have not been filtered through interpretation or evaluation by a second party.	Sources that contain commentary on or a discussion about a primary source.
TIMING OF PUBLICATION CYCLE	Primary sources tend to come first in the publication cycle.	Secondary sources tend to come second in the publication cycle.
FORMATS--depends on the kind of analysis being conducted.	Conference papers, dissertations, interviews, laboratory notebooks, patents, a study reported in a journal article, a survey reported in a journal article, and technical reports.	Review articles, magazine articles, and books
Example: Scientists studying Genetically Modified Foods.	Article in scholarly journal reporting research and methodology.	Articles analyzing and commenting on the results of original research; books doing the same

Taken from University Libraries, University of Albany(https://library.albany.edu/infolit/prisci)

 

------------------------------------------------------------------------------------------------------------------

 

RESOURCES & LINKS

 

Pubmed Central (PMC) online scientific literature database: https://www.ncbi.nlm.nih.gov/pmc/ - this has freely available articles.  When you do a search – it will pull up related articles.  Just under each entry listed you may see a citation tab that you can click on to obtain a properly formatted APA reference – if you don’t see this you can enter the URL into a citation formatter like Zoterobib or the CitationMachine.  

 

Links to citation formatters and citation manager software: https://www.library.cornell.edu/research/citation

 

Citation Formatters: (good for any source including websites)

Zoterobib - https://zbib.org

CitationMachine- for APA formatting: https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/in_text_citations_the_basics.html

 

Guidelines on how to use in-text citations in APA format (basic rules): https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/in_text_citations_the_basics.html

 

 

Guidelines on how to make a final reference list in APA format (basic rules):

https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html

 

In-text citation of a website with no author (APA format): https://apastyle.apa.org/learn/faqs/web-page-no-author

Example Source (full reference for your final list of references)
All 33 Chile miners freed in flawless rescue. (2010, October 13). Retrieved from http://www.msnbc.msn.com/id/39625809/ns/world_news-americas/

 

For the in-text citation of this reference:

Cite within your text the first few words of the reference list entry (usually the title) and the year. Use quotation marks around the title or abbreviated title.: ("All 33 Chile Miners," 2010).

 

 

Citing Bergey’s manual (https://www.biodiversitylibrary.org/item/41848#page/7/mode/1up )

 

Below, in red is a full citation for the TITLE PAGE of Bergey’s Manual that I retrieved on March 3rd (note: you would have a different link at the end of the citation for different pages – so DON’T JUST USE THIS CITATION – I want one that tells the reader which page you contains the information that you are citing. The link to the correct page from where you get your information will be automatically added to your citations if you paste the link from the respective page into some citation formatter (e.g. the CitationMachine above, or Zoterobib).  

Note: you may get slightly different results from the 2 different formatters, so please pick one and use it for all of your citations. Also, make sure that you choose the same format for all of your citations – e.g. there are different versions of the American Psychological Association (APA) format, below you will see examples of APA6 and APA7.

 

CitationMachine - APA6: full citation

Microbiology., A., Bergey, D., & Breed, R. (1970, January 01). Bergey's manual of DETERMINATIVE bacteriology. Retrieved March 03, 2021, from https://www.biodiversitylibrary.org/item/41848#page/7/mode/1up

 

CitationMachine - APA6: in-text citation

(Microbiology., Bergey, & Breed, 1970)

 

CitationMachine - APA7

Microbiology., A. S. for, Bergey, D. H., & Breed, R. S. (1970, January 1). Bergey's manual of DETERMINATIVE bacteriology. https://www.biodiversitylibrary.org/item/41848#page/7/mode/1up  

 

CitationMachine - APA7: in-text citation

(Microbiology. et al., 1970)

 

Zoterobib -APA7: full citation

American Society for Microbiology., Microbiology, A. S. for, Bergey, D. H., & Breed, R. S. (1957 a). Bergey’s manual of determinative bacteriology (7th ed.). Williams & Wilkins Co.,. https://www.biodiversitylibrary.org/item/41848

 

Zoterobib -APA7: in-text citation

(American Society for Microbiology. et al., 1957a) NOTE – you don’t need the a if you have just 1 citation from this source, add letters if you have more than one citation)

 

NOTE: if the text of your report has more than one reference to Bergey’s manual, provide a full citation for each one since the links at the bottom of each will be to different pages – however, add a letter after the date within the in-text citation.

---------------------------------------------------------------------------------------------------------------------------------------------

Guide for making figure legends:https://blog.bioturing.com/2018/05/10/how-to-craft-a-figure-legend-for-scientific-papers/

 

Guide for making table and figure legends: http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWtablefigs.html

 

 

 

 

Bacterial Characteristics Table for Lab Practical-1

 

 

You should use this table in your report (or part of it – e.g. just gram positives or gram negatives and your unknown).  The characteristics of your unknown (based on your data pictures) should be filled in.  

 

You can add this table legend above your table: Table-1: Characteristics of an unknown bacteria and 10 bacterial candidates; Bacillus subtilis (BS), Enterococcus faecalis (EF), Micrococcus luteus (ML), Staphylococcus aureus (SA), Staphylococcus epidermidis (SE), Enterobacter aerogenes (EA), Escherichia coli (EC), Pseudomonas aeruginosa (PA), Proteus vulgaris (PV) and Serratia marcescens (SM).  Information on the characteristics of the 10 bacterial candidates came from Bergey’s Manual and from observations of lab cultures.  (NOTE – you can add text in which you describe the scheme of highlighting that you use to make it easier to see candidates with the greatest number of similar characteristics.)

 

             

	BS	EF	ML	SA	SE	UNK Unknown	EA	EC	PA	PV	SM
Gram stain	+	+	+	+	+		negative	negative	negative	negative	negative
Shape	rods	cocci	cocci	cocci	cocci		rod	rod	rod	rod	rod
Arrangement	short chains	Short chains	Dimers or tetrads	Clusters	clusters		single/ pairs	single/ pairs	single/ pairs	single/ pairs	single/ pairs
Colony color on NA	neutral	neutral	Yellow	Gold	neutral		neutral	neutral	neutral or olive	neutral	neutral or Pink if cool & overgrown
Colony shape & margin	Circular		Circular	Circular	Circular		Circular	Circular	Large, undulate	Irregular	Pinpoint circular
iPLATES
Blood Agar Hemolysis γ ,α, β	α/β	γ	γ	β / α: variable in our lab	γ		α	α /β: variable in our lab	β	γ / α	β / α: variable in our lab
Mannitol Salt (MS) Agar growth	inhibited	+ / Inhibited in our lab	+ / Inhibited in our lab	+	+		inhibited	inhibited	inhibited	inhibited	inhibited
MS Agar color (yellow or red)	Yellow If it grows	Yellow If it grows	Yellow If it grows	Yellow	Red
MacConkey Agar growth	inhibited	inhibited	inhibited	inhibited	inhibited		yes	yes	yes	yes	yes
MCK colony color	-	-	-	-	-		Pink	Pink	neutral or olive	neutral	neutral
MCK agar color (deep red or not)	-	-	-	-	-		-	Deep red/pink	-	-	-
Phenylethanol (PEA)  - growth	+	+	+	+	+		inhibited	inhibited	inhibited	inhibited	inhibited

Neutral colony color = white, grey, cream, tan, etc.