Unknown Report – Term Paper Guidelines - Faculty Websites

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Feb 20, 2013 (4 years and 6 months ago)

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1

Bacterial Unknown Report (150 pts)


Biol
251 and
351 students will identify the genus of one bacterium using morphological,
biochemical, physiological characteristics

and analysis of a 16
S rRNA sequence. The term
paper will emphasize the logical sequence

used to identify the unknown bacterium from a list of
15 possible candidates. The Unknown Table Worksheets will be turned in with the term paper.


Due Date

Biol 351 Microbiology

XXXX


Late Penalty

10 pts will be deducted for each day that the paper is su
bmitted after the deadline.


Cover Page

A cover page is
mandatory

and must include the following information:


Student Name

Lab section number

Lab TA's name

Unknown number


The cover page is not included in the page limit. Papers with an incomplete or mis
sing
coversheet will be returned to the student. Late penalty applies
.



Organization of the Term Paper

The unknown term paper will consist of 5 sections and all sections must be present to receive
full credit. Each section of the paper should be introduced with the appropriate heading or
subheading in bold type. The maximum length of the term paper is 20 p
ages double spaced.
The APA format will be used for citing in
-
text references and students may review examples at
the UNLV Writing Center website (
http://writingcenter.unlv.edu/writing/apa.ht
ml
).



Section I


Introduction and Definition of a
Bacterial

Species
(20 pts)

This section will provide a general overview of the methodology employed to identify a bacterial
unknown. Students should specifically mention the importance of aseptic techni
que,
microscopic examination, the use of differential media, and the importance of using positive and
negative controls for each test.


In their own words, students
must provide an explanation of how bacterial species are
defined.

Students must clearly

state

how the
concept of a bacterial species differs from
that of the biological species concept used with animal and plant species.



All references must be cited.


2

Section II


MATERIALS AND METHODS

(40 pts, 4 pts/test)

This section will contain a concise summation of the microscopic examination,
5 tests not
including the 16S rRNA blast
that were central to the identification of the bact
erial genus
,

and
the results of the 16S rRNA
sequence
analysis. The name of each test

should be listed as a
subheading in bold text, followed by a description of that test, and the results for the unknown.
Results for positive and negative controls for each test
must

be reported.
Tests with negative
results

should be reported if they wer
e important in the identification of the unknown.
The
results of the 16S rRNA sequence analysis should identify the top three matches from a
BLASTn search and a clear description of the significance of the E values and the raw scores.
Examples from past
student
unknown term papers follow.



Microscopic Examination

"Unknown 09 is rod shaped bacterium. The simple stain procedure with
methylene blue allows students to clearly see the shape and arrangement of the
bacterial cells. Methylene blue is a basic

cationic stain and is attracted to the
negative charge of bacterial cells. Cultures of
Staphylococcus
(clusters of
cocci),
Streptococcus
(chains of cocci),
Bacillus

(rod) and
Escherichia

(rod) were
used as controls."



Mannitol Salts Agar

"Unknown 79 wa
s streaked for single colonies onto a mannitol salts agar plate
and incubated at room temperature. The recipe for mannitol salts agar plates
consists of beef extract, peptone, sodium chloride (7.5%) and phenol red. This
high concentration of salt inhibit
s most Gram negative and positive bacteria, but
does not inhibit
Streptococcus
. Mannitol cannot be used as a carbon source by
all bacteria and only species capable of fermenting this sugar are able to grow.
The pH indicator, phenol red turns yellow as an

indication of acid production due
to the fermentation of mannitol. Unknown 79 grew as yellow colonies with a
halo on mannitol salts agar.
Staphyloccocus aureus

was used as a positive
control and grew as single yellow colonies with halos. The negative
control,
E
.
coli

did not grow as

was

anticipated
."



16S rRNA
Sequence
Analysis

"The sequence of the 16S rRNA gene for unknown 43 was submitted to the National
Center for Biotechnology Information (NCBI) database. The sequence was pasted into
the B
LAST

program for nucleotides and the best

three

match
es

were

Burkholderia
fungorum
,
Rhizobium radiobacter,
and
Xanthomonas sp
.

The E
-
value is a measure of
the number of alignments between the submitted…
Burkholderia fungorum

had an E
value of 10
-
5

and this suggests… E
-
values are calculated based upon… Raw scores
are a measure of… The raw score for
Burkholderia fungorum

and

Rhizobium
radiobacter

suggest

that
…"





3


Section III


RESULTS
and DISCUSSION

(40 pts)

This section will consist of a flow chart illustrating the key tests that led to the identification of the
bacterial genus. The flow chart must contain the tests described in
S
ection II
. Flow charts can
be hand drawn, but must be legible. The flow chart
must also demonstrate how closely related
genera were eliminated.



Students must discuss the process of elimination that led to the identification of their unknown.


“A Gram negative, rod shaped, oxidase negative bacterium that is a facultative
anaerobe and able to ferment glucose fi
ts the description of the
Enterobacteriaceae
(Bergey’s Manual, 2001). However, there are more than 20
genera within this family of bacteria (Brock, 2009). The motility agar test was
performed and unknown
5
4 was found to be highly motile. The motility
test
eliminate
d

the genera
Klebsiella

and
Shigella.

A positive citrate utilization test
(bright blue) eliminated
Esherichia
,
Proteus
,
Providencia

and
Morganella
. A
negative litmus milk test (lactose catabolism) eliminated
Citrobacter
and
Enterobacter
. A positive methyl red test further eliminated
Salmonella

as a
possible choice. The logical conclusion is that unknown
5
4 is a member of the
genus
Erwinia
.

The results of the BLASTn search were consistent/not consistent
with the with the results prese
nted in the flow chart."

.

Included in Discussion


I湣潮si獴敮t R敳ults
(
10 pts)

This section will contain an explanation for any test results that were inconsistent with the
identification of the bacterial genus.

Unknown 24

Gram negative, rod, non
-
spore former,
oxidase negative, facultative anaerobe,
glucose fermenter

Unknown 24

4


"All preliminary test results suggested that unknown 46
i
s
E
.
coli
. However, the
result of the Gram stain test indicated that unknown 46 was a Gram positive
coccus and this result was inconsistent with the initial identification. This
inconsistent result

could have been caused by…"


"The best E
-
value from the BLASTn 16S rRNA sequence analysis was for
Pseudomonas fluorescens
.

This result was not consistent since unknown 13
was demonstrated to be a facultative anaerobe and
P
.
fluorescens

is an obligate
aerobe. These results are not consistent and a likely explanation is…"


Part IV


CONCLUSION

Naming the Organism and Background Information
(10 pts)

All students must clearly state the identity of their unknown. In addition,
an explana
tion of the
derivation of the genus and species name must be included.
Discu
ss any particular host,
location, physiological, genetic
and historical
fact that was used to describe the genus.


"Unknown 12 is
Escherichia coli
. The genus
Esherichia

wa
s named after Dr.
Theodor Escherich, the physician that first described this bacterium.
Escherichia

was originally isolated from a child with diarrhea in 1885 (Brock, 2009). The
species,
coli

is derived from the Latin for colon.
Escherichia

coli
is

a co
mmon
commensal and probably inhabits all mammalian digestive tracts (The
Prokaryotes, 2006)."


This section must also briefly summarize the medical, industrial or historical significance of the
unknown. Background information is available in Bergey'
s Manual and other sources.


"Mycobacterium tuberculosis is the bacterium that causes tuberculosis.
Tuberculosis is a s
erious
public health
problem

in many parts of the world. The
World Health Organization estimates that 8 million people are exposed to

this
bacterium and 2 million develop active tuberculosis each year (Brock, 2009)."


(1 page maximum)





References Cited

Reference information is mandatory. Each reference must include the names of all authors (in
the same sequence in which they appear in the publication), the article, journal or book title,
volume number, page numbers, and year of publication. Website add
resses should be use to
identify sources or documents that are only available electronically.


Visit the UNLV Writing Center website for specific examples of how to properly cite a source
(
ht
tp://writingcenter.unlv.edu/writing/apa.html
).


Wikipedia is not an acceptable reference.


There will be a maximum deduction of 10 pts for improper reference citations.


Additional Guidelines

5


Proofread

the term paper


Proper

grammar,
correct
spelling and accurate punctuation are all important and make grading
easier.
25 pts will be deducted from term papers that are that are difficult to read due to a
lack of proofreading.
The UNLV Writing Center is available to review and comment on
student

term paper
s

(
http://writingcenter.unlv.edu/owl/
).


Greek Letters, Special Symbols, Superscripts and Subscripts

Pay attention to the use of special symbols including, Greek letters (

), degree signs
(°C),
and fractions (½). Subscripts (CO
2
) and superscripts (Cu
2+
) should be used with molecular
formulas (C
6
H
12
O
6
) and chemical equations (2H
2
O
2

→ 2 H
2
O + O
2
).


Do not use an ampersand (&) in place of the word "and".


Scientific Names

All scientific nam
es consist of a genus and species. The genus is capitalized and the species is
written in lower case. Scientific names should always be italicized.



Escherichia coli

Staphylococcus epidermidis


The genus and species for every organism should be
spelled out when the organism is
mentioned for the first time. A name can be abbreviated by using the first letter of the genus
and the full name of the species in subsequent entries.



E
.
coli



S
.
epidermidis


Abbreviations for species, both singular
(sp.) and plural (spp.) can be used with the genus.



Escherichia

sp.






Staphyloccus

spp.

(Indicates an unknown species within this genus)

(Refers to several species)


Headings and Subheadings

Identify each section of the paper

with either an appropriate heading or subheading in bold type.


Grammatical Person

Scientific papers are written in the third person. The pronouns I (singular) and we (plural) are
used in first person writing, as in a letter or an email to a friend. The

pronoun you
,

the second
person is used to identify the individual being addressed. He, she, it, and they are pronouns
used in third person writing.


Do not use the first person as exemplified below.


"I performed the Gram stain, anaerobic growth and oxid
ase tests and they were all
negative."


However, do use the third person.


"the results of the Gram stain, anaerobic growth and oxidase tests indicate
d

that
unknown 35
wa
s…"


Formatting

6

Margins in all directions must be one inch

Font size of 1
1


Standard

business font: Arial, Times New Roman, Palatino or Georgia


Text must be double
-
spaced

Pages must be numbered consecutively


Papers not complying with formatting requirements will be returned to the student. Late penalty
applies.


In
-
text Citations

Refer
ences to any sources (textbook, lab manual, Bergey's Manual, scientific journal article,
newspaper or periodical, website) that were employed in any portion of the term paper must be
properly cited. The UNLV Writing Center (
http://writingcenter.unlv.edu/writing/apa.html
) has
specific examples of how to handle in
-
text citations.


Wikipedia is not an acceptable reference.


The UNLV Lied Library has many excellent resources on prokaryotes. Comm
only used
references include, but are not limited to the following:


Bergey's Manual of Systematic Bacteriology

The Prokaryotes

Brock Biology of Microorganisms

Microbiology Laboratory Theory and Applications


Plagiarism

No form of plagiarism is acceptable
and all instances of academic dishonesty will be reported to
the UNLV Office of Student Conduct. Students should familiarize themselves with the UNLV
Writing Center's description of plagiarism (
http://writingcenter.unlv.edu/writing/plagiarism.html
).



7


Item

Grading Scheme

Formatting


1 inch margins in all directions

Font size of 11

Standard business font

Doubled
-
spaced

Pages numbered consecutively

Papers not complying with formatting
requirements will be
returned to the student. Late penalty applies.

Cover Page

Paper with an incomplete or missing coversheet will be returned
to the student. Late penalty applies.

Section I

20 pts

Overview of methodology

Aseptic technique

Microscopic

examination

Differential media

Importance of using + and
-

controls


Definition of a procaryotic species

Explanation of how the concept of a procaryotic species differs
from a
eukaryotic species

Section II

40 pts

Microscopic examination

8 other tests

De
scription of the test and the results for the unknown

Results for + and
-

controls

Identification of three best matches from BLASTn

Results and explanation of E
-
value and raw score for the 16S rRNA
sequence analysis

Section III

40 pts

Legible flow chart

Demonstrates how closely related genera were eliminated

Detailed discussion on the process of elimination

All tests from Section II mentioned

Section IV

10 pts

Clearly stated the identity of their unknown

Explanation of the name (genus & species)

Background information: medical, industrial or historical significance

Section V

10 pts

Complete description of inconsistent results


Unknown Table
Worksheets

30 pts



References

10 pts will be deducted for improper citations



Proofreading

25 pts will

be deducted from poorly proofread papers