To address the prompts, you must first pick a manuscript (see instructions). You mayneed to use credible sources outside of that single manuscript. Please be sure to note
in text the source(s) you used, which will also be placed in the References section at the
end of the worksheet.
Responses will be graded on correctness and thoroughness (see rubric in the Project
Module 3 instructions). Each response should be a small paragraph in length (at least 47 sentences).
Your assigned microbe: _____________________
*ALL responses must be in your own words! Do not use quotes and do not simply
rephrase source material. Instead, summarize the findings from your sources in your
own words.
Manuscript analysis
1) Describe the organism(s)/cell(s) that you microbe is interacting with and state where
these interactions take place. Your description on the other organism(s)/cell(s) should
be more detailed than a single word or sentence. *Note, if applicable, your description
should be more specific than simply “human”…for example, hepatocytes. (2 points)
2) What are the main questions or problems that the researchers are addressing and
what is their overall hypothesis? (2 points)
3) Read the materials and methods sections. Identify 2 methods/techniques that you did
not know before you read the manuscript. Describe how those methods/techniques
work and how they were used by the researchers in their experiments. (You may want
to use methods that relate to your response to question 4 below) *Note, you likely will
need to use other sources to help you describe these methods. Be sure they are
credible sources and cite them using both ways. (4 points)
4) While you should view all figures, for this question choose a single Figure (not Table)
to analyze in detail. If the figure has more than 2 panels, then choose two to discuss
(ex. Panel a and Panel b).
a. Add a screenshot of the figure you are going to focus on. (1 point)
b. Explain why the researchers performed this experiment. What was their
hypothesis or goal when performing this experiment? (1 point)
c. Describe the figure, including what each axis means, what each group is,
etc. All parts of the figure should be included. (2 points)
d. What are your interpretations of the results? This is different than stating
what the authors concluded! Be as specific as possible. You may want to
refer to specific parts of the figure for your response. (3 points)
5) Describe your interpretations of the major findings/conclusions of the manuscript
and explain how the evidence (ie data) supports those findings. You should be
descriptive and specific for this response. It may be helpful to separate different
conclusions into separate paragraphs. (5 points)
Model summary
6) Create an illustration that summarizes at least one of the major findings on how your
microbe interacts with other organisms. Your illustration does NOT need to have all the
conclusions, as some manuscripts are quite extensive. Your illustration should be
approximately half a page in size. More detailed directions are included in the Project
Module 3 instruction guide. (8 points)
7) Write a 3-5 sentence illustration legend that explains what is happening in your
illustration. The legend should be complete and reference all parts, but it should also be
succinct. (2 points)
References
List of properly cited sources (including in-text citations), using both quick reference
format and the extended format/screenshots (see Project Module 1).
Overview
At this point, you should have a good idea of some of the basic aspects of your microbe
and how your microbe is distributed across Sacramento and across the globe. In this
module, you will research ways in which your microbe interacts with other organisms,
whether that is with other microbes or eukaryotic (ex. human) cells. You will return to
PubMed (or other search engines) to find primary manuscripts that help you answer
questions and create a model/image that describes those interactions.
Why are you doing this
The goals of this module are to help you meet the course learning outcomes (listed
below) and to give you practice in finding and reading primary literature articles (rather
than review articles). Additionally, you will have practice creating visualizations that
demonstrate your understanding of the material you find in primary literature articles.
Learning Outcomes (from class Learning Outcomes)
–
Describe host-pathogen interactions mediated by microorganisms.
–
Describe the ecological and symbiotic relationships between microorganisms and
their environment
What to turn in
1) Completed worksheet for Project Module 3 that includes responses to all questions
and a model/image.
2) List of properly cited sources (including in-text citations), using both quick reference
format and the extended format/screenshots (see Project Module 1).
What to do
1) Locate a primary manuscript that explores how your microbe interacts with
other cells (whether Bacterial, Archaeal, or Eukaryotic).
From earlier modules, you should feel comfortable finding primary literature (versus
review articles) on your microbe. However, I’m asking for something very specific, so I
want to help you out.
You have two options to find a single primary manuscript.
a. You are free to find any primary literature manuscript you want to use for this
module. The topic must describe interactions between your microbe and another
1
organism. This could include microbe-microbe interactions, host-pathogen
interactions, or any other combination.
*Note, if you choose your own manuscript, the manuscript cannot already include
a published graphical abstract (see Instruction 3 below)
b. For each microbe, I have listed as least one manuscript that you can use for this
module. The link to these manuscripts will be posted to Canvas. You are
welcome to use one of these manuscripts to answer questions in this module.
2) Read through the manuscript you chose and respond to the questions in the
student worksheet.
The questions on the worksheet are meant to guide you through the manuscript, in the
process giving you practice reading primary literature. Analyzing original data is a skill
that takes time and practice. It might not be easy right away, but you can do this!
3) Create a model that illustrates the major findings of the manuscript you chose.
Many research manuscripts are now requiring graphical abstracts, or models, of the
content of the manuscript. This is because these help to summarize often complex
concepts into a quick, easy to follow visual. With this in mind, for this module you will
need to create a model or graphical-abstract-style illustration that summarizes the key
findings from the manuscript you used for Project Module 3. A complete illustration will
include:
–
The location where the interactions between your microbe and other
organisms takes place.
All relevant organisms, including your own microbe.
At least one of the major findings/conclusions of the manuscript in an
illustration. That means very limited use of text!
Clear labels for all parts. You can think about adding numbers if you are trying
to show a sequence of events
A 3-5 sentence illustration legend that explains what is happening in your
figure. The legend should be complete and reference all parts, but it should
also be succinct.
An example for what a graphical abstract-style illustration looks like:
2
Cell Host & Microbe 2020 2841-53.e8DOI: (10.1016/j.chom.2020.05.004)
Other examples can be found at Cell Host and Microbe, which is a journal that requires
graphical abstracts.
There are multiple ways you can create the illustration
– PowerPoint
– Graphics design software like Adobe Illustrator or Inkscape
– Hand-drawn, as long as you create a digital version that is clear (high
resolution) and legible
– Biorender
o This is a cool program that you can use for free. The downside of the
free version is that the resolution is pretty bad. But that will work for
this assignment. I definitely suggest giving this a try.
***Note, you will receive no points if you just look up a model online and copy it. Your
illustration must be your unique creation.
3
Grading rubric for Project Module 3
Rubric categories
Responses to
questions
*Individual points for
each question are
stated on the
worksheet
Full Points
Partial Points
No points
All questions
appropriately
addressed
Responses lack
sufficient detail or are
too simplistic
outside resources used
appropriately
only part of the
question is
addressed
Questions not
addressed or
responses are not
relevant or
summarized in one
sentence.
student demonstrates
original interpretation of
data and results
responses exceed
expectations
responses are just
rephrasing of
manuscript text
(depending on
severity, little to no
points may be given)
Majority of
responses are
rephrasing or direct
copying/quoting of
manuscript text.
(no points)
(full points)
response meets
minimum or is below
expectations
Illustration/model
*Individual points for
model are stated on
the worksheet
The illustration includes
all details listed in PM 3
instructions.
Illustration accurately
describes the major
results of the study.
Graphics are used
appropriately to show
actions or order, with
limited use of text other
than as labels.
(partial points)
Illustration may be
missing some of the
details listed in the
PM 3 instructions.
Illustration is
missing or does not
show any relevant
information
Labels or important
cells/molecules are
unclear or missing
Difficult or
impossible to
interpret
Overall illustration is
messy, difficult to
interpret, or lacks
professionalism
Messy to the point
that information
cannot be extracted
Illustration is clear, well
organized, aesthetically
pleasing, and
professional.
Text may be used to
describe actions,
rather than graphical
elements.
Labels for all major
cells, molecules, etc
are appropriately used
(partial points)
(full points)
4
Illustration is a copy
or near replica of
published images.
(no points)
Rubric categories
Source citations
Full Points
All sources used are
cited using both
methods described in
instructions; in text
citations used
Partial Points
No points
All sources are cited,
but only one method
is used
Not all sources are
cited
(3 points deducted)
5
(multiple points
deducted)
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