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1 BIO270 Pre-lab 1 Assignment 2014

BI O270 Pre-Lab 1 Assignment

Design of an experiment to test the effect of bioactive compounds
on Daphnia magna heart rate

Learning Objectives:

After completing this assignment, students should be able to:

• Compose a testable hypothesis
• Design an experiment incorporating relevant controls and treatments
• Compile and present the appropriate information of a Materials and Methods
section of a scientific manuscript


Guidelines:

Be sure to follow the standards outlined in, Appendix 1 at the end of this file, the list of
experimental specific considerations in the Pre-lab 1 Manual (p. 13-14), and the
readings from “A short guide to writing about biology” (Pechenik). Completing this pre-
lab assignment will provide you with an opportunity to have your work assessed by
your TA (who will provide valuable feedback) before the Lab 1 assignment is due.
Submit your assignment electronically following the instructions posted on Blackboard
by the submission deadline (28 points: mark recorded out of 6).

Note: Although the Pre-lab will be performed in pairs, you must write your own
individual assignment to be handed in.



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Assignment:

The assignment consists of three parts:

1. Bringing a completed pre-lab exercise to your Pre-lab session (p. 15 of Pre-lab 1
Manual).
2. Writing a Materials and Methods section (to be submitted online after the Pre-
lab) (Question 1 below).

The primary categories in the marking rubric for the Materials and Methods
portion of this assignment are the following:

a) Reasonable Level of Detail 2 marks
b) Format and Style 4 marks
c) Address experimental considerations and Materials and
Methods content (refer to Pre-lab 1 manual, Appendix 1
of the Pre-lab 1 assignment and readings from
Pechenik)

13 marks
d) Data analysis 2 marks

3. Answering questions related to your hypothesis (to be submitted online after the
Pre-lab) (Question 2 below).



Submit this assignment online following the instructions posted on Blackboard. Refer to
the assignment submission deadlines for the specific due date for your assignment. The
written Materials and Methods section should be a maximum of 1.5 pages, 12pt font,
double spaced, standard margins. Assignments over the page limit will be subject to a
10% penalty.

Submit your assignment using this format for your submission title:

1) Your Last name, 2) Assignment (e.g. Lab 1 assignment), 3) Student ID

e.g. J ones-Pre-Lab 1 assignment-888888888

• Failure to do so, will result in a mark deduction

Please use the format below as your template for writing your Materials and Methods
section and answering the questions.
3 BIO270 Pre-lab 1 Assignment 2014


Name: _____________________ Student ID: _____________________
Lab Section: ______________________ Assignment: Pre-lab 1 Assignment
Name of Lab Partner(s):__________________________________________________

1. Materials and Methods [21 marks]:




If your experiment uses multiple bioactive compounds, choose one of those compounds
to answer the following questions.

2. Hypotheses

a. Provide your Hypothesis [3 marks].



b. List the full citation for one peer-reviewed manuscript that provides rationale for
your prediction (see Appendix 2) [1 mark].



c. Write two to four sentences explaining to your TA why you chose this
manuscript. Ensure that you clearly indicate why it supports your hypothesis [3
marks].





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Appendix 1:

Materials and Methods Section of a Scientific report
‘How did you do it?’

The Materials and Methods section is a concise chronological description of the
laboratory procedure you performed in the lab. This section may be the most important
aspect of a research paper because it provides the information by which the validity of
a study is ultimately judged. The complexity of scientific inquiry necessitates that the
writing of the methods be clear, concise and orderly to avoid confusion and ambiguity.

It is usually helpful to structure the Materials and Methods section in the following
manner:

1. Explain how the materials were prepared.

e.g. Source of your organism? How did you set up your experiment? Did you allow any acclimatization
of your subjects? How did you move the subjects to the experimental chamber?

2. Describe the research protocol.

e.g. What did you do? Provide rationale for why particular steps were taken whenever it might not be
obvious (e.g. Why did you use the Daphnia cooling chamber? Why did you restrict movement of
Daphnia?). What variables, treatments and experimental groups did you use? How many samples
were collected and how much replication? What did you control for? This section necessarily includes
any concentrations, volumes, times etc.
• For laboratory calculations, view the file ‘Laboratory calculations review’ posted on blackboard
in the lab manuals tab.

3. Explain how you collected and analyzed data.

e.g. How did you perform your experiment? Did you count for 20 seconds and then multiply by 3 to
get beats per minute? Did you look at percent change from control ((control heart rate – experimental
heart rate)/control heart rate) X 100? Describe how your data will be presented (e.g. mean, SD,
SEM)? If you subjected your data to a statistical analysis you would list the statistical test used with
reference to the variables examined and the p-value used to indicate statistical significance.


Style Tips:

• Writing must be in sentences, no point form or lists.
• Writing should be direct and precise.
• Writing should be in the past tense (this may seem strange for the prelab
assignment as you will not have carried out your study yet!).

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• Write in either active or passive voice.
o We suggest that you ensure that your passive sentences are intentional and not
habitual. Whichever you use or whatever mix you use, make sure your writing
flows, connecting one sentence to the next.
• Experimental organism formatted correctly.
• Avoid descriptions of ‘unimportant’ details (e.g. ‘the microscope was adjusted for
parfocal viewing’ or pipetting procedure or ‘data were recorded’, the colour of
the eppendorf tubes). When standard laboratory procedures are used they are
generally not included.
• There must be enough detail so that the reader understands the study design
and could duplicate it if desired.
• Descriptions of preparations, measurements, and protocol should be organized
chronologically.
• Do not list all of the materials needed for the experiment at the beginning. The
materials and equipment utilized during the experiment should be mentioned
throughout the procedure as they are used.
• For clarity, information should be presented in subsections (e.g. Animals, Sample
Preparation, Data Analysis) according to topic.
• Do not include results (since you have not carried out your experiment yet, this
will not be a problem for the pre-lab assignment!).
• It is not a step by step description of everything you did, nor is it a set of
instructions. In particular, it is not supposed to tell a story.
• Be succinct.


Note: In this laboratory it will not be necessary to list equipment by vendor name
and/or catalog number. However, you should recognize that this is often a requirement
for a Materials and Methods section in a peer-reviewed journal.

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Appendix 2:

Citing Sources

Whenever you quote, paraphrase, summarize, or otherwise refer to the work of
another, whether these are facts or opinions, you are required to cite the source. You
must cite the information in the body of your paper (in-text citations) and then at the
end of your paper in a ‘References’ or ‘Literature Cited’ section. In this course, we will
use the Council of Science Editors (CSE) style of citing sources. This style is used by
many researchers and journals in the Biological Sciences.

In-text citations

In this assignment you are required to provide rationale for your experimental
prediction. You will be expected to provide a one to two sentence summary of the
results of one peer-reviewed paper that supports your prediction. You will need to cite
the peer-reviewed publication in one of those sentences. In addition, you are required
to include a full CSE citation.

In the examples below, the author’s results and/or ideas have been paraphrased; the
results or ideas have been rewritten for the sake of clarity, succinctness or brevity.
Rather than simply restating the text, the author of the paraphrase changes the text to
highlight a particular idea while leaving out the details that are not relevant to the point
being made. You must keep the original meaning from the source material, but use
different vocabulary and a different sentence structure. Remember, the paraphrase
should sound like your own writing, not the source you are quoting. However, you do
not need to change every word when you paraphrase. If there are key words or special
subject related vocabulary, you can retain those in your paraphrase.

Avoiding plagiarism when paraphrasing can be difficult. We recommend you follow
these steps:

1. Read the relevant passage(s) carefully several times until you fully understand the
meaning.
2. Without looking at the passage(s), write your own version, using your own
vocabulary and method of phrasing.
3. Refer back to the original and if necessary rework your version to make sure it is
not copying/plagiarizing the original source, but does say what you want it to say.

When creating your in-text citations, use the ‘author-year’ format of citing. This format
consists of the surname(s) of the author(s) and the year of publication of the
document. Here are three examples:

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Zornik et al. (1999) used an in vivo heart rate assay in Drosophila melanogaster to
demonstrate that injection of serotonin (10
-3
M – 10
-5
M) decreases heart rate at all
life stages.

The inhibition of Cdk8 activity in limiting nutrient conditions stabilizes multiple
transcription factors, including Phd1 and others required for differentiation,
demonstrating the central role of Cdk8 in initiation of differentiation in the yeast S.
cerevisiae (Raithatha et al. 2012).

The primary function of crustacean hyperglycaemic hormone (CHH) is the elevation
of glucose levels in the haemolymph (BIO252 Pre-lab manual, 2005).

Note: If there are two authors, both of their surnames should be included in the in-text
citation.

Full citations

When listing a full print journal citation use the following format: Author(s). Date of
publication. Article title. Abbreviated J ournal title. Volume(issue): pagination. Most
important is to be consistent.

Here are two examples:

Zornik E, Paisley K, Nicholls R. 1999. Neural transmitters and a peptide modulate
Drosophila heart rate. Peptides 20(1): 45-51.

Raithatha S, Su TC, Lourenco P, Goto S, Sadowski I. 2012. Cdk8 regulates stability of
the transcription factor Phd1 to control pseudohyphal differentiation of
Saccharomyces cerevisiae. Mol. Cell. Biol. 32: 664-674.

Note: if you are unsure of the abbreviation used for your journal article, please visit the
following website ISI Web of Science.

Example of Book:

Hill RW, Wyse GA, Anderson M. 2004. Animal Physiology. Sunderland (MA): Sinauer
Associates. p. 50-59.

Example of Lab Manual:

BIO252 Laboratory Manual. 2005. Carbohydrate regulation. University of Toronto,
Toronto, ON. p. 79-87.

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Need more information?

Pechenik, J A. 2012. A Short Guide to Writing About Biology. 8
th
Edition. Toronto:
Pearson. 276p.

Consult the complete CSE Manual, available at the reference desk at the Gerstein
Science Library (call number: T11.S386 2006X).





Documentation and Academic Integrity

In academic communities, including this course, the ethics of research demand that
writers be credited for their work and their writing. Not to do so is to plagiarize. To
plagiarize is to intentionally or unintentionally appropriate the ideas, language, or work
of another without sufficient acknowledgement that such material is not one's own.

You may ask, why do we need to cite sources? Here are a few good reasons why you
must cite your sources:

• Plagiarism is an offence under the Code of Behaviour on Academic Matters.
• Accurate citations help readers of your paper/assignment find the original source
of your information and can therefore read more about it.
• We build our knowledge on the work of those before us. We would also expect
that those who follow us will build on our work. Therefore, we must show
respect and gratitude for the contributions to the body of knowledge of those
before us.
• Citing sources establishes where your own ideas fit into the wider subject area.