辅导案例-LECTURE 15
GEGE2x01 Genetics and Genomics LECTURE 15: Writing your prac report
Writing
Writing your prac report
Gene mapping in Bactrocera tryoni
GEGE2x01 Genetics and Genomics
LECTURE 15
Dr Emily Remnant
[email protected]
Lecture 15
Writing your prac report
• Refresh what we did in Week 3-4 prac
Background, experimental setup and results
• Report format
Each section explained
• Assessment criteria
How the marking criteria relate to the sections of the report
• Question time
Opportunity to ask for direction, not answers!
Here’s what we’ll cover today:
To ask questions throughout,
go to www.menti.com and use
the code 56 28 67
Practical report assessment task
• 25% of final grade. Due October 11th (Canvas)
• Report guidelines: Canvas > Assessments > Practical report
• Report sections, info & marking criteria
Gene mapping with Molecular Markers
What’s the purpose of a scientific
report?
To communicate the results of an experiment clearly and succinctly
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
What’s the purpose of a scientific report?
• To do this you need to:
1. Put the experiment into a biological context
• What is the question? Why is it important? What has been done previously?
2. Describe how the experiment was performed
• The key details required for someone else to independently repeat the experiment
3. Explain the results obtained
• A factual account of your findings, clearly laid out using text, tables and figures
4. Discuss the significance, implications and limitations of the results
• Synthesise your results back into the original context and tie in with future directions
…in a language that is clear, accurate and scientifically appropriate
To communicate the results of an experiment clearly and succinctly
Background
• The Queensland fruit fly or Q-fly, Bactrocera tryoni
Order: Diptera
Family: Tephritidae
... etc.
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Background
• https://www.youtube.com/watch?v=qxfdtr1BMxE
• *PLEASE NOTE: while tiny sensors on the backs of fruit flies are
awesomely cool, the particular strategy in this video is not necessarily
relevant to our study
• For YOUR report, think about:
• Why we need genetic markers, why we need to understand more about the
genetics of Bactrocera tryoni
• Novel and relevant genetic techniques that could be employed to help control
this pest
The Experiment
• Use molecular and phenotypic markers for linkage mapping in
Bactrocera tryoni
• Molecular markers
• RFLP: restriction fragment length polymorphism
• Restriction site in PCR product from white gene
• Microsatellites: short repeat sequences, with short and long alleles
• Data from multiple microsatellites as shown Table 3, pg 12
• Phenotypic marker : white marks
• Determine if the two genes white and white marks are linked, and on
which chromosomes they are located
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Phenotypic and molecular markers
white marks
wm+
Ra and Rb
See also the Figure 3 schematic, page 4 of lab notes
white RFLP
680bp
Ra
130bp 360bp 190bp
RsaI RsaI
Rb
130bp 550bp
680bp
RsaI
Male and Female Backcross
• A test cross is done by crossing a heterozygote with a double-recessive
individual:
AaBb X aabb
• A backcross is when the double-recessive has the same genotype as original
parent (cross ‘back’ to parental genotype)
• Female Backcross: heterozygous female crossed to double-recessive male
AaBb♀ X aabb♂
• Male Backcross: double-recessive female crossed to heterozygous male
aabb♀ X AaBb♂
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Male Backcross in B. tryoni
• Like Drosophila, B. tryoni males do not have recombination during meiosis
• A male backcross* can be used to determine if genes are on the same or
different chromosomes
• *double-recessive female crossed to heterozygous male
Parents
wm Rb
wm Rb ♂♀
X
wm+ Ra
wm+ Ra
P2- Female: homozygous mutant
for white marks and Rb RFLP allele
P1- Male: homozygous for
wild type and Ra RFLP allele
Male Backcross in B. tryoni
F1:
*G2:

Expected ratios:
Phenotype Genotype Unlinked Linked
white marks, b b wm Rbwm Rb 1 1
white marks, a b wm Rawm Rb 1 0
wild type, b b wm+ Rbwm Rb 1 0
wild type, a b wm+ Rawm Rb 1 1
P: Xwm Rb
wm Rb
♀ wm+ Ra
wm+ Ra

wm+ Ra
wm Rb
* G2: different from F2, (F2
are specifically offspring
from an F1 x F1 cross)
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Outcomes of B. tryoni Male Backcross
Rawm+
wm Rb
wm+ Rb
wm Ra
1 wm+ Ra
1 wm+ Rb
1 wm Ra
1 wm Rb
Rawm+
wm Rb
2 genes;
Different chromosomes;
Unlinked:
Independent
assortment
Four types of gametes
with parental and non-
parental phenotypes
wm+ Ra
wm Rb
Rawm+
wm Rb
wm+ Rb
wm Ra
2 genes;
Same chromosome;
Linked:
No Recombination
in males
1 wm+ Ra
0 wm+ Rb
0 wm Ra
1 wm Rb
2 types of gametes
with parental
phenotypes only
Linked Unlinked
à Male backcross: Great way for mapping genes to chromosomes with limited offspring
What is happening in the F1 (heterozygous) male? ♂
wm+ Ra
wm Rb
How did we determine if white marks and
white are linked? Our strategy:
• DNA was provided from a male backcross:
• Parent 1 (male, wild-type, Ra Ra)
• Parent 2 (female, white marks, Rb Rb)
• F1 (male, wild-type, Ra Rb)
• Sixteen G2 offspring (F1 male x female P)
• Each with known phenotype at white marks but unknown RFLP genotype at white
gene
• PCR of the white gene (lab notes, p6-7)
• Restriction enzyme digest of PCR product with RsaI (p8)
• Gel electrophoresis of uncut and cut PCR products (p9)
Gel electrophoresis results:
• Size standards: known fragment sizes shown in Figure 5, pg 16
• Use size standards to estimate your sample RFLP fragment sizes, based on the
expected band sizes- are they similar to expected?
• Fill out Table 3 (pg 12) with RFLP ‘phenotypes’ (AB or BB)
♀P♂P F1 G2-1 G2-2 G2-3 G2-4 G2-5 G2-6 G2-7 G2-8 G2-9 1kbpUC19/
HpaII
250bp
500bp
750bp
1000bp
489bp
404bp
501bp
331bp
242bp
190bp
147bp
110bp
multiple bands
(2000-10000bp)
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Table 3: Microsatellite data/chromosomes
S = short allele
L = long allele
Bt1 = a microsatellite
marker known to be
located on B. tryoni
chromosome 2
Bt2 = chromosome 5
Bt5 = chromosome 3
… etc
Microsatellite question: Prelab exercises (p3):
Each microsatellite (Bt1, Bt2, etc.) will
have a similar format, with short and
long alleles segregating in the offspring
Note the difference between prelab
question (F2 offspring from F1xF1
intercross) vs our results (G2 offspring
from male backcross)
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Same or different chromosomes?
Lwm+
wm S
wm+ S
wm L
1 wm+ L
1 wm+ S
1 wm L
1 wm S
Lwm+
wm S
2 genes;
Different chromosomes;
Unlinked:
Independent
assortment
Four types of gametes
with parental and non-
parental phenotypes
wm+ L
wm S
Lwm+
wm S
wm+ S
wm L
2 genes;
Same chromosome;
Linked:
No Recombination
in males
1 wm+ L
0 wm+ S
0 wm L
1 wm S
Two types of
gametes with parental
phenotypes only
Linked Unlinked
à Linkage analysis: Examine segregation of your genes with the microsatellite markers
Any questions so far?
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Report format
• Scientific report similar to a research journal article
• 1500 words of written text, plus figures, tables, references, and
supplementary information
• Contains the sections:
• Introduction
• Methods
• Results
• Discussion
• Supplementary
Read some journal articles
• To help you get used to the ‘scientific voice’- how scientists write
• Note: you are not required to write an abstract in your report
• Journal: Biology letters: short-format, brief articles.
Introduction
• Include a relevant, informative title for your article
• Not just the generic name of the prac
• Approximately 2-3 written paragraphs to set the scene of the report
• Describe the background and put the experiment into context. Think
about the big picture:
• Study organism- significance: why do we want to understand this species?
• Describe molecular markers, how their use has aided in genetic mapping
• Include references to support your statements
• State the aims of the experiment.
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Introduction: some tips
• The introduction moves from the general to the specific in 2-3
paragraphs and should cover the following areas:
• Identify the main context and draw on background literature to summarise key
points of previous related research
• Explain: ‘why this study?’; ‘what are the aims?’
• Think carefully about what to include and what to leave out
• Choose relevant background to the topic – no need to go into a history of
genetic mapping, or to assure us of the benefits of human genome sequencing
• Cover briefly what molecular markers are and their uses, not a complete
theoretical background
Methods
• Describe the experiment
• What cross was set up, which samples were examined?
• Which molecular techniques were used? Which analytical/statistical techniques?
• Write as a paragraph, not a protocol, briefly describing the key
information so it can be understood/repeated.
• Include necessary details
• concentrations of reagents, temperatures, incubation times
• Don’t include unnecessary information that is obvious
• no need to say that you used PCR tubes, or equipment that is implied.
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Methods: some tips
DON’T: Write it like a protocol, recipe or set of instructions:
• “First, put 10ul of buffer into a PCR tube, then add ….”
DO: Write a brief paragraph, essential details only
• “The PCR reaction contained…”
DON’T: State only the volumes used
• “The PCR reaction contained 2µl of PCR buffer”
DO: Include reagents used at their final concentration in the reaction
• “The PCR reaction contained 67mM Tris (pH 8), 16.6mM[NH4]SO4 … etc”
Which one sounds more like a journal
article?
• Take 1.5ml of bacterial cells and put
into an eppendorf tube.
• Centrifuge for 5 minutes until a pellet is
formed, then pour off the supernatant
into the waste bins provided.
• Next, add 1ml of sterile minimal media
to the pellet and vortex to resuspend.
• Repeat the above steps, resuspending
in 0.5ml of media the second time
• Take four agar plates and streak out
bacterial suspensions using a sterile
swab…
Bacterial cells from four E. coli strains
(wild type, mutants 1, 2 and 3) were
pelleted by centrifugation from 1.5 ml
liquid culture. Cells were rinsed in 1 ml of
sterile minimal media and re-centrifuged,
followed by resuspension in 0.5 ml of
sterile media.
Swabs of each strain were plated onto
four sterile minimal medium L-agar plates,
including three plates that had each been
supplemented with a different
component of the tryptophan
biosynthetic pathway (tryptophan, indole
or anthranillic acid). Plates were
incubated at 37°C for 24 hours.
Option 1: Option 2:
Discussion board question about methods:
• Q: “In explaining the PCR and gel methods, I was unable to determine a few
concentrations such as concentration of template DNA (which was reported
as 3 uL in the notes) as well as the concentration of white PCR product
used in the restriction digest. Would it be acceptable to report just the
volumes used?”
• A: Yes- absolutely. We have not provided concentrations of the DNA
template used in the PCR, and we did not measure the DNA
concentrations of our white PCR product, so it is acceptable to
report the volume used in this instance.
Discussion board question about methods:
• Q: “How do we display the genetic cross? Should we make a diagram similar
to the one in the lab notes or just summarise with words?”
• A: Up to you! There is often not one single way to represent each
element of the report, and this is a good example. Think about the
clearest way to represent the information.
• Note that using figures taken directly from the lab notes is
discouraged- you always need to adapt a diagram in your own way,
using your own words.
Any other questions so far?
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Results
• Clear, precise description of your findings that includes:
• data presentation such as figures and tables
• linked to a verbal summary of your findings
• This section describes but does not explain your results.
• It provides a factual account of your findings, for example: outcomes
and data produced as well as any analysis and tests performed on the
data, described clearly (but the implications are not discussed)
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Results: some tips
• Include a written paragraph detailing the results obtained
• Use data from your group where possible. If data is missing, observe from other
groups. Check all results against ‘perfect cut gel’.
• Exercise 5, questions 1-4* on page 11 of the lab notes provides a good
guideline of what should appear in the results
• * don’t write the question followed by the answer; incorporate your answers into a written
paragraph
• Present a summary of the results in a concise table
• Refer to all tables/figures that you include somewhere throughout the text
• Include the analysis of how you determined linkage
• Statistically test your hypothesis and include in results
• Non-essential figures/tables can be placed in the Supplementary
Discussion board question about Results:
• Q: “Processed results for linkage analysis - is there a specific format for this
results table or is this up to us? Would this table simply summarise the
linkage relationships or also show how we were able to deduce those
relationships? ”
• A: The format is again up to you. The table can summarise the linkage
relationships, though I would recommend explaining somewhere
(perhaps in an accompanying paragraph) how you deduced the linkage
relationships. If you can find a way to include this information in the
table, that is fine too.
Discussion board question about Results vs
Discussion:
• Q: “Should we be interpreting the results in the Results section or is that
reserved for the Discussion section? For example, instead of just stating
there was an x # of bands in a lane and their respective sizes, can we
interpret these results and say which allele they represent in the 'Results'
section? I'm a bit unclear what extent of analysis should be in the Results
and the Discussion sections.”
• A: Results include analysis of the data, so in this case you would
include the number of bands, AND which allele they represent in
results. You would also include your linkage analysis to determine
which chromosome the genes are on.
Discussion
• An informed commentary based on your actual results
• Relates back to your introduction and the key context/background
literature/ related research
• Tells the reader what your results mean in terms of the context,
background and aims.
• To enable this you must include
• Key points of your results and discussion of how they allowed you to achieve
your aim
• Limitations of your results, e.g. what you would do differently if you revisited the
research and/or what you would explore further
• Suggestions for future research in this area
• A final summary of the main findings and why they are important
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Discussion: some tips
• Demonstrate a clear understanding and interpretation of the results and
their biological significance
• Exercise 5, questions 5-6, pg11 provides some important discussion points that
should be considered
• Consider limitations and future directions
• Could you improve the methodology used?
• Think about which modern techniques are now available that could complement
this research.
• What would you do next to increase our understanding of the genetics of B.
tryoni?
• Finish with a brief conclusion to the report bringing it back to the aims
References
• Both the Introduction and Discussion are opportunities to integrate
your report with the literature.
• You should cite at least 2-3 relevant primary references that support
any factual statements that you make about previous work, or provide
inspiration for techniques that you propose as future directions
• Citing the lab manual: Generally not encouraged unless the
information does not appear elsewhere (eg. something specific about
our methods)
• Author-date referencing system:
• Pleska, M. and Guet, C.C. (2017). Effects of mutations in phage restriction sites
during escape from restriction-modification. Biol Lett 13(12): 20170646
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Supplementary section
• Comes at the end of the report
• Contains information that you used to determine the results, but are
too detailed to include in the results
• Raw data such as
• Labelled gel photos
• Table recording approximate band sizes for each genotype
• Large table where you recorded all the results (eg. a completed Table 3 from
lab notes)
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Discussion board question about Supplementary:
• Q: “In reference to "summary of the banding pattern for each individual" in
the Supplementary section, is this referring to including a table like Table 3
from our lab notes?”
• A: You can certainly include a summary of the gel banding patterns
within a similar table to Table 3, which I would consider to be a
record of the raw data, and too large to be included in the Results
section.
Any more questions?
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Assessment criteria
• Context (20%): Place the experiment into context in the introduction and
throughout the report. Provide relevant background information on the study
organism, the techniques used and the aims.
• Technical accuracy (25%): Presentation of the methods and results in a
technically accurate way, including tables, figures and Supplementary
information.
• Understanding, interpretation and extension (40%): Demonstrate
understanding and interpretation of the results, and discussion of the
implications, relevance, and suggestions of future directions/experiments.
• Presentation (15%): Overall clarity of presentation, appropriate scientific
style, good use of English and appropriate use of references.
Context (20%)
• Largely represented by the Introduction, also elements of the
Discussion
• Description of the relevance and importance of the study
• Explanation of key points in a clear and concise way
• Lack of irrelevant information
• Source information is appropriately referenced
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Technical accuracy (25%)
• Largely represented by the Methods description, also includes
presentation of the Results (and Supplementary)
• Correct, scientific description of the Methods used
• Accurate, concise representation of all necessary results and analysis
• Figures and tables presented clearly and labelled correctly, with figure
legends and table headings
• Inclusion of raw data in the supplementary section
• (the point above still applies for supplementary- figures/tables labelled etc…)
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Understanding, interpretation, extension (40%)
• Largely represented by the analysis, understanding and interpretation of
Results and Discussion.
• Analysis of results provided the correct biological explanation (Did you get
the ‘correct’ result?)
• Adequate coverage of questions from Exercise 5, pg 11of the lab notes and
include a discussion of these points in your results and discussion section
• Consideration of the implications, relevance, and suggestions of future
directions/experiments.
• Extend from this study to suggest ways of expanding on the results, using
modern techniques
Presentation (15%)
• Clarity of writing throughout the report
• Correct use of genetic nomenclature and scientific style – not too wordy, clear and
concise, information is easy to interpret from what has been written
• Overall layout
• Ordering of sections
• Information placed in correct sections
• Placement of figures/tables in a linear order, integrated with written paragraphs
• Spelling, grammar, and correct use of english
• Choice of relevant references that have been correctly cited and referred to
within the report
• Adherence to word count
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
Questions?
• See Canvas for Report Guidelines > Assignments > Practical Report
• Discussion Board for any other questions
To ask questions throughout,
go to www.menti.com and
use the code 56 28 67
External report writing tools
• Help with structure, scientific language, general guidelines for each
section* of the report, with interactive questions and examples:
http://learningcentre.usyd.edu.au/wrise/biochemistry3/overall_structure/os
_structure.html
• work through each screen by clicking ‘next’
• *Note: we don’t require an Abstract/Summary in your report
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