Kyushu University
Department of Agriculture
Session 6 – Writing Your Manuscript
Kyushu University
10 July 2014
Andrew Jackson, PhD
Senior Editor
Seminar series
June 5
Effective presentations
June 12
June 19
June 26
July 3
July 10
July 17
July 24
Reviewing the literature
Academic publishing
Research and publication ethics
Effective writing
Manuscript structure
Communicating with journals
Peer review and revisions
Section 1
Professional writing
strategies
Coverage
Writingand
Staffing
Plan
strategies
Use your figures to
structure your manuscript
Where to start?
 Your findings are
why you want to
publish your work
 Form the basis of
your manuscript
 First step, is to
logically organize
your findings
Figure 1
Logical
presentation
Table 1
Figure 2
?
Figure 3
Is anything
missing?
Additional
analyses?
Coverage
Writingand
Staffing
Plan
strategies
Use your figures to
structure your manuscript
Where to start?
 Your findings are
why you want to
publish your work
 Form the basis of
your manuscript
 First step, is to
logically organize
your findings
Figure 1
Logical
presentation
Table 1
Figure 2
Figure 3
Figure 4
New data
Coverage
Writingand
Staffing
Plan
strategies
I.
II.
III.
IV.
Prepare an outline
Introduction
A.
General background
B.
Related studies
C.
Problems in the field
D.
Aims
Methods
A.
Subjects/Samples/Materials
B.
General methods
C.
Specific methods
D.
Statistical analyses
Results
A.
Key points about Figure 1
B.
Key points about Table 1
C.
Key points about Figure 2
D.
Key points about Figure 3
E.
Key points about Figure 4
Discussion
A.
Major conclusion
B.
Key findings that support conclusion
C.
Relevance to published studies
D.
Unexpected/negative findings
E.
Limitations
F.
Implications
G.
Future directions
Introduction
What background information
you will introduce
Methods
What analyses you will describe
Results
What findings you will present
Discussion
What interpretations, limitations,
and implications you will discuss
Coverage
Writingand
Staffing
Plan
strategies
Getting feedback
 After completing your outline, discuss it with your colleagues
 Make the necessary changes before you begin writing
 Write your manuscript section-by-section, do not get
overwhelmed by thinking about writing an entire manuscript
 Set deadlines as to when the first draft of each section will be
completed
 Get feedback from you colleagues after each section and make
changes before beginning the next section
Coverage
Writingand
Staffing
Plan
strategies
The ‘write’ order
Manuscript sections
Writing order
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Title
Abstract
Introduction
Methods
Results
Figures
Discussion
Methods
Figures
Results
Discussion
Introduction
Abstract
Title
Coverage
Writingand
Staffing
Plan
strategies
Methods
The ‘write’ order
• Write as you are doing experiments
• Include any changes you’ve made
• Methods sections are usually consistent
Figures
• Prepare figures after choosing journal
• Repeat experiments if necessary
Results
• Based on prepared figures
• Subsections based on each figure
Coverage
Writingand
Staffing
Plan
strategies
The ‘write’ order
Discussion
• Conclusions based on presented data
• Discuss relevant studies
Introduction
• Narrow- or broad-focused journal
• Introduce ideas necessary for
understanding the Results/Discussion
Abstract
• Concisely summarize manuscript
• According to author guidelines
Title
• Concisely summarize key finding
• Include key words
Section 2
Target the journal
Broad vs. narrow focus
Target the journal
Aims and scope
Broad focus
Make sure your findings
will be of broad interest
Narrow focus
Make sure your findings
will be of interest to
specific area(s)
Target the journal
Broad focus
Aims and scope
Planta
Planta publishes timely and substantial articles on all aspects
of plant biology. We welcome original research papers on
any plant species.
Target the journal
Broad focus
How did related articles target the journal?
The control of chlorophyll levels in maturing kiwifruit
Chlorophyll is present in many plant organs, including immature fruit where it
is usually degraded during ripening. Mature green kiwifruit (Actinidia
deliciosa) are an exception, with high concentrations of chlorophyll remaining
Broad interest
in the fruit flesh. In gold-fleshed kiwifruit (A. chinensis), chlorophyll is
degraded to colourless catabolites upon fruit ripening, leaving yellow
carotenoids visible. We have identified candidate genes for the control of
chlorophyll degradation in kiwifruit…
Broad interest
Pilkington et al. Planta. 2012; 236: 1615−1628.
Target the journal
Narrow focus
Aims and scope
Paddy and Water Environment
The aim of Paddy and Water Environment is to advance the
science and technology of water and environment related
disciplines in paddy-farming. The scope includes the paddyfarming related scientific and technological aspects in
agricultural engineering such as irrigation and drainage, soil
and water conservation, land and water resources
management, paddy multi-functionality, agricultural policy,
regional planning, bioenvironmental systems, and ecological
conservation and restoration in paddy farming regions.
Target the journal
Narrow focus
Aims and scope
Paddy and Water Environment
The aim of Paddy and Water Environment is to advance the
science and technology of water and environment related
disciplines in paddy-farming. The scope includes the paddyfarming related scientific and technological aspects in
agricultural engineering such as irrigation and drainage, soil
and water conservation, land and water resources
management, paddy multi-functionality, agricultural policy,
regional planning, bioenvironmental systems, and ecological
conservation and restoration in paddy farming regions.
Target the journal
Narrow focus
Aims and scope
Paddy and Water Environment
The aim of Paddy and Water Environment is to advance the
science and technology of water and environment related
disciplines in paddy-farming. The scope includes the paddyfarming related scientific and technological aspects in
agricultural engineering such as irrigation and drainage, soil
and water conservation, land and water resources
Make sure your manuscript specifically
management, paddy multi-functionality, agricultural policy,
of these areas
of interest!
regionaltargets
planning,one
bioenvironmental
systems,
and ecological
conservation and restoration in paddy farming regions.
Target the journal
Narrow focus
How did related articles target the journal?
Effects of tillage and irrigation on the occurrence and establishment of
native wetland plant species in fallow paddy fields
Traditional weed management, such as tillage and irrigation, has led to an
enhanced maintenance of wetland plant species in fallow paddy fields.
Recent herbicide usage and improvements in irrigation and drainage systems
however have caused habitat loss of these species, especially in fields on
open lowlands…
Keywords from the Aims and Scope
Takanose et al. Paddy Water Environ. 2013; 11: 1−4.
Target the journal
Your references
Related articles from the journal
Include references to those articles in
your manuscript
Shows the journal editor that your
study is building on research already
published in their journal
Section 3
Manuscript structure
Manuscript
structure
Introduction
General introduction
Current state of the field
Problem in the field
Aims
Specific aims
Manuscript
structure
Your aims should
address a problem
Problem
However, information on major nutrient balances driven by underlying
socioeconomic factors is lacking in peri-urban areas.
Aims
The objectives of the research were: (1) to monitor agricultural inputs
and outputs of N, P, and K, to quantify and assess element balances at
the field level for a two-year period; (2) to identify the main
contributory factors causing element imbalances; and (3) to assess
socio-economic factors that drive nutrient management. This will
allow future research to explore risks for soil accumulation and
potential losses to the water environment.
Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.
Manuscript
structure
Most common reason
for rejection?
Analyzed 42 manuscripts rejected from
8 biomedical journals
Flaws found in:
Introduction
66.7%
Methods
Results
Discussion
85.7%
66.7%
71.%
Experimental design
Ezeala et al. Ann Med Health Sci Res. 2013; 3: 376–379.
Manuscript
structure
Methods –
What/who was used
Participants
Age and gender
Enrollment
Inclusion/exclusion criteria
Animals, cells
Species/cell type
Age, gender, weight
Living/incubation conditions
Materials
Where purchased
[city, state (if US), country]
How much was used
Manuscript
structure
Methods –
How it was done
Order
• General methods first
• Specific techniques in order
of appearance
Previously
used methods
• Cite previous publications
• XXXX was done as previously
described23. Briefly…
New methods
• Give enough detail to be
reproducible
• Validation for new technique
Always state sample number and controls
Manuscript
structure
Methods –
How it was analyzed
Quantification
methods
• Explain how the data
was quantified
• Rationale
Computer
programs
• Where obtained
• Which version
• Specific parameters
Statistical
analyses
• Choose right test!
• P-value for significance
• Consult with a statistician
Manuscript
structure
Results
Logical presentation
1. Initial observation
2. Characterization
3. Application
Example:
1. New gene expressed in the heart
2. Regulation of gene expression, when it is
expressed, function of the produced protein
3. Role of the gene in heart development
Manuscript
structure
Results
Logical presentation
1. Initial observation
2. Characterization
3. Application
Subsections
Each subsection
corresponds to
one figure
Factual description
What you found, not
what it means
Manuscript
structure
Display items
Present large amount
of data quickly and
efficiently
Usually the first thing
readers will look at
Figures, graphs
& tables
Keep it simple: use
separate panels if
necessary
Must be able to stand
alone: clear labels
and figure legends
Manuscript
structure
Figures
Clear figure legend
Kindlin-2 knockdown and focal adhesion localization.
Confocal immunofluorescent microscopy with anti-β1
integrin and anti-paxillin on C2C12 cells transfected
with RNAi and then changed to differentiation media
for 2 days. Control cells show linear staining consistent
with localization to costameres (arrows), as well as
punctate focal contact staining (arrowheads). Focal
contact proteins in the kindlin-2 RNAi cells fail to form
linear structures and instead are concentrated in
unusual appearing puncta (*). (Scale bar = 20 μM).
Title of the experiment
Brief methodology
Key findings
Clear indicators
Dowling et al. (2008) BMC Cell Biol 9:36.
Manuscript
structure
Discussion
Summary of findings
Relevance of
findings
Similarities/differences
Unexpected results
Limitations
Implications for
the field
Manuscript
structure
Writing the beginning
of your Discussion
Beginning should state the major
conclusion of the study
Re-introduce the topic
Re-introduce the problem
State major conclusion to answer the problem
Summarize key data to support conclusion
Manuscript
structure
Writing the beginning
of your Discussion
Beginning should re-state problem and
your conclusion that answers that problem
Current management practices caused a large quantity of nutrient inputs
on both sites. Two recent one-year studies, one in the same study area
and the other in Hanoi, Vietnam, showed similar nutrient balances for N,
Problem
P, and K. However, it is hard to show main control factors on element
balances based on one-year study because of short-term observation.
This paper shows that positive net N and P balances in conjunction with
negative net K balances on these plots are most likely because of the
irregularity of organic manure application…
Answer
Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.
Manuscript
structure
Writing the end of
your Discussion
End should state the major conclusion of
the study
Re-state your major conclusion
Describe the key implications
Recommend future research
Manuscript
structure
Writing the end of
your Discussion
Why your work is important to your readers
The Spanish version of AIDA showed good psychometric
properties in Mexico and can be used to assess the construct
“pathology-related identity integration vs. diffusion” with
reliability, validity, and content equivalence in comparison
with the original AIDA questionnaire. This finding supports
the cross-cultural generalizability of the underlying concept
and confirms the importance of culture-specific test
adaption in addition to literal translation of the
questionnaire. Nevertheless, some items should be
improved. Therefore, the test version of “AIDA Spanish –
Mexico” should be further adapted and should be tested in a
more heterogeneous population.
Conclusion
Implications
Future
directions
Kassin et al. Child Adolesc Psychiatry Ment Health. 2013; 7: 25.
Manuscript
structure
Linking your ideas in
your manuscript
General background
Introduction
Current state of the field
Problems in the field
Objectives
Methods
Results
Methodology
Results and figures
Summary of findings
Discussion
Relevance of findings
Implications for the field
Logically link your ideas throughout your manuscript
Manuscript
structure
Linking your ideas in
your manuscript
Introduction
New ways to treat or prevent lung cancer
are therefore needed.
Problem
This study explored the hypothesis that inhibition
of TNKS…would inhibit lung cancer growth…
Objectives
Discussion
Pharmacological or genetic inhibition of TNKS1
and TNKS2…reduces lung cancer proliferation...
Conclusion
Busch et al. BMC Cancer. 2012;13:211.
Manuscript
structure
Writing effective
conclusions
Your conclusion is a summary of your findings
Your conclusion should be the answer to your
research problem that is supported by your findings
Emphasizes how your study will help
advance the field
Section 4
Titles and abstracts
Titles & abstracts
Effective titles
Important points
Avoid
 Summarize key finding
 Contains keywords
 Less than 20 words
Questions
Describing methods
Abbreviations
“New” or “novel”
Your title should be a concise summary of
your most important finding
Titles & abstracts
Relevance of
your aims
Abstract
Importance of
your results
Validity of your
conclusions
First impression
of your paper
Judge your
writing style
Probably only part
that will be read
Titles & abstracts
Sections of an abstract
Concise summary of your research
Background
Why the study was done
Aims
Your hypothesis
Methods
Techniques
Results
Most important findings
Conclusion
Conclusion/implications
Titles & abstracts
Abstract
Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The
resistance mechanism is an important nonhost reaction in plants that can block the invasion of
filamentous pathogens such as fungi and oomycetes. However, it remains unclear whether the
mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance,
whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used
microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation
transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to
demonstrate that microwounds derived from fungal penetration attempts may trigger induced
penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and
Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe
that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with
the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein
HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal
penetration or artificial microwounds. These results strongly suggest that microwounding may trigger
actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may
be a promising target to improve basic disease resistance in plants.
Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
Titles & abstracts
Abstract
Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The resistance
mechanism is an important nonhost reaction in plants that can block the invasion of filamentous pathogens such as
fungi and oomycetes. However, it remains unclear whether the mechanical stimuli accompanying fungal penetration
play a role in induced penetration resistance, whereas the perforation of the cell wall may provide significant stimuli to
plant cells.
Here, we used microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation
transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to demonstrate that
microwounds derived from fungal penetration attempts may trigger induced penetration resistance in plant cells.
When preinoculated with the nonpathogenic fungi Erysiphe pisi and Colletotrichum orbiculare, which were unable to
penetrate a barley cell, the penetration of a bio-probe that was transferred by micromanipulation onto the same cell
was completely blocked…Treatment with the actin polymerization inhibitor cytochalasin A or expression of the actin
depolymerizing protein HvPro1 caused complete ablation of the induced penetration resistance triggered by either
failed fungal penetration or artificial microwounds.
These results strongly suggest that microwounding may trigger actin-dependent induced penetration resistance.
Manipulation of induced penetration resistance may be a promising target to improve basic disease resistance in
plants.
Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
Titles & abstracts
Abstract
Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The
resistance mechanism is an important nonhost reaction in plants that can block the invasion of
filamentous pathogens such as fungi and oomycetes. However, it remains unclear whether the
mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance,
whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used
microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation
transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to
demonstrate that microwounds derived from fungal penetration attempts may trigger induced
penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and
Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe
that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with
the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein
HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal
penetration or artificial microwounds. These results strongly suggest that microwounding may trigger
actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may
be a promising target to improve basic disease resistance in plants.
Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
Titles & abstracts
Abstract
Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The
resistance mechanism is an important nonhost reaction in plants that can block the invasion of
filamentous pathogens such as fungi and
oomycetes. However, it remains unclear whether the
Background
mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance,
whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used
microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation
transfer technique of the bio-probe, a germling
of Blumeria graminis hordei, to the wounded cells to
Methods
demonstrate that microwounds derived from fungal penetration attempts may trigger induced
penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and
Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe
that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with
Results
the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein
HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal
penetration or artificial microwounds. These results strongly suggest that microwounding may trigger
actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may
Conclusions
be a promising target to improve basic disease
resistance in plants.
Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
Activities
Manuscript structure exercise
Based on the following problem identified in the field, chose
which aims are most appropriate.
Problem: Currently it is not clear which weight management
program is most efficient to prevent weight gain after smoking
cessation in men.
Unrelated variable
A) In this study, we evaluated the effect of working hours on
the efficacy of three popular weight management programs
for the prevention of weight gain in men after smoking
cessation.
Manuscript structure exercise
Based on the following problem identified in the field, chose
which aims are most appropriate.
Problem: Currently it is not clear which weight management
program is most efficient to prevent weight gain after smoking
cessation in men.
B) In this study, we evaluated the efficacy of three popular
weight management programs implemented in a working
environment for the prevention of weight gain in men after
smoking cessation.
Unrelated variable
Manuscript structure exercise
Based on the following problem identified in the field, chose
which aims are most appropriate.
Problem: Currently it is not clear which weight management
program is most efficient to prevent weight gain after smoking
cessation in men.
C) In this study, we evaluated the efficacy of three popular
weight management programs for the prevention of weight
gain in men after smoking cessation.
Directly addresses the identified problem
Manuscript structure exercise
Match the aims from an Introduction with the most
appropriate major conclusion (to be used in a Discussion).
Aims: To date, few studies have investigated the influence of
literacy on economic growth. In this study, we aimed to
evaluate how literacy rates affected the economic growth of
various countries from 2000 to 2010.
A) Our results demonstrate the need to improve education to
promote literacy in developing countries.
Implications
Manuscript structure exercise
Match the aims from an Introduction with the most
appropriate major conclusion (to be used in a Discussion).
Aims: To date, few studies have investigated the influence of
literacy on economic growth. In this study, we aimed to
evaluate how literacy rates affected the economic growth of
various countries from 2000 to 2010.
B) This study showed that increased literacy rates are
positively correlated with economic growth.
Conclusion answers the problem
Manuscript structure exercise
Match the aims from an Introduction with the most
appropriate major conclusion (to be used in a Discussion).
Aims: To date, few studies have investigated the influence of
literacy on economic growth. In this study, we aimed to
evaluate how literacy rates affected the economic growth of
various countries from 2000 to 2010.
C) In this study, we showed that economically developed
countries spend more money on education, leading to
improved literacy rates.
Key finding
Manuscript structure exercise
Presentation of ideas in the Discussion
This study showed that increased literacy rates are positively
correlated with economic growth.
Conclusion
In this study, we showed that economically developed countries
spend more money on education, leading to improved literacy
rates.
Key findings
Our results demonstrate the need to improve education to
promote literacy in developing countries.
Implications
Manuscript structure exercise
Which is the best title, and why?
A) Characterizing the fungal infection of wheat in high altitude
environments
Describes methodology
B) High altitude reduces fungal infection of wheat
Summary of key finding
C) Does high altitude affect the fungal infection of wheat?
Don’t use questions
D) Low oxygen and cold temperature in high altitude
environments affects the growth rate of a variety of fungi
and reduces the fungal infection of wheat
Too long (25 words)
Manuscript structure exercise
True or false?
F A) The Introduction of your manuscript does not depend
on the type of journal.
F B) Because most readers do not read the Methods section,
it is not a very important part of the manuscript.
T C) Figure legends should provide enough information for
the reader to understand the figure without having to
refer to the main text.
Manuscript structure exercise
True or false?
F D) You should not emphasize the limitations of your study
in you manuscript because it makes your findings look
less important.
T E) You should write you conclusion to be an answer to the
problem you identified.
F F) Because you want people to download and read your
article, you should not give too much information (e.g.,
implications) in the abstract.
Any questions?
Thank you!
Andrew Jackson: [email protected]
Jeffrey Robens: [email protected]
edanzediting.co.jp/kyushu_140710
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