20140826 Edanz Kyushu Session 2

Kyushu University Department of Agriculture Seminar Series – Session 2

Dr Jeffrey Robens

26 August 2014

Seminar series

Session 1 Session 2

Effective writing Manuscript structure

Journal selection Cover letters

Methodology Peer review

Figures and Results

Section 1

Figures & Results

Present large amount of data quickly and

efficiently

Keep it simple: use separate panels if

necessary

Must be able to stand alone: clear labels and figure legends

Usually the first thing readers will look at

Figures, graphs & tables

Figures & Results 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).

Dowling et al. (2008) BMC Cell Biol 9:36.

Clear indicators

Title of the experiment

Brief methodology

Key findings

Figures & Results

Data aligned and formatted

Table formatting

Muñoz et al. New Engl J Med. 2003;348:518−527.

Clear and concise table caption

Abbreviations defined

Figures & Results Is this a good table?

Alignment and formatting problems

Alignment of text

Alignment of parentheses

Alignment of decimals

Data similarity

Lines

Tumor size (mm3) before treatment Mean (±SD)

Tumor size (mm3) after treatment

Mean (±SD)

% decrease

Treatment time

Group 1 423.2 (6.23) 232.8 (3.18) 44.99 4 months

Group 2 286.43 (4.8) 157.32 (2.29) 45.08 14 weeks

Group 3 342.7 (6.88) 218.4 (5.2) 36.27 3.5 months

Group 4 404 (3) 302 (4.21) 25.247 90 days

Figures & Results Making a good table

Tumor size (mm3) before

treatment Mean (±SD)


Mean (±SD)

% decrease

Treatment time

(weeks)

Group 1 423.20 (6.23) 232.80 (3.18) 44.99 16

Group 2 286.43 (4.80) 157.32 (2.29) 45.08 14

Group 3 342.70 (6.88) 218.40 (5.20) 36.27 14

Group 4 404.00 (3.00) 302.00 (4.21) 25.25 12

Tumor size (mm3) before treatment Mean (±SD)


Mean (±SD)

% decrease

Treatment time

Group 1 423.2 (6.23) 232.8 (3.18) 44.99 4 months

Group 2 286.43 (4.8) 157.32 (2.29) 45.08 14 weeks

Group 3 342.7 (6.88) 218.4 (5.2) 36.27 3.5 months

Group 4 404 (3) 302 (4.21) 25.247 90 days

Figures & Results

0

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35

0 1 h 2 h 3 h 4 h 5 h 6 h

Drug A

Drug Bng

/ml

0

5

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0 1 h 2 h 3 h 4 h 5 h 6 h

Use high contrasting colors Clearly label axes Clear legends

Graphs

Figures & Results Graphs

Drug A

Drug B

0

5

10

15

20

25

30

01 h

2 h3 h

4 h5 h

6 h

NEVER use 3-D graphs for 2-D data

Figures & Results Results

1. Novel observation 2. Characterization 3. Application

Logical presentation

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

Figures & Results

1. Novel observation 2. Characterization 3. Application

Each subsection corresponds to

one figure

What you found, not what it means

Logical presentation

Subsections

Factual description

Results

Figures & Results Factual description

Drug A is more effective in treating liver cancer as we observed a 32.7% decrease in tumor size compared with only a 22.1% decrease after Drug B treatment.

The efficacy of Drug A was significantly higher than that for Drug B, with decreased tumor size 32.7% or 22.1%, respectively.

Belongs in the Discussion

Exception is when the Results and Discussion sections are combined

Figures & Results Group repetitive results

Drug A reduced tumor volume by 32.7%, increased blood pressure by 12.3%, and decreased the patient’s weight by 7.3 kg. Drug B reduced tumor volume by 22.3%, increased blood pressure by 15.6%, and decreased the patient’s weight by 2.4 kg. Drug C reduced tumor volume by 38.1%, increased blood pressure by 6.9%, and decreased the patient’s weight by 9.2 kg.

Figures & Results

Patients treated with Drug C showed the greatest reduction in tumor volume (28.1%) compared with those treated with Drug A (32.7%) or Drug B (22.3%). Drug C also had the lowest increase in blood pressure (6.9%) compared with that seen after treatment with Drug A (12.3%) or Drug B (15.65). However, patients treated with Drug C had the highest weight gain among the three groups (Drug A, 7.3 kg; Drug B, 2.4 kg; Drug C, 9.2 kg).

Group repetitive results

Activities Please see accompanying

handouts

Results

Results activity

In the following Results section, identify any common errors you can find.

Results activity

Results Food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Results activity

Results Food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

More descriptive heading

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

“significant increase”

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Belongs in Introduction

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Belongs in Methods

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Results activity


No problems

Results activity


Results activity


Belongs in Discussion

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.

Should show the data

Results activity

Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). Even though food consumption continued for over one month with an average daily consumption of 2.3±0.12 g, the body weight of earthquake-experienced mice increased only slightly during that period (186.3±1.2 g on day 1 and 188.2±1.6 g on day 30).

Introduction and Discussion

Section 2

Introduction & Discussion

General introduction

Specific aims Aims

Current state of the field

Problem in the field

Introduction


Major nutrient balances in small-scale vegetable farming systems in peri-urban areas in China

Nutrient Cycling in Agroecosystems

Nutrient Cycling in Agroecosystems (formerly Fertilizer Research) considers manuscripts dealing with aspects of carbon and nutrient cycling as well as management, their effect in ecological, agronomic, environmental and economic terms. Contributions may deal with subjects in agronomic, agro-forestry and fallow systems or system components such as plants and the fertility, chemistry or microbiology of soils, as well as with system inputs and losses.

Aims and Scope

Key point

Target your journal


Beginning should demonstrate relevance/interest

Cities in China and other developing countries continue to expand as people migrate from rural to urban areas, and agricultural land in peri-urban areas decreases rapidly as a result. Farmers are challenged to intensify production per unit area with decreasing amounts of land to satisfy food production demands and increase revenue. This intensive production will inevitably cause serious nutrient imbalances, exacerbated by the limited nutrient-retention capacity of soils in peri-urban areas. Moreover, inefficient nutrient management and concomitant nutrient enrichment of agro-ecosystems have contributed to agriculture’s impact on aquatic systems. Specifically, soils in vegetable lands are often characterized by continuous and large quantities of organic and inorganic fertilizer application, which inevitably lead to a serious pollution threat to the water environment.

Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.

Interest

Writing the Introduction

Introduction & Discussion Writing the Introduction

Beginning should demonstrate relevance/interest

Cities in China and other developing countries continue to expand as people migrate from rural to urban areas, and agricultural land in peri-urban areas decreases rapidly as a result. Farmers are challenged to intensify production per unit area with decreasing amounts of land to satisfy food production demands and increase revenue. This intensive production will inevitably cause serious nutrient imbalances, exacerbated by the limited nutrient-retention capacity of soils in peri-urban areas. Moreover, inefficient nutrient management and concomitant nutrient enrichment of agro-ecosystems have contributed to agriculture’s impact on aquatic systems. Specifically, soils in vegetable lands are often characterized by continuous and large quantities of organic and inorganic fertilizer application, which inevitably lead to a serious pollution threat to the water environment.


Interest

Keywords from the Aims and Scope


Clearly state an interesting problem in the field

Therefore, the large net balances [of N, P, and K] indicate a substantial risk of long-term effects on soil fertility, because of soil accumulation and losses to ground and surface waters. However, information on major nutrient balances driven by underlying socioeconomic factors is lacking in peri-urban areas.




Your aims should directly address this problem

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.


However, information on major nutrient balances driven by underlying socioeconomic factors is lacking in peri-urban areas.


Introduction & Discussion Flow of information

Lung cancer is the leading cause of cancer mortality for men and women. Despite smoking prevention and cessation programs and advances in early detection, the 5-year survival rate for lung cancer is only 16% with current therapies. Although lung cancer incidence rates have recently declined in the United States, more lung cancer is now diagnosed when considered together in former- and never-smokers than in current smokers. Thus, even if all of the national anti-smoking campaign goals are met, lung cancer will remain a major public health problem for decades. New ways to treat or prevent lung cancer are therefore needed. One potential therapeutic target for lung cancer is the Wnt signaling pathway. The canonical Wnt signaling pathway in mammals consists of a family of secreted lipid-modified Wnt protein ligands that bind to a family of 7-pass transmembrane Frizzled (Fzd) receptors, as reviewed…

Busch et al. BMC Cancer. 2012; 13: 211.

Topic sentence

Stress sentence

Topic sentence

Support

Introduction & Discussion Discussion

Summary of findings

Relevance of findings

Implications for the field

Similarities/differences Unexpected results Limitations


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

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, 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…


Writing the Discussion

Problem

Answer



End should state the major conclusion of the study

Re-state your major conclusion

Describe the key implications

Recommend future research



In summary, we identified a P. infestans RXLR-WY–type effector, PexRD2, which interacts with MAPKKKε and perturbs plant immunity associated signaling pathways dependent on this kinase. Either overexpression of PexRD2 or knockdown of MAPKKKε supports enhanced pathogen growth and suppression of MAPKKKε-triggered or -dependent cell death readouts in N. benthamiana. This study represents a step toward understanding how oomycete RXLR-type effectors directly interact with MAPK cascades, which are well established as key regulators of plant immunity. The next challenge is to better understand the role of PexRD2 and PexRD2-like effectors, and their targets, in the progression of disease in important host crop plants, such as tomato and potato. The ultimate aim of this would be to manipulate these interactions to tip the balance in the coevolutionary arms race between pathogen and host in favor of the plant.

End should summarize your conclusion and clearly state implications

King et al. Plant Cell. 2014; 26: 1345−1359.



In summary, we identified a P. infestans RXLR-WY–type effector, PexRD2, which interacts with MAPKKKε and perturbs plant immunity associated signaling pathways dependent on this kinase. Either overexpression of PexRD2 or knockdown of MAPKKKε supports enhanced pathogen growth and suppression of MAPKKKε-triggered or -dependent cell death readouts in N. benthamiana. This study represents a step toward understanding how oomycete RXLR-type effectors directly interact with MAPK cascades, which are well established as key regulators of plant immunity. The next challenge is to better understand the role of PexRD2 and PexRD2-like effectors, and their targets, in the progression of disease in important host crop plants, such as tomato and potato. The ultimate aim of this would be to manipulate these interactions to tip the balance in the coevolutionary arms race between pathogen and host in favor of the plant.

End should summarize your conclusion and clearly state implications

King et al. Plant Cell. 2014; 26: 1345−1359.

Implications

Conclusions

Future directions

Field advancement

Key findings



Linking your ideas in your manuscript

General background

Objectives

Methodology

Results and figures

Summary of findings

Implications for the field

Relevance of findings

Problems in the field

Logically link your ideas throughout your manuscript

Current state of the field Introduction

Methods

Results

Discussion


Linking your ideas in your manuscript

Contamination of the soil by heavy metals is a serious

environmental problem...

Little is known how heavy metals affect membrane lipid metabolism…

Our results showing changes in total fatty acids, profiles of individual polar lipids, and unsaturation levels suggest that

Cd stress might alter membrane structure and function.

Background

Problem

Conclusion

Discussion

Introduction

Elloumi et al. Botanical Studies. 2014; 55: 61.

Our aim was to assess how Cd stress affects the composition and biosynthesis of lipids and fatty acids……

Objective


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

Introduction activity

S

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.

1. 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.

2. 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.

3. In this study, we evaluated the efficacy of three popular weight management programs for the prevention of weight gain in men after smoking cessation.

Introduction activity

S

Based on the following problem identified in the field, chose which aims are most appropriate.

Problem: Current climate change is mainly driven by historic emissions. The countries responsible for the majority of historic emissions are not necessarily the same as those responsible for the dominant share of current emissions.

1. We report on historical trends in climate change to better understand future changes.

2. This paper provides an original quantitative analysis of historic emissions by tracing sources of industrial CO2 and methane, to compare with current emissions.

3. In this paper, we identify those countries responsible for the dominant share of current emissions.

Discussion activity

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 different tissue pressures on tumor growth. In this study, we aimed to evaluate how varying the pressure within brain, liver, and lung tissues affected the growth of transplanted tumors.

A) Our results demonstrate the need to monitor pressures within different tissues when determining effective treatments.

Implications

Discussion activity


B) This study has shown that the increasing the pressure within tissues significantly reduces tumor growth.

Conclusion answers the problem

Discussion activity


C) In this study, we have shown that high pressure environments reduce the vascularization of growing tumors.

Key finding

Discussion activity

This study has shown that the increasing the pressure within tissues significantly reduces tumor growth. In this study, we have shown that high pressure environments reduce the vascularization of growing tumors. Our results demonstrate the need to monitor pressures within different tissues when determining effective treatments.

Key findings

Conclusion

Implications

Presentation of ideas in the Discussion

Titles and abstracts

Section 2

Titles & Abstracts

Important points

Summarize key finding Contains keywords Less than 20 words

Avoid

Effective titles

Your title should be a concise summary of your most important finding

Questions Describing methods Abbreviations “New” or “novel”

Titles & Abstracts Abstracts

First impression of your paper

Importance of your results

Validity of your conclusions

Relevance of your aims

Judge your writing style

Probably only part that will be read

Titles & Abstracts Sections of an abstract

Aims

Background

Methods

Results

Conclusion

Why the study was done

Your hypothesis

Techniques

Most important findings

Conclusion & implications

Concise summary of your research

Titles & Abstracts Writing your 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. Fungal penetration was essential to the triggering of induced penetration resistance because a

penetration-peg-defective mutant of C. orbiculare completely lacked the ability to trigger resistance. The

artificial microwounds significantly, but not completely, blocked the penetration of the bio-probe. 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

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.


Writing your 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.

Implications

Titles & Abstracts Writing your Abstract




















Titles & Abstracts




















Why this study needed to be done

What you did

What you found

How can advance the field

Writing your Abstract

Titles & Abstracts SEO

Search Engine Optimization

Identify 7–8 keywords (include synonyms)

Use 2 in your title, 5–6 in the keyword list

Use 3 keywords 3–4 times in your abstract

Use keywords in headings when appropriate

Be consistent throughout your paper

Cite your previous publications when relevant • Google Scholar ranks results by citations


handouts

Title and Abstract

Title activity

Which is the best title, and why? A) Characterizing the fungal infection of wheat in high altitude

environments

B) High altitude reduces fungal infection of wheat

C) Does high altitude affect the fungal infection of wheat?

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

Summary of key finding

Don’t use questions

Describes methodology

Too long (25 words)

Abstract activity

Activity : Your colleague has written an abstract and has asked you to review it for them. How would you recommend improving this abstract?

Abstract activity

A devastating earthquake and tsunami hit Japan on March 11, 2011. In the present study, the effects of this earthquake on laboratory mice behavior were investigated. “Earthquake-experienced” mice displayed a marked increase in food consumption without gaining body weight. The food was purchased from a company based in New Zealand. The mice also displayed enhanced anxiety. Maze performance of earthquake-experienced mice showed quicker acquisition of the task compared with that of earthquake-naive mice. Stress hormone levels, which were measured three times, were elevated compared with the naive mice. This indicated that the earthquake and aftershocks were stressful for the mice.

How is this related to mice?

Abstract activity


Unnecessary information


Abstract activity


Unnecessary information

How was this measured?

No conclusions


Cover letters

Section 8

Coverage and Staffing Plan Cover letters

Cover letter: First impression for journal editors

Significance Relevance

Writing style Interesting to their readers?

Why your work is important!


Read the aims and scope

Plant Molecular Biology is an international journal dedicated to rapid publication of original research articles in all areas of plant biology. The Editorial Board welcomes full-length manuscripts that address important biological problems of broad interest, including research in comparative genomics, functional genomics, proteomics, bioinformatics, computational biology, biochemical and regulatory networks, and biotechnology. Because space in the journal is limited, however, preference is given to publication of results that provide significant new insights into biological problems and that advance the understanding of structure, function, mechanisms, or regulation.

Plant Molecular Biology

Broad interest

Biological problems


Building your cover letter

Dr Wilhelm Gruissem Editor-in-Chief Plant Molecular Biology 2 September 2013 Dear Dr Gruissem, Please find enclosed our manuscript entitled “Identification of the histone acetyltransferase HAF2 as a factor involved in natural variation for seed dormancy in Arabidopsis thaliana”, which we would like to submit for publication as a Research Article in Plant Molecular Biology.

Journal editor’s name

Manuscript title

Article type

• Have you read the aims and scope? • Have you read the author guidelines?



Seed dormancy is an important life-history strategy that allows plants to select favorable conditions for germination, thereby affecting long-term survival. Dormancy can be released by specific environmental factors, such as cold or dry-storage (after-ripening). However, the genetic factors that regulate this process have not been clearly elucidated. The model plant Arabidopsis has substantial natural variation in seed dormancy, and identifying genes associated with this trait is of broad interest to geneticists, ecologists, and agricultural researchers.

Introduction Problem Relevance

Second paragraph:

Current state of the field Problem researchers are facing


We combined genome-wide association (GWA) mapping with transcriptome analyses to screen candidate single nucleotide polymorphisms correlated with variation in seed dormancy in 108 accessions of Arabidopsis. The most likely candidate was a plant-specific histone acetyltransferase gene, HAF2. HAF2 expression was down-regulated by cold and after-ripening, which break seed dormancy, and was up-regulated in accessions with high levels of dormancy. When the HAF2 gene from a non-dormant accession was inserted into a dormant accession…


Methods Key results

Third paragraph:

Briefly describe your methodology Summarize your key findings



These findings are significant in elucidating the genetic mechanisms underlying a fundamental life-history trait of plants and will be of interest to Plant Molecular Biology readers, especially those focused on Arabidopsis seed dormancy. Furthermore, our integrated approach combining GWA mapping and transcriptomics offers a promising strategy to identify candidate loci in future studies.

Relevance Implications

Fourth paragraph:

Why interesting to the journal’s readership



We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript, including authorship and order of authorship, and agree with submission to Plant Molecular Biology. This study was funded by the Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to declare.

Ethics Conflicts of interest

Last paragraph:

Disclaimers related to publication ethics Funding Conflicts of interest

Funding



We would like to recommend the following reviewers to evaluate our manuscript: 1. Reviewer 1 and contact information 2. Reviewer 2 and contact information 3. Reviewer 3 and contact information 4. Reviewer 4 and contact information Please address all correspondence to:

Reviewers Contact information

Other important information:

Recommended reviewers Author’s contact information


Dr Wilhelm Gruissem Editor-in-Chief Plant Molecular Biology 2 September 2013 Dear Dr Gruissem, Please find enclosed our manuscript entitled “Identification of the histone acetyltransferase HAF2 as a factor involved in natural variation for seed dormancy in Arabidopsis thaliana”, which we would like to submit for publication as a Research Article in Plant Molecular Biology. Seed dormancy is an important life-history strategy that allows plants to select favorable conditions for germination, thereby affecting long-term survival. Dormancy can be released by specific environmental factors, such as cold or dry-storage (after-ripening). The model plant Arabidopsis has substantial natural variation in seed dormancy, and identifying genes associated with this trait is of interest to geneticists, ecologists, and agricultural researchers. We combined genome-wide association (GWA) mapping with transcriptome analyses to screen candidate single nucleotide polymorphisms correlated with variation in seed dormancy in 108 accessions of Arabidopsis. The most likely candidate was a plant-specific histone acetyltransferase gene, HAF2. HAF2 expression was down-regulated by cold and after-ripening, which break seed dormancy, and was up-regulated in accessions with high levels of dormancy. When the HAF2 gene from a non-dormant accession was inserted into a dormant accession, seed dormancy was increased and HAF2 expression levels reduced. Finally, we sequenced HAF2 from 78 accessions and found that mutations were enriched in the promoter region. These findings are significant in elucidating the genetic mechanisms underlying a fundamental life-history trait of plants and will be of interest to Plant Molecular Biology readers, especially those focused on Arabidopsis seed dormancy. Furthermore, our integrated approach combining GWA mapping and transcriptomics offers a promising strategy to identify candidate loci in future studies. We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript, including authorship and order of authorship, and agree with submission to Plant Molecular Biology. This study was funded by the Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to declare. We would like to recommend the following reviewers to evaluate our manuscript: Reviewer 1 and contact information Reviewer 2 and contact information Reviewer 3 and contact information Reviewer 4 and contact information Please address all correspondence to: We look forward to hearing from you at your earliest convenience. Yours sincerely,

A good cover letter


Dr Wilhelm Gruissem Editor-in-Chief Plant Molecular Biology 2 September 2013 Dear Dr Gruissem, Please find enclosed our manuscript entitled “Identification of the histone acetyltransferase HAF2 as a factor involved in natural variation for seed dormancy in Arabidopsis thaliana”, which we would like to submit for publication as a Research Article in Plant Molecular Biology. Seed dormancy is an important life-history strategy that allows plants to select favorable conditions for germination, thereby affecting long-term survival. Dormancy can be released by specific environmental factors, such as cold or dry-storage (after-ripening). The model plant Arabidopsis has substantial natural variation in seed dormancy, and identifying genes associated with this trait is of interest to geneticists, ecologists, and agricultural researchers. We combined genome-wide association (GWA) mapping with transcriptome analyses to screen candidate single nucleotide polymorphisms correlated with variation in seed dormancy in 108 accessions of Arabidopsis. The most likely candidate was a plant-specific histone acetyltransferase gene, HAF2. HAF2 expression was down-regulated by cold and after-ripening, which break seed dormancy, and was up-regulated in accessions with high levels of dormancy. When the HAF2 gene from a non-dormant accession was inserted into a dormant accession, seed dormancy was increased and HAF2 expression levels reduced. Finally, we sequenced HAF2 from 78 accessions and found that mutations were enriched in the promoter region. These findings are significant in elucidating the genetic mechanisms underlying a fundamental life-history trait of plants and will be of interest to Plant Molecular Biology readers, especially those focused on Arabidopsis seed dormancy. Furthermore, our integrated approach combining GWA mapping and transcriptomics offers a promising strategy to identify candidate loci in future studies. We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript, including authorship and order of authorship, and agree with submission to Plant Molecular Biology. This study was funded by the Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to declare. We would like to recommend the following reviewers to evaluate our manuscript: Reviewer 1 and contact information Reviewer 2 and contact information Reviewer 3 and contact information Reviewer 4 and contact information Please address all correspondence to: We look forward to hearing from you at your earliest convenience. Yours sincerely,

A good cover letter

Manuscript information

Background

Key findings

Relevance

Disclaimers

Recommended reviewers


Specific cover letter styles

http://www.nature.com/nature/authors/submissions/subs/#a6

Coverage and Staffing Plan Cover letters Recommending

reviewers

“Authors will be asked to submit, with their manuscript…ii) the names and contact details (including e-mail address) of three potential qualified reviewers...

“The system requires authors to supply the names, e-mail addresses, and affiliations of at least four recommended reviewers.

Coverage and Staffing Plan Cover letters PNAS

http://www.pnas.org/site/authors/editorialpolicies.xhtml


Why recommend reviewers?

Reviewers recommended by authors are usually more favorable

1. Scharschimidt et al. J Clin Invest. 1994; 93: 1877–1880.

2. Earnshaw & Farndon. Ann R Coll Surg Engl. 2000; 82: 133–135.

3. Grimm. Science 2005; 309: 1974.

4. Wager et al. BMC Med. 2006; 4: 13.

5. Schroter et al. JAMA 2006; 295: 314–317.

6. Rivara et al. J Pediatr. 2007; 151: 202–205.

7. Bornmann & Daniel. Res Eval. 2009; 18: 262–272.

8. Bornmann & Daniel. PLoS One 2010; 5: e13345.

Coverage and Staffing Plan Cover letters Recommending

reviewers

Where to find them?

From your reading/references, networking at conferences

How senior? Aim for mid-level researchers

Who to avoid? Collaborators (past 5 years),

researchers from Kyushu University

International list: 1 or 2 from Asia, 1 or 2 from Europe, and 1 or 2 from North America

Choose reviewers who have published in your target journal

Peer review & revisions

Section 5

Customer Service Peer review What reviewers are looking for

The science

The manuscript

Relevant hypothesis Good experimental design Appropriate methodology Good data analysis Valid conclusions

Logical flow of information Manuscript structure and formatting Appropriate references High readability

Customer Service Peer review

Group similar comments together

Organize the reviewers’ comments

Reviewer 1: “Re-analyze the data in Figure 3 using a Mann–Whitney U test.”

Reviewer 3: “Repeat the experiments in Figure 3 with additional controls.”

Note: the comments of one reviewer may affect the comments of another

• Mann–Whitney U test: 2 groups • Kruskal–Wallis test: >2 groups

Experimental References Writing


Respond to every reviewer comment

Easy to see changes

Refer to line and page numbers

Use a different color font

Highlight the text

Writing response letters

Read by the journal editor, not the reviewers


Fernando L. Cônsoli Editor-in-Chief Neotropical Entomology 2 September 2013 Dear Dr Cônsoli, Re: Resubmission of manuscript reference No. WJS-07-5739 Please find attached a revised version of our manuscript originally entitled “Population dynamics of Drosophilids in response to humidity and temperature,” which we would like to resubmit for consideration for publication in Neotropical Entomology. The reviewer’s comments were highly insightful and enabled us to greatly improve the quality of our manuscript. In the following pages are our point-by-point responses to each of the comments. Revisions in the manuscript are shown as highlighted text. In accordance with the first comment, the title has been revised and the entire manuscript has undergone substantial English editing. We hope that the revisions in the manuscript and our accompanying responses will be sufficient to make our manuscript suitable for publication in Neotropical Entomology.

Address editor personally

Manuscript ID number

Thank reviewers

Highlight major changes

Writing response letters


Reviewer Comment: In your analysis of the data you have chosen to use a somewhat obscure fitting function (regression). In my opinion, a simple Gaussian function would have sufficed. Moreover, the results would be more instructive and easier to compare to previous results.

Response: We agree with the Reviewer’s assessment of the analysis. Our tailored function, in its current form, makes it difficult to tell that this measurement constitutes a significant improvement over previously reported values. We describe our new analysis using a Gaussian fitting function in our revised Results section (Page 6, Lines 12–18).

Agreeing with reviewers

Agreement

Revisions

Location

Why agree


Reviewer Comment: In your analysis of the data you have chosen to use a somewhat obscure fitting function (regression). In my opinion, a simple Gaussian function would have sufficed. Moreover, the results would be more instructive and easier to compare to previous results.

Response: Although a simple Gaussian fit would facilitate comparison with the results of other studies, our tailored function allows for the analysis of the data in terms of the Smith model [Smith et al., 1998]. We have now explained the use of this function and the Smith model in our revised Discussion section (Page 12, Lines 2–6).

Disagreeing with reviewers

Revisions

Location

Evidence


Reviewer comment: The authors looked for polymorphisms in the promoter region of the gene; however, they didn't evaluate the untranslated regions. That is one of my concerns about this methodology.

“Hidden” questions

Rephrased question: Why didn’t the authors evaluate polymorphisms in the untranslated regions of the gene?


Reviewer comment: The authors looked for polymorphisms in the promoter region of the gene; however, they didn't evaluate the untranslated regions. That is one of my concerns about this methodology.

“Hidden” questions

Response: In this study, we decided to focus on the promoter region of this gene because previous studies [Yajima et al., 2010; Jackson et al., 2011] have shown that its transcription was particularly affected. This has now been clarified in the Discussion section of our manuscript (Page 16, Line 24–28).

Evidence

Location

Revisions


Reviewer comment: Currently, the authors’ conclusion that this model is appropriate for the predicting deforestation rates worldwide is not valid because they only addressed deforestation in Asia. The authors need to include deforestation data from Africa and South America as well.

“Unfair” comments

Reasons why reviewers might make these comments

Current results are not appropriate for the scope or impact factor of the journal

Reviewer is being “unfair”


What you should do

First, contact the journal editor if you feel reviewer is being unfair

Do the experiments, revise, and resubmit

Withdraw submission and resubmit current manuscript to a journal with a different scope or lower impact factor

“Unfair” comments


handouts

Cover letters and peer review

Peer Review Exercises

The Journal Editor has returned your manuscript along with questions from the reviewers. Write an appropriate response for each one, and then share with your group. One member of each group will then read their best response for one of the comments.


Reviewer #1: Although the author provided controls for the first two sets of experiments, it appears that control subjects were not included in the third set. Repeat the experiments with the proper controls and update your manuscript accordingly.

We would like to thank Reviewer #1 for their comment. We agree that it is important to include the controls. Therefore, we have repeated the third set of experiments with the proper controls. We have now updated Figure 3 and revised the Results section (page XX, lines YY–ZZ) of our revised manuscript.

Agreement

What was done

Revisions

Location

We would like to thank Reviewer #2 for identifying this oversight. We have now discussed the work from Robertson and colleagues (Robertson et al. Biophys Comm; 2005, 13: 18–29 and Robertson et al. Anal Biochem; 2008, 24: 243–252) in our revised Introduction (page XX, lines YY–ZZ).


Reviewer #2: In the Introduction, the authors failed to discuss the studies published by Robertson and colleagues regarding non-parametric analyses. These should be added to the revised manuscript.

Revisions

Location


Reviewer #3: The authors have proposed a very interesting model to explain consumer behavior in foreign countries. I wonder how this might impact the tourism industry.

Revisions

Location

We would like to thank Reviewer #3 for their comment regarding our model. We also agree it would be of interest to the tourism industry. We have added a discussion about the impact our model might have for tourism-based marketing in our revised Conclusion (page XX, lines YY–ZZ).

Agreement

Next steps

Section 6

Next steps If rejected, what should you do?

Option 1: New submission to the same journal

Fully revise manuscript Prepare point-by-point responses Include the original manuscript ID number

Option 2: New submission to a different journal

Revise manuscript Reformat according to the author guidelines

Next steps Promote your work

Promote your work on social networks

NEJM BMJ Nature

Facebook ○ ○ ○

LinkedIn ○ ○ ○

Twitter ○ ○ ○

YouTube ○ ○ ○

Blogs ○ ○ ○

Podcasts ○ ○ ○



Cell (IF, 32) posting on Facebook

Next steps


Promote your work

Sharing published papers on LinkedIn

Next steps


Promote your work

Allen et al. PLoS ONE 2013; 8: e68914.

• 16 PLOS ONE articles were promoted on social networks on one randomly chosen date

• 16 PLOS ONE articles were not

Views* Downloads*

Promoted 18±18 4±4

Not promoted 6±3 1±1

*per day

Next steps

Respond to post-publication comments

Promote your work


Present your work at conferences

Allows you to discuss your work personally with your peers

Get feedback about your work and future directions

Networking and collaborations

Be an effective communicator

Write effectively

Increase the readability of your manuscript

How to choose the most appropriate journal

How to logically present your research

How to write effective cover letters

Successfully navigate peer review

How to actively promote your work

Your goal is not only to be published, but also to be widely read/cited

Thank you!

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Jeffrey Robens: [email protected]

20140826 Edanz Kyushu Session 2

Education

Transcript of 20140826 Edanz Kyushu Session 2