Zhengzhou Tobacco Research Institute 20141028

Author Academy: Effectively Communicating your Research

Zhengzhou Tobacco Research Institute28 October 2014Dr. Jeffrey Robens

Download at: liwenbianji.cn/ZTRI_2014

About Jeffrey…

Author

Senior Research ConsultantEducation Group Leader

Peer reviewer

University of Pennsylvania

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Publication Output of ZTRI

SCOPUS

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Be an effective communicator

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

Write effectively

Choose the best journal to reach your target audience

Logically present your research in your manuscript

Convey the significance of your work to journal editors

Properly revise your manuscript after peer review

Effective writing

Section 1


Effective writing Improving readability

Use short sentencesLimit your sentences to 15–20 words

One idea per sentence

Use active voiceMore simple, direct, and easier to read

AMA Manual of Style: “In general, authors should use the active voice…”. (10th ed., pg. 320)

Effective writing Stress position

Readers focus at the end of the sentence to determine what is important.

1. You deserve a raise, but the budget is tight.

Which sentence suggests that you will get a raise?

2. The budget is tight, but you deserve a raise.

http://writingcenter.unc.edu/handouts/flow/

Effective writing

The budget is tight, but you deserve a raise. Your salary

will increase at the beginning of next year.Stress position Topic position

The topic position introduces the idea of the current sentence

The stress position also introduces the topic of the next sentence

Stress position

Effective writing Topic position

The patient went to the hospital to see a gastroenterologist. The doctor then performed a series of diagnostic tests. The results showed the patient suffered from a bacterial infection. Antibiotics were prescribed to treat the infection before the patient developed an ulcer.

idea ideaideaidea

Topic link

sentence

Ready to write manuscript!

Ready to write manuscript?

1. Write manuscript first, and then choose the journal

2. Choose the journal first, and then write the manuscript

Author guidelines• Manuscript structure• Word limits• Reference style

Aims and scope• Topics• Readership• Be sure to emphasize

Relevant references Writing style

Choose journal before you write!

Journal selection

Section 2


Journal selection Evaluating significance

How new are your findings?Low or high impact?Novelty

How broadly relevant are your findings?International or regional? Specialized or general?Relevance

What are the real-world applications?Appeal

Journal selection Factors to consider when choosing a journal

Which factor is most important to you?

Aims & scope Readership

Open access Impact factorIndexing

Titles and abstracts

Insert your proposed abstract

Journal Selector – www.liwenbianji.cn/journal_selector


Matching journals

Filter by:• Impact factor• Publishing frequency• Open access



Journal’s aims and scope, IF, and frequency Similar published articles

Have they published similar articles recently?Have you cited some of these articles?


springer.com/gp/authors-editors/journal-author

Journal selection Tips to identify the most suitable journal

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Identify the interests of the journal editor

• Editorials• Review articles• Special issues


S• Editorials• Review articles• Special issues



Manuscript

Journal editor’s interests

Journal A Journal B Journal C


S

Identify the interests of the journal editor

Identify the interests of the

readers


• Most viewed• Most cited


S • Most viewed• Most cited



Manuscript

Reader’s interests

Journal A Journal B Journal C

Manuscript structure

Section 3


Coverage and Staffing PlanManuscript

structure Prepare an outline

I. IntroductionA. General backgroundB. Related studiesC. Problems in the fieldD. Aims

II. MethodsA. Subjects/Samples/MaterialsB. General methodsC. Specific methodsD. Statistical analyses

III. ResultsA. Key points about Figure 1B. Key points about Table 1C. Key points about Figure 2D. Key points about Figure 3E. Key points about Figure 4

IV. DiscussionA. Major conclusionB. Key findings that support conclusionC. Relevance to published studiesD. LimitationsE. Unexpected resultsF. ImplicationsG. Future directions

Knowing what you need to discuss, write down the key ideas

Use short bullet points to list ideas

Don’t let “writing correct English sentences” get in the way of outlining your ideas

List important information from your reading in the appropriate section with citations


structure Introduction

General introduction

Specific aimsAims

Current state of the field

Problem in the field


structure

The purpose of this work was to evaluate the morphological responses of N. tabacum pollen tubes subjected to osmotic stress through the analysis of different cell wall components.

Aims

Although the above-mentioned model supports turgor pressure in promoting pollen tube growth (at least in the so-called fast phase), it is not yet clear how changes in the osmolarity of the growth medium might modify the cell wall or affect its composition.

Problem

• Identify an important problem• State aims that directly address this problem

Writing the Introduction

Biagini et al. Plant Reprod. 2014; 27: 129–144.


structure Methods

Study design

How it was done

General methodsSpecific techniques

Discuss controls

Quantification methodsStatistical tests

Consult a statistician

What/who was used

Samples or participantsMaterials

How it was analyzed


structure

1. Novel observation2. Characterization3. Application

Logical presentation

Example:1. New gene expressed in the heart2. Regulation of gene expression, when it is

expressed, function of the produced protein3. Role of the gene in heart development

Results


structure

1. Novel observation2. Characterization3. Application

Each subsection corresponds to

one figure

What you found, not what it means

Logical presentation

Subsections

Factual description

Results


structure Discussion

Summary of findings

Relevance of findings

Implications for the field

Similarities/differencesUnexpected resultsNegative resultsLimitations


structure

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.

Writing a strong conclusion paragraph

Why your study is important

Implications

Conclusions

Future directions

Field advancement

Key findings

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


structure Linking your ideas

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 fieldIntroduction

Methods

Results

Discussion


structureWriting 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

Who’s hungry?

First impressions are important!


Section 4



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

QuestionsDescribing methodsAbbreviations“New” or “novel”

Titles and 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


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 and 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.


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


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.


Why this study needed to be done

What you did

What you found

How advances the field

Writing your Abstract

Journal editors are busy!

Cover letters

Section 5


Cover letters

Abstract:First impression for readers

Cover letters are the first impression for the journal editor

SignificanceRelevance

Writing styleInteresting to their readers?

Is your work important?

Cover letters

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). 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.

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.

Why study needs to be

done

What was done and what

was found

Interest to journal’s readers

A good cover letter

We would also like to suggest the following reviewers for our manuscript…

Editor’s name Manuscript title

Article type

Recommend reviewers

“Must-have” statements

Cover letters

“Must-have” statements

Not submitted to other journals

Source of funding

Authors agree on paper/journal

Original and unpublished

Conflicts of interest Authorship contributions

Disclaimers about publication ethics

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 ZTRI

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

Have they published in your target journal?

Peer review

Section 6

Peer review What reviewers are looking for

The study

The manuscript

Relevant hypothesis Good study design Appropriate methodology Good data analyses Valid conclusions

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

Abstract and IntroductionMethodsResults and FiguresDiscussion

Peer review

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

Highlight the text

Peer review

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.

Agreeing with reviewers

Agreement

Peer review Agreeing with reviewers

Agreement

RevisionsLocation


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).

Peer review Disagreeing with reviewers


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).

Peer review


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).

Evidence

Revisions

Location

Disagreeing with reviewers

Peer review

Reviewer comment: Currently, the authors’ conclusion that this questionnaire is appropriate for cross-cultural analyses is not completely valid because their participants all resided in the UAE. They should also show the questionnaire’s validity in participants living in other countries.

“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”

Peer review

Reviewer comment: Currently, the authors’ conclusion that this model is appropriate for the predicting growth rates worldwide is not valid because they only measured tobacco growth in Asia. The authors need to include data obtained from other regions, such as the United States, as well.


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”

Peer review

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 of lower impact factor


Be an effective communicator

S

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

Good experimental design

Write effectively

Choose the best journal to reach your target audience

Logically present your research in your manuscript

Convey the significance of your work to journal editors

Properly revise your manuscript after peer review

The Springer Author Academy

S

Free online courses

• Publishing a journal article

• Preparing a book manuscript

• Being an effective peer reviewer

谢谢！

Any questions?

下载完整版 PDF讲义liwenbianji.cn/ZTRI_2014

Jeffrey Robens: [email protected]

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