Research presentations. A short (7 slides maximum) presentation on the topic of the grant - the point is to educate the audience so that they are informed.

Research presentations. A short (7 slides maximum) presentation on the topic of the grant - the point is to educate the audience so that they are informed reviewers of your grant. Suggested format: introduction to the topic, why the field is interesting, what isn’t known, what I’d like to do.

Grant proposal.  Written in four steps: outline, pre-proposal, a preliminary and a final grant. There will be feedback at each step in the process - each participant will edit some of the other grants, and I will edit them all. Some of the scheduled classes will include discussion of the outlines, pre-proposals, and preliminary grants, and the last class will be organized as a grant panel, with students assigned as primary and secondary reviewers. Editing will be with track changes in Word. All students will be able to see all comments, since you can learn from comments on other grants.

Outline (1 page, single-spaced). hypothesis to test, brief description of background information, significance (why it is worth doing), long range goal of project, specific objectives.

Pre-proposal (2-3 pages, single-spaced). expand on outline, add methods sections and possible outcomes of experiments designed to test hypothesis.

Preliminary and final grants (minimum of 7, maximum of 10 single-spaced pages). Abstract, Specific aims, Background, Significance, Experimental design and methods. References are needed, but don’t count in the page limit).

Things on B-space (so far) SyllabusWriting tips (mostly taken from Mimi Zeiger’s book)Grant writing tips from Ira Herskowitz

Not posted, but also see Article from Trends in Cell Biol. About grant writing, by Liane Rief-LehrerTrends in Cell Biology Volume 10, Issue 11, 1 November 2000, Pages 500-504

The infectiousness of pompous prose  (Nature, 1992, vol.360:11-12)For centuries, scientists have been bombarded with pleas for plain language. Why have these pleas had no effect, when the problem of unreadable prose could be solved at a stroke? Martin W. Gregory, doi:10.1038/360011a0, References | PDF (290K)

See also http://www.amstat.org/publications/jcgs/sci.pdf

Writing: the clear choice Sheila McCormick CONTEXT: Sir It would be interesting to know the accessibility score for G. D. Gopen and J. A. Swan's paper ”The science of scientific writing“ (Am. Sci.78, 550–558; 1990), cited in your News Feature about clarity (Nature 423, 376–378; 2003). I... Nature 424, 128 - 128 (10 Jul 2003) Correspondence Full Text | PDF | Rights and permissions | Save this link2.Scientific literacy Clear as mud Jonathan Knight SUMMARY: It's not surprising that some academic papers seem to swim before our eyes ? the scientific literature has become steadily less accessible over the past half-century. Can we stop this tre CONTEXT: ...now runs workshops to help scientists to improve their papers. Swan's courses stem from a collaboration with George Gopen, a lecturer in English at Duke University in Durham, North Carolina, in which the pair developed principles of... Nature 423, 376 - 378 (22 May 2003) news feature Full Text | PDF | Rights and permissions | Save this link

You should be able to find lots of these at used book stores. I highly recommend 1, 3, 4, 6 and 12.

1. Essentials of Writing Biomedical Research Papers, Mimi Zeiger (the second edition, has less clinical and more mol. biol. examples) – most examples from came from this book

2. Writing a Successful Grant Application, Liane Reif-Lehrer 3. Style, Toward Clarity and Grace, Joseph M. Williams. 4. The Craft of Scientific Writing, Michael Alley5. Prose Style, A Handbook for Writers, Wilfred Stone and J.G. Bell6. Writing for your Peers, The Primary Journal Paper. Sylvester P.Carter7. How to Write and Publish a Scientific Paper, Robert A. Day8. Woe is I, the Grammarphobe’s guide to better English in plain English,

Patricia T. O’Conner9. The Well-Tempered Sentence, A punctuation handbook for the innocent,

the eager, and the doomed, Karen E. Gordon10. Elements of Style, W.I. Strunk and E.B. White11. Elements of Grammar, Margaret Shertzer12. Visual Display of Quantitative Information, Edward Tufte

Important ?s in Biology

?s that can be addressedexperimentallythe

grant

Problems: question is too narrow; or, question is too broad not hypothesis-driven (e.g., put a transgene already shown

to work elsewhere into a plant it has not been testedin)

grants in which, if step 1 doesn’t work, there is no hope for the rest of the grant (you need parallel approaches)

Grant writing tips title: descriptive, specific and appropriateabstract: Write it last. Format: The broad term objectives are... (not something like I want to cure diabetes: this is too broad an objective and therefore it is hard to quantify interim successes).

The specific aims are... (develop a method to measure blood sugar levels).

Specific aims: Write them in the form of a hypothesis to be tested.Good: test hypothesis that reaction X is rate-limiting for the mechanism of Y.Bad: Study effect of X on system Y.Be concise: what specific research is intended to accomplish, and the hypothesis to test in each aim (avoid narrative paragraphs)Background: 1)review work of others - don't be too selective or controversial (you don't want reviewers to think that you are biased or arrogant). Try to convince the reader that you haven't just looked up papers but that you really understand and are familiar with the techniques and results.2) evaluate the knowledge to date (display your thinking).3) say how your work will fill gaps in #2.4) explain importance by relating specific aims to long-term objectives.5) use references, but pick important ones.

Preliminary studies - are mandatory; or at least state why you will be able to do the work (establish your competence).

Experimental design and methods:Make sure they match specific aimsRepeat specific aim and then describe experiments

If you are using new methods say why they are better

Include controls and discuss them

Say how you will collect and interpret results

State limitations and difficulties with technique

List alternative approaches - describe potential outcomes and what you would do in that case

Don't speculate if the experimental result could lead to a dead end

Each section of the grant should have a closing paragraph with a conclusion, a summary, a recommendation, or a plan for future direction.

Be positive but don't overstate your case

Things that help get a grantyour publication record previous work in the area or with the techniques (or a letter

of support or collaboration from someone who is familiar with the area or techniques) Think about the reviewer as a person! don't irritate them with unclear writing and confusing organization

avoid ambiguity (indefinite antecedents)repeat key termsdon't abbreviate only some of the time (be consistent with

terminology)write in active voiceomit unnecessary words

style – use topic sentences (the reader should be able to read the first 1-2 sentences of each paragraph and get a general idea of the grant).

Think about what the reader needs to know, not about what you want to write.

Who should read your grant before you submit itsomeone in your labsomeone not in your lab ( probably a better judge of clarity)a good editor (scientist not necessary)

What reviewer should do:write ?? in the margins if something seems missing

point out what other information you would like to see on the next draft

point out jargon

point out where figures would be useful

mark out irrelevant information

Getting startedwhat will you do (hypothesis to test)is work original?are you aware of other's work? (background)why is it worth doing? (significance)what is the long-range goal?what are the specific objectives and do these connect with

the long-range goal?is methodology state-of-the-art?what are your qualifications? - why you and not someone else?how long will it take?what are the expected results?what are your contingency plans?

Write an outline:logical progression of ideasparallel constructionadequate detail (if you discuss 3 topics, give similar information in

the same sequence about each topic)

Example Outline. Sophia Chen’s project (Ph.D., 1997), I wrote itAsymmetric cell division and cell fate determination in plant microsporogenesis

Hypothesis(es) to test: 1) The vegetative and generative cells take on different cell fates because of an

intrinsic difference (cytoplasmic elements, gene expression) in the two cells that occurs because of the unequal partitioning of the cytoplasm

2) The two cells are initially equivalent in developmental potential, but take on different fates because of signaling induction.

Background information: During normal pollen development, the first microspore mitosis give rise to two

sister cells with distinct fates, a generative cell and a vegetative cell. The generative cell has reduced cytoplasmic volume relative to the vegetative cell, and is completely embeeed within the vegetative cell. The fate of the generative cell is to undergo another haploid mitosis, giving rise to the two sperm cells, while the vegetative cell generates a pollen tube which grows through the female tissue towards the ovary to deliver the two sperm cells to the central cell and the egg cell, for fertilization. In vitro, this asymmetric divisions can be disturbed, giving rise to cells that display alternative cell fates. There is evidence from EM that the vegetative cell nucleus has more nuclear pores on the face nearest the generative cell, suggesting that the cells may communicate.

Significance: A molecular understanding of the regulation of cell identity during pollen development could be used to manipulate gametogenesis and/or pollen embryogenesis in crop plants.

Long-range goals: Identify the gene products of genes altering nuclear or cell identity in microsporogenesis and identify cytoplasmic components that regulate cell identity (these two goals may merge, if we are lucky).

Specific objectives: 1) A screen of mutagenized Arabidopsis will be performed, seeking

phenotypes that appear to alter the asymmetrical cell division, as judged by nuclear morphology in mature pollen. Genetic and cell biological characterization of such mutants will focus on determining the time of action and mechanism of the defect (i.e. is DNA replication altered, is nuclear migration altered, are cytoskeletal components altered, etc.), and on mapping the gene(s).

2) Attempt to reproduce the published in vitro culture methods that can alter the developmental fates of uninucleate microspores. Attempt single cell manipulations with laser tweezers or laser ablation of in vitro cultured microspores.

Revelations occur in the Bible

People suggest, results indicate

Drama is for the theater

… These results revealed that …showe

d

… These results suggest that …

… A dramatic increase in …steep

… Exogenously applied hormone … Applied hormone is exogenous

indicate

From Anton Lang (via Harry Klee)

Word choiceWords should be preciseThe pollen tubes continued to grow for several hours

Words should be simpleAll heat stable materials utilized in the isolation and processing of solutions were sterilized prior to use.

Words should be necessaryCalcium content in response to drugs was examined and found to vary considerably.There is a new method that helps to purify proteins.The progress report was in need of additional data.

Words should be familiarWe vortexed the tubes.Protein was added to properly pH'd solution.

Don't use jargonScintillation fluid was added to the hot samples.

Express the core of the message in the verb, subject and completer

Make the topic the subjectThe patient showed no change in symptoms

Action inappropriately in the subjectEvaporation of ethanol from the mixture takes place rapidly.

An increase in heart rate occurred.

Action inappropriately in the objectWe made at least two analyses on each specimen.The new drug caused a decrease in pollen germination.

Action inappropriately in a prepositional phrase Calcium is translocated across the membrane along with the formation of a phosphorylated enzyme intermediate. Calcium is then released into the lumen with the simultaneous decomposition of the phosphorylated intermediate enzyme into the unphosphorylated enzyme and ADP plus phosphate.

When ….is formed. as…. is decomposed.

Do not pile nouns into noun clustersNoun clustersfilament length variability

Adjectives added to noun clusterslong-term greenhouse experiments

Noun being modified is missing from clusterTo assess for zero drift, we checked the control in each set of tubes.

Untangle noun clustersThe precipitate was further purified by sucrose density gradient centrifugation.

The antigen was prepared from whole rat liver homogenates.

Normal and mutant samples were studied by paper electrophoresis.

Talk about 1 thing at a timeThe elution order and extent of separation of these two isoenzymes are quite different from those achieved on DEAE-cellulose chromatography of chymotrytic-digested S1, where light chain 1 emerges first, followed by a well-resolved second peak of light chain 3.

Revision: The elution order of these two isoenzymes, light chain 3 followed by light chain 1, is the reverse of that achieved by DEAE. Similarly, the extent of separation is reversed, the peak of light chain 1 being much better resolved than the peak of light chain 3.

Watch out for indefinite antecedentsThe presence of disulfide bonds in oligopeptides may restrict the formation of ordered structures in sodium dodecyl sulfate solution. Once they are reduced, the predicted conformation can be fully induced.

Make sure you have an antecedentAfter repeated ultracentrifugation, the apolipoprotein A-I content of high density lipoproteins was reduced to about 65% of the original serum value, but no A-II was lost. This suggests that the binding environments of these two apolipoproteins in high-density lipoproteins differ.

Put parallel ideas in parallel form(infinitive and object and infinitive and object; noun and noun; prepositional phrase and prepositional phrase)This lack of response could have been due to damage of a cell surface receptor by the isolation procedure, but it could also be that isolated cells do not respond normally because the cells are isolated.Problems with comparisonsOveruse of compared toExperimental plants had a 28% decrease in water content as compared to normal plants.Comparisons of unlike things These results are similar to previous studiesAbsolute statements disguised as comparisonsThis medium contains 50 mM boric acid compared to Brewbaker's medium.

ParallelismPairsIce nucleation was less in the E. coli group than the Pseudomonas group.Confusion between pair and seriesThe Gaude modification contains 12.5 mg of cysteine HCl, 50 mg of methionine and has a final volume of 115 ml.HybridsThe fractions were centrifuged, resuspended in a small volume of buffer, and a sample of cells was counted in a cell counter.

Avoid writing flawsVerb and subjects should make sense together The appearance of nondialyzable 35-S in the medium was measured.

Verb-subject agreementThe pistil, anthers and petals of each plant was dissected.

Don't omit helping verbsThe tissue was homogenized and the samples incubated.

Avoid dangling modifiers (modifiers without a noun, or modifying the wrong noun)In changing from a standing to a recumbent position, the heart expands noticeably in all directions.

Make sure that sentences containing information in parentheses make senseAuxin (1 mM) had no effect, 10 mM slightly depressed the response, and 50 mM almost abolished the response.

Avoid turning verbs into nounsending with -tion; -ment;-ence;-al

Bad: The discovery of a method for the manufacture of artificial skin will have the result of an increase in the survival of patients with severe burns.Good: If researchers can discover how to manufacture artificial skin, more patients will survive severe burns.Avoid weak verbsOccurred; showed; caused; produced; was achieved; was observed; was noted.

Active vs passive voiceActive: We conducted this study at UC-BerkeleyPassive: This study was conducted at UC-BerkeleyActive: Dumas first observed this phenomenon in 1987Passive: This phenomenon was first observed in 1987

When Passive voice is usefulIf doer of activity is indefinite or unimportant

The topics covered by this guide include....If result of activity is more important than the doer.

These statistics were drawn from 12 clinical studies.Otherwise, try to use active voice.It has been determined that.... (raises question of who determined it?)

Weak predication (core assertion of the sentence)

Impersonal constructionsWeak: It is worthwhile to reexamine Dickinson's results.Stronger: Dickinson's results are worth re-examining.

Demoting to subordinate clauseWeak: I think that Smith is underrated as a force in scientific thought.Stronger: Smith is underrated as a force in scientific thought. The scientific community still underrates Smith's contributions.

Overuse of "to be"Weak: I am in receipt of the new information, and it is very interesting.Stronger: The new information I received greatly interests me.

I have received extremely interesting new information.

Use of articles• A (an), for something non-specific

Before a non-specific singular noun; not before a proper noun; not before a non-countable noun, such as water.

• The, for something specificBefore a specific noun (usually singular);NOT before a proper noun, such as Berkeley;Before a proper noun that proceeds a common noun, such as the Oakland Airport;Before a noun that has been mentioned before, so the reader knows it is specific;Before the name of an organ, tissue, or cell; Not before the name of a molecule (DNA);Before “first” or “second”, not before “one” or “two”Before a noun followed by a preposition, like of

Which or ThatPollen development, which is fascinating, is the research topic of the McCormick lab.

“which is fascinating” is a non-restrictive clause – i.e. the sentence doesn’t need those words for the sentence to make sense.

A comma should be placed before the word which (exceptions: in which or for which)

Do you always need a that? It depends – yes, if the sentence is confusing without it.

The president said the pledge of allegiance should be recited every day

The president said that the pledge of allegiance should be recited every day

I know that I can do it or I can do it – either is ok

former and latter -

don’t use them, the reader has to go back and re-read the sentence to make sure they have it right. It is much better to repeat the nouns.

Please take care of my cat and my son. The former can stay out all night, the latter should stay in the house.

Paragraph structure (taken from Mimi Zeiger’s book) OrganizationUse topic sentences, put topic sentences first if possibleOrganize other sentences in logical way that supports point made in topic sentenceIn science papers – talk about specifics - most to least important or vice versa; in order announced in topic sentence, pro-con; comparison and contrast; parallel structure; funnel, and chronological order.

ContinuityDo not skip stepsRepeat key terms – repeat them exactly, or use a category term plus “this” or “these”

repeat early in the sentence. Use different terms for different meanings.Keep a consistent order – don’t change order, or add or leave out items Keep a consistent point of view for similar ideasUse parallel form for parallel ideasSignal the subtopic (i.e. the organization of the paragraph) at the beginning

sentenceUse transition words or phrases to indicate the logical link between ideas

Telling the storyState the messageDisplay your thinkingUse transition words to make it clear which sentences move the story forward and which don’tUse “I” or “we” when displaying judgmentOmit unnecessary detail

Introductions (paraphrased from Mimi Zeiger’s book)

Funnel from what is known to the question. Tell a story.Start with what is known.Move to the unknown or to a problem with the known. End with the question. Make sure that the question follows from the preceding sentences.

If there are 2 questions, introduce them both.State experimental approach. State the answer to the question. Make clear what sentences move the story forward. Make clear the function of any sentences that do not move the story forward.

Cite references that reflect the key work that led to your question.Keep references to a minimum.

Be sure the importance of the work is evident and state it if necessary.

Keep the introduction short, aim to awaken interest.

Tips on Titles I

State topic of paperEffect of X on Y in Z, or Y in Z

State the point in the titleUse an adjective or noun based on the verb in the question and in the answer.

If the question was to determine whether pollen tube growth rate is increased when the moon is full, and the answer is yes, then you can say "Increased pollen tube growth rate during full moons".

Distinguish between adjectives that modify quantitative words and those that modify qualitative words. (The word increased should modify something measurable, such as a rate; improved should be used to modify words signifying concepts that can get better or worse, such as function or performance).

Or use a complete sentence to state the point.The Centromere is Alphoid DNA (sentences are stronger and therefore more controversial).

Titles II:

Titles should be:Accurate - use the same terms in the title that you used in the question and the answer.Complete, but not too long - if there are 2 or more points, it is better to pick the most important, or to use category terms to group the different variables that were measured.Specific - avoid and (as in X and Y in Z - there is no relationship between X and Y)

- avoid with

Unambiguous - avoid noun clusters, misplaced adjectives, abbreviations (exception - you can use a noun cluster for the species, a la tobacco flowers, instead of flowers of tobacco). Omit unnecessary words (The, nature of, studies of, etc. at the beginning of the title); try to compact words by using category words (expression of gene X in pistils, petals, anthers and sepals - replace with expression of gene X in flowers). But don't omit the and an in the rest of the title.Put the important word first (an easy way is to use the form General topic: specific topic)

R. L. Thilmony, Z. Chen, R. A. Bressan, and G. B. Martin Expression of the Tomato Pto Gene in Tobacco Enhances Resistance to Pseudomonas syringae pv tabaci Expressing avrPto Plant Cell 1995 7: 1529-1536.   or

CMT. Rommens, J. M. Salmeron, GED. Oldroyd, and B. J. Staskawicz Intergeneric Transfer and Functional Expression of the Tomato Disease Resistance Gene Pto Plant Cell 1995 7: 1537-1544.  

Sheng, D’Ovidio and Mehdy. Negative and positive regulation of a novel proline-rich protein mRNA by fungal elicitor and wounding. Plant J. 1991. 1: 345-354

V. F. Irish and Y. T. Yamamoto

Conservation of Floral Homeotic Gene Function between Arabidopsis and Antirrhinum Plant Cell 1995 7: 1635-1644.  

V. Shulaev, J. Leon, and I. RaskinIs Salicylic Acid a Translocated Signal of Systemic Acquired Resistance in Tobacco? Plant Cell 1995 7: 1691-1701.  

Tips on Abstracts

The abstract should stand on its own. State the question (if there was more than one, maybe only state the most important one)State what was done - state approach or protocolState what was found- only results that answer the question. Give data, if at all, only for the most important results.State the Answer -don't say something vague, like "The causes of this response are discussed".If readers might wonder why you are asking the question, include 1-2 sentences of background at the beginning of the abstract (this background info. should match the beginning of the introduction, but should be shorter).If your paper is important because of an implication of the answer, then state the implication at the end of the abstract.

Use continuity to make the abstract flow. Signal the different parts of the abstract,We found...; We conclude that ....or Thus....; We suggest that......Write short sentences and avoid noun clusters.

Science, Vol 294, Issue 5550, 2372-2375 , 14 December 2001

A Prokaryotic Voltage-Gated Sodium Channel Dejian Ren,1* Betsy Navarro,12* Haoxing Xu,1* Lixia Yue,1* Qing Shi,1 David E. Clapham1 The pore-forming subunits of canonical voltage-gated sodium and calcium channels are encoded by four repeated domains of six-transmembrane (6TM) segments. We expressed and characterized a bacterial ion channel (NaChBac) from Bacillus halodurans that is encoded by one 6TM segment. The sequence, especially in the pore region, is similar to that of voltage-gated calcium channels. The expressed channel was activated by voltage and was blocked by calcium channel blockers. However, the channel was selective for sodium. The identification of NaChBac as a functionally expressed bacterial voltage-sensitive ion-selective channel provides insight into both voltage-dependent activation and divalent cation selectivity. 1

Spatial expression dynamics of Men-9 delineate the third floral whorl in male and female flowers of dioecious Silene latifoliaShona E. Robertson, Yi Li, Charles P. Scutt, Malcolm E. Willis and Philip M. Gilmartin* 

Sex determination in Silene latifolia is controlled by heteromorphic sex chromosomes. Female flowers have five fused carpels and ten arrested stamen primordia. The male-determining Y chromosome overrides female development to suppress carpel formation and promote stamen development. The isolation and characterization of two S. latifoliaMale enhanced cDNAs, Men-9a and Men-9b, which probably represent different alleles of a novel gene are reported here. The why is missing Men-9a and Men-9b share 91.8% coding sequence nucleotide identity, yet only 85.4% amino acid identity. Are these details important? The Men-9 cDNAs are related to the previously reported MROS3 cDNA from S. latifolia. However, MROS3 is not present in the S. latifolia population used in these studies and the expression dynamics of Men-9a and Men-9b contrast dramatically with those reported for MROS3. all of these explanations do not belong in the abstract Men-9 cDNAs are expressed primarily in anthers of young male flowers, with highest expression in 1 2 mm buds. Men-9 expression is also observed at a low level in female flowers. In situ hybridization analysis reveals two phases of Men-9 expression. The first phase is during a common stage of early stamen development in male and female flowers prior to stamen arrest in female flowers. The second phase of Men-9 expression is maximal in the epidermis and endothecium of Y chromosome- and Ustilago violacea-induced what the devil are these? stamens; expression in male and female flowers extends to the epidermis of the staminal nectaries with strict boundaries at the second and fourth whorls. Men-9 gene expression therefore delineates the boundaries of the third floral whorl in S. latifolia flowers. Ok, so the punchline is that they have a marker for the third floral whorl, but why do we need such a marker?

Tips for ResultsOnly report results that are pertinent to the question posed in the introduction.Include all results, even if some don't support your hypothesis. Results are different from data. Data are facts, results are general statements that interpret data. Most data should be in tables or figures. Present data after stating the result, not instead of stating the result.

Organize the entire section, and each paragraph from most to least important. The result should be the topic sentence. Say the result first, the supporting details second.

Make sure that every result has a method in the methods section.

Give clear ideas of differences by reporting percent change rather than exact data (don't make the reader have to re-calculate this information).

You should subordinate control results, methods, figure and table citations and data. Control results sometimes need to be described first, for instance if you need to establish the baseline. However it is better to try to put control results in the table or graph and not in the text, or at least incorporate them into the same sentence as the result, but in a different clause of the sentence.

Don't make the method the topic sentenceBad: We administered ethylene to the plants. This hormone decreased transpiration.

Better: Ethylene administered to the plant decreased transpiration, orEven better: When ethylene was administered to the plant, transpiration decreased.

Don't make what should be a figure legend a topic sentenceBad: A summary of the transient assays is shown in figure 2. The promoter fusions with the 35S enhancer show up to 300-fold higher GUS activity.

Better: The promoter fusions with the 35S enhancer show up to 300-fold higher activity (Figure 2). (or, for Plant Cell: "Figure 2 shows that the 35S enhancer....")

Data should not overwhelm results. If the data are in a table or figure, don't repeat them in the text, except maybe for 1 or 2 especially important values. If there are secondary data that are not in the table or figure, you can put them in parentheses in the results, after you have stated the result.

Use precise words. Ability vs.Actuality. We could not demonstrate binding sites for SRK in pollen extracts (means they might have been there, but the technique was not sensitive enough). There were no binding sites (means they don't exist).

Don't use qualitative words unless you later quantify them Pollen tube growth rate increased markedly after addition of calcium, from 10 mm per hour to 40 mm per hour.

Verb tense -Results are past tense, because they are discrete events that happened in the past.

Comparisons - use the word than rather than compared with

Tips for Figures and TablesSchematic drawings should be kept simple.Micrographs should be just enough larger than the interesting features so that a context is possible.

Use the appropriate graph for the type of data you have.Line graph: X and Y axes, show relationship between 2 variables, scale each axis accurately.

Scattergrams: 2-axis graph with data points and line drawn to show strong relationship

Bar graphs: one-axis graph, amounts or frequencies of a discontinuous variable or a relative scale variable. Axis must include zero. Bars should be same width, no tick marks on base line (the baseline is not an axis).

Histogram: 2-axis graph, shows frequency distribution by series of contiguous rectangles. Rectangles should be of equal widths.

Readability - make letters clear and shapes easy to distinguish.

Emphasis - use different line weights; curves should be the darkest, letters in axis labels less dark, tick marks, error bars, etc., the least dark. For graphs, open and closed circles are the easiest. It is a good idea to label each line that connects points with a phrase, especially if there are more than 2 lines.

Point - make sure each figure makes a clear point. A decrease should look like a decrease.

Figure legends (title, experimental details, definitions of symbols, abbreviations)For drawings, diagrams, photos, Titles should identify the type of figure (e.g.; Bright field micrograph....)

Titles that state the point (Inhibition of Y by X) are better than those that don't (The effect of X on Y). The title should be a short phrase, don't overload it with experimental details.Put experimental details in a separate sentence. It is not necessary to say "For details, see methods".

Make all the figures in the paper parallel in structure, if possible. Then you can use the same symbols and define them just in figure 1.

Cornelis Spelt, Francesca Quattrocchio, Joseph N. M. Mol, and Ronald Koes anthocyanin1 of Petunia Encodes a Basic Helix-Loop-Helix Protein That Directly Activates Transcription of Structural Anthocyanin Genes Plant Cell 12: 1619-1632.

Tables (title, column headings, body, footnotes)Title should be a short phrase, but should include the point and all the variables (therefore, use a category term to lump the variables).

Every column should have a heading

Left hand columns (usually independent variables, list them in a logical order, control should be first).

Right hand columns (dependent variables, arrange them to show trends or permit easy comparison). Numbers should align on the decimal point (even if there isn't one).

Simplify complicated tables by omitting columns of less important data, columns in which most or almost all of the data are the same value, etc.

Put footnotes in same order as in figure legend (experimental details in sentences, then abbreviation definitions, then statistical details).

Make all the tables parallel in structure, if possible.

Could be more user-friendly

Nature 414, p. 517 (2001).

Tips for DiscussionsThe beginning (first paragraph or 2) should state the answer to the question in the introduction and support it with results

The middle should discuss topics in order of most to least important to the answer (and you should give hints to the reader as to why you organized the discussion this way)

The end (last paragraph) should restate the answer, make a special point, or both.Make sure you signal the answer with a phrase such as "this study shows", otherwise the reader might mistake your answer for something that is already known. If it seems too abrupt, you can re-state the question and then answer it (but be sure the question in the introduction and the discussion are identical), or you can provide a brief context and then answer it.

Verb tense: use present tense for answers and for signals of the answer. Use strong verbs for conclusions and weaker verbs for implications.

include support for the answer, explain it and defend it.Explain any results that don't support the answer, indicate why the work is new, explain any discrepancies with results of others, explain unexpected findings, explain limits of the methods, and the validity of the assumptions

Tips for Discussions (slide 2) Don't begin with a summary of results. Usually the answer is not the same as the result, but is more likely to be a generalization based on the result. Cite the relevant result after the answer, but don't summarize all the results.

You can lead the reader through the story of the discussion either by providing an overview at the beginning (or at the beginning of several paragraphs on a topic), or step-by-step. With the overview the reader knows what to expect, but the step-by-step is more interesting to read because it makes the reader think they are there while the story is unfolding.

For step-by-step: use a key term topic sentence (repeating a key term from the previous paragraph) at the beginning of every paragraph.

For the overview: use a section topic sentence at the beginning of each section and a transition topic sentence at the beginning of each paragraph.

To keep the story going later in the discussion you should use transition phrases or clauses rather than transition words (phrases are stronger). Repeating several key terms is stronger than one or none.

Tips on discussions (slide 3) You should be able to read the first sentence or two of every paragraph in the discussion and get an idea of the whole story - if you can't (if the paragraphs seem independent), then you need to add transitions. But, if you have a paragraph that needs to be included but isn't really part of the story (for example, if you need to explain a discrepancy or unexpected finding), then you can either start a new paragraph without a transition phrase connecting it to the previous paragraph, or use a subtopic sentence and make the point in another relevant paragraph.

How to end: Saying that further studies are needed isn't the best.

You can summarize conclusions (this is an especially good idea if your discussion didn't answer all the questions in the first paragraph, but did it in successive paragraphs).

You can state applications, implications, or speculations in order to indicate the importance of the work.

Give credit to yourself and others. If other work confirms your point say so; if what you did ties up loose ends from other work, say so.

Subtitles or subheadings aren't substitutes for topic sentences.

Tips for Materials and MethodsMaterials: chemicals, buffers, etc; what was examined (plants)

Methods: what was done to answer the question (protocol); independent variables (manipulations done to cause a change); dependent variables (changes measured or observed); controls of independent variables

Why it was done (purpose -it may not be obvious how the method relates to the question of the paper)

How it was done (methods and apparatus of manipulation and of measurement and observation). If it is well known be brief, if it is less well known or modified, be explicit, and say why it was modified - be helpful to the reader.

How it was analyzed (methods of analyzing the data and how it is summarized in the results: sample size, 6 experiments, mean and standard deviation)Methods should also include preparation (things you had to do before you could do the experiment), and any assumptions (state them and why you consider them to be valid).Don't include results unless they are intermediate (that is, the results used in calculations done to obtain results that answer the question). In some fields (e.g. biochemistry) the outcome of one experiment determines what the next will be - in that case the protocol is described in the results, not in the methods.

More on Methods (slide 2) Signal the organization -

Visual signals -subtitles, new paragraphs, new sentences.Verbal signals -topic sentence (the effect of X on Y was examined)

transition phrases (to prepare the enzyme solution)words (verbs and key terms)

Verb tense Use past tense, except when describing how data are presented (then use present tense, because the information is still true) For example data are summarized as mean +/- SD.

Sample size: When you have different sample sizes (sub-groups within a group), make sure the numbers add up correctly. If you say you had 39 transgenic plants and then you say that 25 had one phenotype and 13 had a different phenotype, the reader will wonder about that other plant.

More on methods (slide 3)

Use precise words: measured, calculated, estimated. Use determined if you need to describe 2 or more procedures together

Avoid interchanging these terms: study: a long-term inquiry into a question - a paper is equivalent to a study. experiment: a test done to examine the validity of a hypothesis. series: two or more related experiments. group: number of plants treated similarly or with similar characteristics.

Point of view: of the experiment: Plants were assayed. of the experimenter: We assayed the plants.

From the view of the experimenter sounds more lively, but you don't want too many We did this, we did that, because it sounds obnoxious. Therefore, start some sentences with a reason or a purpose or a subordinate clause, a la "After fixing the tissue to the slides, we processed......"

You can mix the point of view, but don't change back and forth in one paragraph for no reason. If possible, use the Experimenter point of view for the parts that move the story forward.

Tips for ReferencesThey should be the most valid (refereed journals, not abstracts or non-refereed conference proceedings)generally available (not conference proceedings, not obscure journals) and as few as possible (use review articles if you can - otherwise, select the first, most important, most elegant and most recent papers). But be fair to other workers in the field.

You can cite by emphasizing the science: Pollen development is fascinating (23) or the scientist: McCormick (1993) has reviewed the reasons why pollen development is fascinating.

Author names are not good beginnings to a paragraph and don't keep the story going, so it is better to avoid using names unless you have a particular reason to do so.

Put references after the idea you are referring to, not in the middle of an idea or after general indications of published work.

Don't pile all the references at the end of the sentence - instead you should intersperse the relevant ones at the relevant points.

If you draw a conclusion based on the work of others, put the reference after their work, not after your conclusion.