11. Dangling Clauses (Robert A. Day, Bryan A. Garner, Joseph M. Williams, & Stan Fields).

1. 11. Dangling Clauses (Robert A. Day, Bryan A. Garner, Joseph M. Williams, & Stan Fields). Danglers are verbs ending in –ing or –ed that do not relate to the nouns or pronouns they are supposed to modify. When the noun or pronoun that is modified by the verb doesn’t appear where it logically should, the verb is said to “dangle.” Example: Walking down the street, the house was seen. Implies that the house was walking down the street. Danglers can often be remedied by simply recasting the sentences: Hoping to find some cause of the flaw, the results of the test were reviewed. Change to: Hoping to find some cause of the flaw, we reviewed the results of the tests.

2. Watching from the ground below, the birds flew ever higher until they disappeared. Change to: Watching from the ground below, we saw the birds fly higher until they disappeared. By watching closely, the birds became visible. Change to: By watching closely, we were able to see the birds.

3. A common manifestation is to begin the main clause with it or there: Applying these principles to the present situation, it is clear that the company must reimburse its employee. (implies that “it” is applying these principles) One possible revision: If we apply these principles to the present situation, it becomes clear that the company must reimburse its employee. A better revision: Given these principles, the company must reimburse its employee. Turning to England, it ought to be noted that that country, though late in doing so, participated fully in the medieval development…. Change to: Although England was late in doing so, it participated fully in the medieval development…. By instead examining the multigenerational ethnic group, it becomes clear that the Irish had fully adapted… Change to: By instead examining the mutigenerational ethnic group, we see that the Irish…

4. 12. Sexist Language (David Porush & Stan Fields). The biochemist must learn how the chromatograph works before he designs the methods section. One possible revision: The biochemist must learn how the chromatograph works before he/she designs the methods section. A better revision would be to change to plural: Biochemists must learn how the chromatograph works before they design the methods section. An anthropologist often finds that she is caught between cultures. Revise to first or second person: As anthropologists, we often find… As an anthropologist, you will often find…

5. If he understands chromatography, the biochemist will have an easier time setting up his experiment. Revise with an indefinite pronoun: A biochemist who understands chromatography… Some other suggested revisions: The average man…  The average person… To man a project…  To staff a project… Man-machine interface…  User-system interface…, User- machine Manpower…  Work force…, Personnel…, Workers…

6. 14. Manuscript Organization (Robert A. Day, J.R. Matthews & Stan Fields) A. TITLE Describes the paper in the fewest possible words; Avoids abbreviations and jargon. Article titles have evolved from statements declaring the nature of the study (e.g., “Molecular Structure of Nucleic Acids,”“Mutations of bacteria from virus sensitivity to virus resistance”) to statements actively declaring the results (e.g., “DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45” (recent issue of Cell), “Phosphorylation of the Translation Initiation Factor eIF2α Increases BACE1 Levels and Promotes Amyloidogenesis” (recent issue of Neuron)). Which style you prefer is a matter of personal preference B. ABSTRACT Provides a brief (often 250 words or less) summary of each of the main sections of the paper: Introduction, Materials and Methods, Results and Discussion. Does not include information that is not stated in other parts of the manuscript. Probably the most important part of a manuscript or grant application. -Many people will read only the abstract. -The abstract of a grant application will direct the grant to the appropriate reviewers; will create the first impression of the quality of the application.

7. A few (bad) examples from the literature: Portion of the first sentence from an abstract in a recent issue of PNAS: Two approaches, one novel, are applied to analyze the divergentevolution of … -One approach is new and interesting; the other is old and boring Portion of the last sentence from an abstract in a recent issue of Molecular Biology and Evolution: …our results have some implications regarding the means by which terpene synthases specify product outcome. “some implications” suggests that the implications were not important enough to mention in the abstract-not really a great way to end the abstract

8. Middle portion of an abstract in a recent issue of Cell: … Liver stages of the parasite containing thousands of merozoites grow inside hepatocytes for several days without triggering an inflammatory response. We show here that Plasmodium uses a PEXEL/VTS motif to introduce the circumsporozoite (CS) protein into the hepatocyte cytoplasm and a nuclear localization signal (NLS) to enter its nucleus. CS outcompetes NFκB nuclear import, thus downregulating the expression of many genes controlled by NFκB, including those involved in inflammation. CS also influences the expression of over one thousand host genes involved in diverse metabolic processes to create a favorable niche for the parasite growth… Liver stages of the parasite containing thousands of merozoites grow inside hepatocytes… -Do the liver stages contain thousands of merozoites or does the liver? -Can the liver stages grow inside anything besides hepatocytes? …Plasmodium uses a PEXEL/VTS motif…and a nuclear localization signal (NLS) to enter its nucleus -Does Plasmodium enter the nucleus or does the CS protein? CS outcompetes NFκB nuclear import… -Does CS outcompete NFκB nuclear import or does CS nuclear import outcompete NFκB nuclear import? …over one thousand host genes involved in diverse metabolic processes to create a favorable niche for the parasite growth -Are the one thousand genes creating a favorable niche, or are the diverse metabolic processes creating the niche?

9. C. INTRODUCTION • Supplies sufficient background information to allow the reader to understand and evaluate the results of the present study without needing to refer to previously published work. • Provides rationale for the present study: What is the purpose of this paper? • Some rules for a good introduction: • 1. Present the nature and scope of the problem investigated; why is the problem important? • 2. Briefly review the pertinent literature to orient the reader. • 3. State the method of the investigation; if necessary, the reasons for the choice of method. • 4. State the principal results. • 5. State the principal conclusions. • Examples: • Release of neurotransmitter from chemical synapses is the primary method of communication between neurons, and the regulation of this process is crucial for plastic changes within the nervous system. • DiAntonio, A. (1993) Cell 73, 1281. • VAMP or synaptobrevin, syntaxin, and SNAP-25 bind to each other in vitro in a complex that is thought to be at the heart ofvesicle docking and fusion. • Deitcher, DL. (1998) J. Neurosci. 18, 2028.

10. D. MATERIALS AND METHODS Describe the experimental design and provide enough detail so that the experiments can be repeated. The usual order of method presentation is chronological; however, related methods should be described together. If a method has been published, only the literature reference need be given, although it is useful to identify the method briefly (e.g., “cells were broken by ultrasonic treatment as previously described (9),” rather than, “cells were broken as previously described (9).”) Be precise: exact temperature, quantity, time, etc; animals, plants, and microorganisms usually identified by genus, species and strain designation When large numbers of strains, mutants or chemicals are used, prepare tables identifying sources and properties Do not include results in the Materials and Methods section

11. E. RESULTS Probably the easiest part of a manuscript to write (and often a good place to begin your writing) Begin (usually) by providing a big-picture description of the experiments Useful to provide a rationale for each new set of experiments Present results in the past tense If there are only one or a few determinations, present them descriptively in the text; for multiple determinations, use a figure, graph or table. Do not present identical data in the text and in the figures/graphs/tables. The paper stands or falls on the basis of the results

12. If data show pronounced trends or make an interesting picture, use a graph. If numbers show no exciting trend, or you need to present exact numbers, use a table Some additional guidelines: Tables and figures should both stand alone and be an indispensable part of the text. Readers should be able to understand figures without referring to the text; ideally figures should be understandable without reading the figure legend.

13. Readers can compare items down a column easier than across a row. Place independent variable in rows and dependent variables in columns. • Determination S. fluoricolor S. griseus S. coelicolor S. nocolor • Optimal growth -10 24 28 92 • temperature (ºC) • Color of mycelium Tan grey red purple • Antibiotic flurocillinmycin streptomycin rholmondelay neomycin • Produced • Yield of antibiotic 4,108 78 2 0 • (mg/ml) • vs. • Organism Optimal growth Color of Antibiotic Yield of antibiotic • temperature (ºC) mycelium produced (mg/ml) • S. fluoricolor -10 tan flurocillinmycin 4,108 • S. griseus 24 grey streptomycin 78 • S. coelicolor 28 red rholmondelay 2 • S. nocolor 92 purple neomycin 0

14. Raychaudhuri, S. et al.,(2006) J. Cell Biol 173, 107–119.

15. F. DISCUSSION Often the hardest part of a manuscript to write Should present principles, relationships and generalizations shown by the Results Discuss, but do not recapitulate the Results Point out exceptions or lack of correlation and define unsettled points. Don’t try to cover up or fudge data that don’t fit Show how results and interpretations agree or contrast with previous publications Discuss theoretical implications, or practical applications State conclusions as clearly as possible Summarize evidence for each conclusion Reference to current work or findings traditionally uses the past tense (e.g., “we showed”). Use of present tense (e.g., “We show”) has become popular in recent years

16. Large-Scale Survey of Cytosine Methylation of Retrotransposons and the Impact of Readout Transcription From Long Terminal Repeats on Expression of Adjacent Rice Genes Discussion In this study, we pinpointed methylated LTRs and detected tissue-specificLTR methylation, and then we tested the impact of readout transcriptionfrom unmethylated LTRs on the expression of adjacent genes.Dasheng was the focus of this study because of its young age,high copy number, and the high level of polymorphism among Oryzaspecies (JIANGet al. 2002b). Dasheng elements are classifiedas nonautonomous LTR retrotransposons because they do not encodeany of the proteins necessary for retrotransposition (JIANGet al. 2002b).The transposition intermediate for both autonomous and nonautonomousLTR retrotransposons is a transcript that initiates from a promoterin the 5' LTR and terminates in the 3' LTR. Note that if active,the promoter in the 3' LTR (or in a solo LTR) could initiatetranscription into flanking host DNA. A promoter in the DashengLTR was predicted with a high degree of certainty by employinga consensus Dasheng LTR as the input sequence for a promoteridentification program (supplemental Figure 5 at http://www.genetics.org/supplemental/).We hypothesized that unmethylated LTRs adjacent to host genesmight impact host gene expression. We searched for and foundevidence of Dasheng LTR-promoted transcripts among the riceESTs and full-length cDNA collections (our unpublished data).The EST and cDNA libraries from which the Dasheng transcriptswere identified were prepared from tissues of rice plants grownin normal conditions, suggesting that Dasheng LTRs do not needstress conditions to be transcribed. Several studies show thatLTRs of retroelements in both human and plant genomes have retainedtheir promoter activity (DOMANSKYet al. 2000; KASHKUSHet al. 2003;DRUKERet al. 2004; MACKet al. 2004; OKAHARAet al. 2004; STEINHOFF and SCHULZ 2004;LAVIEet al. 2005). Promoters of HERVs LTRs were shown to beactivated in various human tissues during development, and thatthis promoter activity is correlated with the LTR methylation(OKAHARAet al. 2004; LAVIEet al. 2005).

17. Key Principles: • Make your main characters the subjects of your sentences. • Try to place the subjects and verbs near the beginning of your sentence. •  Sentences are cohesive with one another when we see at the beginning of a second sentence information that appeared toward the end of the preceding sentence. • Passages are coherent when we see that the topics of each sentence in the passage constitute a relatively small set of related ideas. • Motivate your work (e.g., to test the hypothesis that XXX, we performed YYY)