Download 547-5(2015)

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.
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.
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…
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…
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…
To man a project…
Man-machine interface…



Manpower…

The average person…
To staff a project…
User-system interface…, Usermachine
Work force…, Personnel…,
Workers…
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.
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 divergent evolution 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
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?
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 of vesicle docking and fusion.
Deitcher, DL. (1998) J. Neurosci. 18, 2028.
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
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
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.
Readers can compare items down a column easier than across a row. Place
independent variable in rows and dependent variables in columns.
Determination
Optimal growth
temperature (ºC)
Color of mycelium
Antibiotic
Produced
Yield of antibiotic
(mg/ml)
S. fluoricolor
-10
S. griseus
24
S. coelicolor
28
S. nocolor
92
Tan
flurocillinmycin
grey
streptomycin
red
rholmondelay
purple
neomycin
4,108
78
2
0
vs.
Organism
S. fluoricolor
S. griseus
S. coelicolor
S. nocolor
Optimal growth
temperature (ºC)
-10
24
28
92
Color of
mycelium
tan
grey
red
purple
Antibiotic
produced
flurocillinmycin
streptomycin
rholmondelay
neomycin
Yield of antibiotic
(mg/ml)
4,108
78
2
0
Raychaudhuri, S. et al.,(2006) J. Cell Biol 173, 107–119.
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
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-specific LTR methylation, and then we
tested the impact of readout transcription from 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 Oryza species (JIANG et al. 2002b). Dasheng elements are classified as
nonautonomous LTR retrotransposons because they do not encode any of the proteins necessary for
retrotransposition (JIANG et al. 2002b). The transposition intermediate for both autonomous and
nonautonomous LTR retrotransposons is a transcript that initiates from a promoter in 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 initiate
transcription into flanking host DNA. A promoter in the Dasheng LTR was predicted with a high degree of
certainty by employing a consensus Dasheng LTR as the input sequence for a promoter identification
program (supplemental Figure 5 at http://www.genetics.org/supplemental/). We hypothesized that
unmethylated LTRs adjacent to host genes might impact host gene expression. We searched for and found
evidence of Dasheng LTR-promoted transcripts among the rice ESTs and full-length cDNA collections (our
unpublished data). The EST and cDNA libraries from which the Dasheng transcripts were identified were
prepared from tissues of rice plants grown in normal conditions, suggesting that Dasheng LTRs do not need
stress conditions to be transcribed. Several studies show that LTRs of retroelements in both human and
plant genomes have retained their promoter activity (DOMANSKY et al. 2000; KASHKUSH et al. 2003;
DRUKER et al. 2004; MACK et al. 2004; OKAHARA et al. 2004; STEINHOFF and SCHULZ 2004; LAVIE et
al. 2005). Promoters of HERVs LTRs were shown to be activated in various human tissues during
development, and that this promoter activity is correlated with the LTR methylation (OKAHARA et al. 2004;
LAVIE et al. 2005).
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)