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What’s in a paper?
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How to write:
Format
Abstract
Introduction
M&M
Results & Discussion
Conclusions
References
Figures/Tables
Final touches
What’s Publishable?
New ideas
New compounds (not likely)
New topics (less likely)
New data
Address current issues
Issues of regional interest
Small but provable topics
Small improvements
Field vs. Laboratory
Field data:
Monitoring, scattered data – less publishable
Field plot studies (expensive) – highly publishable
Lab studies:
Inexpensive
Publishable, if done right
Lab-field combinations
Complementary
Most publishable
Example: Analytical methods + field samples
What’s in a Paper?
How long?
12-15 text pages, double spaced
1-4 tables
5-2 figures
15-25 references
2-4 core references
To Make It Easy
Always read other people’s papers first!
Avoid “reinvent the wheel”
Avoid wasting time on developing old methods
Avoid becoming “narrow minded” - fair evaluation
of your own work
Really get the “handle” or “angle”
Aim low, aim small, aim specific
Really, really understand “why?”
To be used in Introduction
To Make It Easy
Always prepare a study protocol
Notebooks: date/time
Plan 1, plan 2, …, keep updating
Objectives
Detailed methods, exact conditions, references
Detailed statistics, design
Incorporate changes
Record problems, unexpected observations
Store all info in specific folders
To be used in M&M
To Make It Easy
Analyze data when still “hot”
Get data off instruments right away!
Plot after 3 time points!
Group curves by treatments
What do you want to compare?
Temperature? In one graph
Compounds? In one graph
Soil type? In one graph
Keep samples for 6 months after finish
Recap if punctured
Always use replicates (n ≥ 3) and statistics
r or r2
Try to use internal standards, or run samples at
approximately the same time
Format
Always:
Double space
Page number
Add line number
Left justified
Font: 12 pt, Times New Roman
1st page: Title, author info
2nd page: Abstract, (keywords)
3rd page: Introduction (< 2 page)
M&M: < 5 pages
Do not place figures in text!
Do not start a sentence with a numerical or abbreviation!
Habits, habits…
Abstract
Most important (go over 10+ times)!
Write after finishing most of manuscript
<200 words or <18 lines
Start with “why” (2-3 sentences)
Followed by “In this study, …” (what was done; 2-3
sentences)
Followed by results (2-3 sentences): include numbers!
Followed by conclusions
End with “significance”
Emphasize uniqueness, impact
Spelling check!
ABSTRACT
Halogenated fumigants are some of the most heavily used pesticides
worldwide. A number of studies have shown that fumigant transformation in
soil is correlated with soil organic matter content. However, relatively little is
known about the mechanisms of fumigant interaction with soil organic matter.
In this study, we used 14C-labelled 1,3-dichloropropene (1,3-D) and methyl
bromide (MeBr) to characterize their incorporation into soil organic matter and
the association of bound radioactivity with the different organic matter
components. The 14C activity of bound residues increased with time, and
reached 38-49% for 1,3-D and 37-42% for MeBr after 72 d of incubation at
25ºC. More bound residues were produced for 1,3-D than for MeBr in the same
soils. The distribution of 14C activity in soil humic substances followed the
order of fulvic acids >> humin > humic acids. These observations suggest that
incorporation into soil organic matter is the predominant pathway for
transformation of halogenated fumigants in soil, and fulvic acids are likely the
most significant sink of all soil organic matter fractions. It is further speculated
that bound residues formed as a result of alkylation of organic matter by the
fumigants through nucleophilic replacement.
ABSTRACT
Chiral pesticides currently constitute about 25% of all pesticides used, and this
ratio is increasing as more complex structures are introduced. Chirality occurs
widely in synthetic pyrethroids and organophosphates that are the mainstay of
modern insecticides. Despite the great public concerns associated with the use
of insecticides, the environmental significance of chirality in currently used
insecticides is poorly understood. In this study, we resolved enantiomers of a
number of synthetic pyrethroid and organophosphate insecticides on chiral
selective columns, and evaluated occurrence of enantioselectivity in aquatic
toxicity and biodegradation. Dramatic differences were observed between
enantiomers in their acute toxicity to freshwater invertebrates Ceriodaphnia
dubia and Daphnia magna, suggesting that the aquatic toxicity is mostly
attributable to only a specific enantiomer in the racemate. In field sediments, the
(–) enantiomer of cis-bifenthrin or cis-permethrin was preferentially degraded,
resulting in relative enrichment of the (+) enantiomer. Enantioselective
degradation was also observed during incubation of sediments under laboratory
conditions. Enantioselectivity in these processes is expected to result in
ecotoxicological effects that cannot be predicted from our existing knowledge,
and must be considered in future risk assessment and regulatory decisions.
Introduction
Most difficult to write
Write after M&M
Key point: justify “why”
Aim low, aim small, aim specific
Thorough understanding of published studies
Fair evaluation of existing information
Start with problems, sources, big picture issues, …(1st paragraph)
Followed by specific review
Do not undermine other researchers!
Only include useful/relevant studies
Always “praise” previous findings
Followed by a gap or an unclear topic
Followed by “In this study, we …”, or “The main objective of this study
was …”
End by the potential usefulness of the expected information: “The
results from this study may be used …”
About 4 paragraphs; < 2 pages!
INTRODUCTION
Halogenated hydrocarbons form the majority of soil fumigants. In particular, methyl
bromide (bromomethane, MeBr) has been heavily used for several decades due to its broad
spectrum of activity against nematodes, arthropods, weeds, fungi, and bacteria. However, the
potential contribution of MeBr to stratospheric ozone depletion will result in a complete MeBr
phase-out in 2005 in the U.S. and other industrialized countries (1). Most of the probable
chemical alternatives are also halogenated fumigants. These include 1,3-dichloropropene (1,3-
D) and chloropicrin, which are already in widespread use, and methyl iodide (iodomethane,
MeI) and propargyl bromide (bromopropyne, PBr), which are being considered as potential
alternatives (2-4). All of these compounds have very high vapor pressures, and have been
shown to quickly volatilize after soil incorporation (5-8). Atmospheric emission of fumigants is
an environmental or health hazard, because many fumigants are acutely toxic and potentially
carcinogenic (7). Evaluation of fumigant emissions and mechanisms has attracted great
research interest over the last decade. Transformation in soil has been identified as the most
important process in reducing fumigant emissions (9).
Fumigant transformation can be mediated by both chemical and microbial processes (10-
12). For halogenated fumigants, the rate of fumigant transformation has been shown to depend
closely on soil organic matter content (10, 13-16). For instance, transformation of MeBr, 1,3-
D, and MeI was more rapid in soils with higher organic matter content or after amendment of
organic materials such as compost, and the enhanced transformation occurred also in sterilized
soils (13-14, 17). All these observations suggest that soil organic matter is involved in the
abiotic transformation of fumigants in soil. In separate studies, Papiernik et al. (15-16) showed
that transformation of PBr or MeBr proceeded at similar rates in sterile and non-sterile soils,
and little propargyl alcohol or methanol was produced from the transformation. This
implies that abiotic processes predominated fumigant transformation, and hydrolysis
was not the main transformation pathway. In a recent study, using solid-state 13C
NMR, Tao and Maciel (18) observed bond interactions between MeBr and whole soil
samples or soil organic matter components. While the study offered direct evidence to
the hypothesis that MeBr alkylated organic matter in soil, the actual contribution by this
pathway to the overall abiotic transformation was not known.
The main objective of this study was to evaluate the role of organic matter in
fumigant transformation in soil by following the formation and distribution of non-
extractable or bound residues. Bound residues are defined as the fraction of pesticides
that is non-extractable after exhaustive extraction (19). Bound residues commonly
occur as a result of irreversible interactions between pesticides and soil organic matter.
The fumigants 1,3-D and MeBr were used as the test compounds in this study. The
same mechanisms should apply also to the other halogenated fumigants of similar
structures, including MeI, PBr, and chloropicrin.
Introduction
The significance of molecular chirality is widely recognized in life sciences (1, 2). A
lesser known fact is that many modern pesticides also contain chiral structures and thus consist
of enantiomers (3, 4). About 25% of currently used pesticides are chiral, and this ratio is
increasing as compounds with more complex structures are introduced into use (3).
Enantiomers of the same compound have identical physical-chemical properties, thus appearing
as a single compound in standard analysis. For economic reasons, chiral pesticides are mostly
used as mixtures of enantiomers, or racemates. However, enantiomers are known to selectively
interact with biological systems that are usually enantioselective, and may behave as drastically
different compounds. The role of enantioselectivity in environmental safety is poorly
understood for pesticides, and the knowledge gap is reflected in that the great majority of chiral
pesticides are used and regulated as if they were achiral, that is, as single compounds.
Studies on chiral pesticides started to appear in the early 1990s (4, 5-12). Studies so far
show that microbial degradation of chiral pesticides is commonly enantioselective. As one
enantiomer is preferentially degraded, the enantiomer ratio (ER), defined as the ratio of (+)-
enantiomer over (–)-enantiomer, increasingly deviates from the original value (typically 1.0)
(8, 9). Enantioselectivity was found to result in changes of ER of α-HCH along the polar bear
food chain, causing ER to increase from about 1.0 in cod to 2.3 in liver samples of polar bear
(10). In the brain tissue of seals around Iceland, often only (+)-α-HCH was found, while (–)-α-
HCH was absent, giving indefinitely large ER values (5, 13). Enantioselectivity has also been
observed under laboratory conditions for the soil degradation of some chiral herbicides and
fungicides, including metolachlor, metalaxyl, and dichlorprop (4, 8, 14).
Most environmental research on chiral pesticides has thus far been limited to a
few legacy chlorinated insecticides whose use was discontinued decades ago, and some
herbicides or fungicides. Little is known about currently used chiral insecticides. Many
current insecticides have high activity against non-target organisms and are also chiral.
In particular, two classes of insecticides, synthetic pyrethroids (SPs) and
organophosphates (OPs), are acutely toxic to a wide range of aquatic organisms at trace
levels (15, 16). Contamination of surface aquatic ecosystems by these compounds is a
great environmental concern (17, 18). All known SPs have chiral structures and contain
4 or 8 enantiomers (19), while many OPs are also chiral, consisting typically of 2
enantiomers (20). However, although these compounds are in wide use,
enantioselectivity in their environmental behavior is almost unknown (21).
In this study, we developed chiral-selective chromatographic methods to separate
and isolate enantiomers from a number of SPs and OPs. Individual enantiomers were
used for characterizing their differences in acute toxicity to two indicator aquatic
invertebrates, Ceriodaphnia dubia and Daphnia magna. Enantioselectivity was further
evaluated for SPs during their biodegradation in sediments under field and laboratory
conditions.
Materials & Methods
Easiest to write
Write first
Structure/arrangement
Sub-headings:
Add “experiments”…
Chemicals (1 paragraph; no structures; no properties)
Soils (source, properties, brief description of handling
and analysis)
Group treatments so they correspond to Results and
Discussion
Info on exact steps, word by word description
Avoid general statements
Details, details, details!
Write so that other people can repeat!
M&M
Flow chart:
Chemicals: names, full chemical names, purity, sources
company name without “Inc.” or “Co”, city, state
abbreviation
Soils/sediments: source, handling (size, air drying),
properties (OM, pH, texture), analysis
Scientific names for soils
Specific treatments/experiments
Chemical analysis
May be combined into experiments
Spell out terms (HPLC, GC,…) when first used; abbreviate
thereafter
Exact conditions: temperatures, flow rate (double check)
Retention times
Calibration methods
Recoveries, detection limits
MATERIALS AND METHODS
Soils. Two different types of soil were used in this study, a Chualar loam (fine-
loamy, mixed, thermic Argixerol) from Salinas, California, and a Waukegan silt loam (fine silty,
over sandy or sandy-skeletal, mixed, mesic Typic Hapludoll) from Rosemont, Minnesota. The
basic soil properties were analyzed before the study (Table 1). The soil organic carbon content
was determined using the Walkley-Black method (20), and particle sizes were determined using
the hydrometer method (21). These soils were passed through a 2-mm sieve without air-drying
and stored at 4ºC before use.
Chemicals. Methyl bromide (>99% purity) was obtained from the Great Lakes
Chemical Company (West Lafayette, IN). Carbon-14 labelled MeBr with a specific activity of
3.1 mCi mmole-1 and radiochemical purity of >97% was synthesized by the New England
Nuclear Co. (Boston, MA). The standard of 1,3-D (48% cis isomer and 49% trans isomer) was
purchased from Chem Service (West Chester, PA). Carbon-14 labelled 1,3-D with specific
activity of 1.11 mCi mmole-1 and radiochemical purity 98.6% was provided by Dow
AgroSciences, LLC (Indianapolis, IN).
Incubation Experiments. The moist soil samples were pre-incubated for a
week at room temperature to revive soil microbial activity. To prepare the spiking solutions, both
14C-labelled and unlabelled MeBr or 1,3-D were dissolved in ethyl …
Preparation of 14C-bound Residue Samples. The soil samples were thawed
at room temperature and transferred to 50-ml centrifuge tubes, followed by aeration in a fume
hood overnight to remove any untransformed parent compound or volatile …
Fractionation of 14C-bound Residues. Bound residues derived from the previous
incubation experiments were fractionated into fulvic acids (FA), humic acids …
Radioactivity Measurement. The radioactivity in HA and FA fractions was
measured directly on a Packard Tri-Carb 1600TR Liquid Scintillation Analyzer (Packard
Instrument Company, IL) after mixing with 5 ml Ultima Gold Cocktail (Packard, CT).
Combustion of solid samples was carried out on an OX-500 biological oxidizer (R.J. Harvey
Instrument Corp., Hillsdale, NJ). The total time of oxidation was 4 min, and the temperature was
900ºC. The 14CO2 evolved from combustion was trapped in 15 ml Carbon-14 Cocktail (Harvey,
Hillsdale, NJ), and the radioactivity was determined by LSC. The efficiency of 14CO2 recovery,
as determined by combusting 14C standards, was determined to be >97%. A 5-minute interval was
used for all samples for radioactivity counting by LSC.
Materials and Methods
Chemicals. Analytical standards of racemic (Z)-cis-bifenthrin [> 96%, 2-methylbiphenyl-3-
ylmethyl (Z)-(1RS)-cis-3-(2- chloro-3,3,3-trifluoroprop-1-enyl) -2,2-
dimethylcyclopropanecarboxylate)], fonofos [99.4%, O-ethyl S-phenyl (RS)-
ethylphosphonodithioate], and profenofos [> 93.7%, O-4-bromo-2-chlorophenyl …
Chromatographic Separation and Analysis. Enantiomers were resolved and isolated
on an Agilent 1100 Series high pressure liquid chromatography (HPLC) (Wilmington, DE) with
chiral columns. After testing with a suite of commercially available columns, resolution of SP
enantiomers was achieved on a Sumichiral OA-2500I column (Sumika Chemical Analysis
Service, Osaka, Japan), using 99.5% hexane and 0.5% 1,2-dichloroethane as the mobile phase.
Resolution of OP enantiomers was achieved on a Chiralcel OJ column (Daicel Chemical
Industries, Tokyo, Japan) using 98% hexane and 2% ethanol (containing 5% methanol and 5%
isopropanol) as the mobile phase. The injection volume was 20 μl and the UV wavelength for
detection was 230 ± 15 nm. The polarity (i.e., rotation sign) of the resolved enantiomers was
determined by an in-line laser polarimeter detector (PDR-Chiral, Lake Park, FL). The light
source for the chiral detector was a laser (675 nm) and the cell path was 50 mm. The resolved
enantiomers were individually collected at the HPLC outlet, evaporated to dryness, and used in
aquatic toxicity bioassays. Concentrations were determined using peak area, by assuming the
same response factor for enantiomers originating from the same compound. …
Aquatic Toxicity Assays. Enantioselectivity in aquatic toxicity was evaluated through 96-
h acute toxicity assays using Ceriodaphnia dubia and Daphnia magna. The overall procedure for
the test was similar to the EPA guidelines (22). Test animals were supplied by Aquatic
Biosystems (Fort Collins, CO). Briefly, test solutions (15 mL) containing a given …
Analysis of Field Sediments. Sediments containing residues of cis-bifenthrin and
cis-permethrin were collected at a site next to a nursery in southern California, and were used for
evaluation of changes in ER as a result of natural attenuation. The dried sediment was
accumulated from surface runoff over a four year period. Samples were taken using …
Incubation Experiments. Enantioselectivity in SP degradation was further evaluated
through incubation experiments. Sediment samples were collected from a sedimentation pond and
a runoff channel at a nursery site in southern California. The pond sediment contained 0.65%
organic carbon and 5% clay, while the channel sediment contained 6.4% organic carbon and 19%
clay. Compared to sediments used in the above experiment, sediments from the sedimentation
pond and channel were newly deposited. The sediments were sampled from the surface layer (0-5
cm) and used without air-drying to preserve the original microbial activity. Five grams (dry …
Results and Discussion
Relatively difficult to write
Think through what’s important
Combine Results and Discussion
Break into 2-3 sections with headings
Some results followed by some discussion
Followed by extrapolation
Avoid pure speculation!
Leave major conclusions to the end
Use references for argument (2-4 references)
Use topic sentences
RESULTS AND DISCUSSION
Mass balance. In this study, the recovery of 14C activity after organic matter fractionation
ranged from 86 ± 4.0% to 112.7 ± 7.9% for 1,3-D-derived bound residues, and from 82.5 ± 2.8% to
109.9 ± 7.2% for MeBr-derived bound residues. …
Total bound residues in soil. Figure 1 shows accumulatio
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