GROISMAN LAB PROCEDURES
PART ONE
In the Lab
I.
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
X.
XI.
XII.
XIII.
Working in the Lab
Laboratory Safety and Security
Storing Primers
Storing Strains
Notebooks
Computer Backups
Meetings and Presentations
Ordering
Shipping
Travel
Lab Departure
Lab Duties
The Basics
PART TWO
Out of the Lab
I.
II.
III.
IV.
V.
VI.
Posters
Figures and Graphics
Manuscript Guidelines
Abstract Outline
Guidelines for Reviewers
EAG: On Writing Manuscripts
I. Working in the Lab
A. Media preparation
Elaine prepares certain media and solutions. These include LB broth as well as LB agar plates with
various antibiotics, minimal M63 liquid and agar plates, and MacConkey agar plates. Other media
must be prepared by the individual performing the experiment.
We keep a stock of sterilized solidified LB agar media with a stir bar ready for melting in a microwave.
All media should be prepared in glass bottles and autoclaved except in those very few instances in
which the protocol calls for filter sterilization rather than autoclaving.
B. Using disposable plastic tubes versus washable glass tubes
Plastic tubes should be used only for biochemical/molecular biology experiments.
Experiments involving growth of bacteria should be carried out in glass test tubes. For example, you
should use glass test tubes when the bacteria are going to be used for:
 Phage transduction
 Preparation of phage lysates
 DNA transformation
 Preparation of plasmid DNA
 Inoculation of a large volume for gene expression/protein purification
 Conjugation
 Gene expression studies (measurement of b-galactosidase or fluorescence from GFP)
 Invasion and/or survival within eukaryotic cells
 Inoculation of mice
C. Use of restriction enzymes
Enzymes are located in the –20˚C freezers.
When you want to use a restriction enzyme or ligase, you should go to the –20˚C freezer with an ice
bucket, put the enzyme in the ice (or put it in one of the coolers), go to your bench, pipette the
required amount into the Eppendorf tube (you must change tips every time you go into the restriction
enzyme tube), put the enzyme back in the freezer in its original location.
You must not pipette enzymes at the freezer door.
Check the New England Biolabs (NEB) catalog for the appropriate buffer and incubation temperature
and other reaction conditions. You must have your own copy of the NEB catalog, which you can get
for free. This catalog has lots of useful information for cloning and other DNA manipulations.
D. Working with radioactivity
All staff is required to take a radiation safety examination prior to working with radioactive materials.
The current radiation safety officers for the lab are Kerry and Guy.
E. Including controls in the experiments
Every experiment must include the relevant controls, which most likely will vary from experiment to
experiment. Here I will include some general examples of controls.
 Controls for a DNA plasmid transformation/electroporation
o competent cells + NO plasmid DNA (use equivalent volume of TE)
o plasmid DNA + NO competent cells (use equivalent volume of LB broth)
o You must include as many competent cell controls as there are competent cells in the
experiment and as many plasmid DNA controls as plasmids you are using in the transformation.
 Controls for phage transductions
o phage lysate + NO bacterial cells (use equivalent volume of LB broth)
o bacterial cells + NO phage lysate (use equivalent volume of LB broth)
You must do as many phage lysate controls as there are phage lysates in the experiment, and as
many bacterial cell controls as there are bacterial cells in the experiment.
 Controls for conjugation
o donor cells + NO recipient cells (use equivalent volume of LB broth)
o recipient cells + NO donor cells (use equivalent volume of LB broth)
 Controls for a restriction enzyme digest during a cloning experiment
After inoculating with restriction enzyme, run an aliquot corresponding to 1/10 the total volume in an
agarose gel to make sure the DNA was digested. You should run next to it an equivalent amount of
uncut DNA and the appropriate size standard (1 kb ladder for DNA fragments ≥ 1 kb or the 100 bp
ladder for fragments ≤ 1 kb).
II. Laboratory Safety and Security
 If you are the last person to leave the lab in the evening or on the weekend, please make sure
that all Bunsen burners and lights are turned off, and the doors to the lab are locked.
 For the safety of people in our lab and the security of our equipment, supplies and personal
belongings, if you see someone unfamiliar in the lab, please don’t hesitate to question them on who
they are and why they are there. You can ask them politely, “Can I help you with something?” or
something else to that effect.
 Please do not give out passwords to our computers, online subscriptions or other secure
information to anyone outside of the lab.
III. Storing Primers
 Use 2 tubes for each primer: the original tube with the primer in it, and one empty tube.
 Resuspend primer from original tube in TE to 100 uM. Take 1/3 from the original tube and put
it in the empty tube. Leave remaining 2/3 in the original tube.
 The tubes should be stored in boxes in the refrigerator in lab (4 C) and in the hallway outside
the lab (-80 C). The original tubes should be stored in boxes marked “A” and duplicate tubes should
be stored in boxes marked “B”.
 Use the primer in the duplicate tube first. If you need more, take some from the original tube.
 Complete the Primer Form and give it to Jenny. She will return it to you with the database
numbers. The updated Primers database is on our website. FileMaker Pro is on one computer
in each lab.
IV. Storing Strains
It is critical that every strain constructed in the lab be stored in the freezer and entered in our
computer database. This is because we are obligated to provide researchers with our published
strains and also because it allows new lab members to start their projects readily (the same way you
had that opportunity when you joined the lab.)
A. Complete the Strains Excel Form (except Freezer location) and email it to Jenny. Please complete
every field in as much detail as possible. Use Helvetica, 9pt, black for all fields. The first row should
contain field names in the same order as the database:
Name, Species, Pedigree, Genotype, Plasmid, Phenotype, Selection, Construction, Origin, Date,
Reference, Other Notes, Notebook, Freezer Location.
B. Jenny will enter your strain information into the database and assign freezer locations. The
updated Strains database is on our website. FileMaker Pro is on one computer in each lab.
C. To prepare frozen stock cells, use the following protocol.
a. Streak single colony on LB with antibiotics (if needed).
b. Next day, add 1.5 ml 10% skim milk
c. Scrape colonies off plate with spatula or spreader
d. Place skim milk & colonies in screw cab tube
e. Place tube in crushed dry ice until frozen
f. Place tube in –70˚C freezer for storage
When the tube has been prepared, store it in the proper box in the –70˚C freezer according to the
location number Jenny has given you.
D. To prepare stab, pick colony from fresh plate, then stab into agar in vial. Incubate overnight at
37˚C with cap partially unscrewed. The next day, close cap tightly and store in appropriate box on
shelf.
E. All plates must have the date written on them.
F. Strain numbers must be written on the plates.
G. Plates must be checked after an overnight incubation. This is true even if you think you will need to
keep them there longer. Bacteria do NOT know the day of the week. Thus, if you streak colonies on
Friday, you must check them on Saturday.
H. You must make sure streaks for individual colonies do NOT touch. Otherwise, we will NOT have
purified colonies.
I. If you are comparing the phenotype of two isogenic strains that differ, say in a mutation, plasmid or
other, the colonies must be streaked onto the same plate (not two separate plates of the same kind).
J. After a P22 transduction, you must purify your colonies onto the same type of plate in which the
original selection was carried out. Then, you purify them one more time onto Green plates and onto
any other plates of interest and onto the same type of plate where they came from. The only results
that count are those obtained with colonies that are free of P22 phage. Therefore, you may want to
consider doing the second purification only onto Green plates.
K. If you have any questions, do not hesitate to ask Eduardo.
INDIVIDUALS WHO FAIL TO STORE STRAINS OR RECORD THE INFORMATION IN THE COMPUTER DATABASE
WILL NOT BE ALLOWED TO REMAIN IN THE LAB.
STRAINS DATABASE ERRORS:
You may find errors in strains database entries made prior to 09/10 (fonts/symbols displaying
incorrectly, incomplete fields, incorrect or switched details, etc.) Please give Jenny any necessary
corrections as you find these errors. She may also be able to find the original strain information and
correct the database entry. (Duplicate but correct entries are a lesser concern.)
V. Notebooks
A description of the laboratory protocols and results from experiments must be written in laboratory
notebooks. Each experiment must have a date and include enough detail for somebody else to
reproduce the results. The information in your notebook must be in English.
Notebooks may be saved electronically (e.g., Omni Outliner for notebooks, Keynote for
presentations). Consult Eduardo if considering this option.
VI. Computer Backups
Most computers in our lab have the Tivoli centralized backup system (TSM) installed.
All (new) data is backed up to the Yale server automatically every night at 7:30 p.m.
 Backup status
Jenny will receive error messages and notify you if any computers do not successfully complete
backups. She will also label computers that are not part of the backup system. You can use your
computer’s nodename (“EGLAB#” from Jenny) to check backup status, change settings and get more
information at: http://www.yale.edu/its/accounts/backup.html.
 To add a computer to the backup system
1) Connect the computer to the network via ethernet cable. Also notify ITS 2-9000 if registering a
new device on the network or registering device to new user.
2) Give Jenny:
Computer Name/Processor
MAC: System Preferences – Network – Advanced – WINS – NetBIOS name
or
PC: Start – Type “system” in search box – System Information – Processor
IP/Physical Address
MAC: System Preferences – Network – Advanced – Hardware – MAC address
or
PC: http://www.yale.edu/its/network/ip_and_nic/.
3) PCs especially must have current anti-virus software (Yale Software Library)
4) Your computer must be powered on and connected to the network during the scheduled
backup time. Do not use sleep mode, system standby or hibernate. Increase power
management inactivity timeout to ensure your system is awake for the scheduled backup
window.
 To change or cancel backups
Notify Jenny if a computer no longer needs backups (this impacts our ITS charges) and if a computer
is moved. (Also notify ITS at 2-9000 if computer moved to a new building.)
VII. Meetings and Presentations
All meeting schedules are posted on our lab website.
 Hosting Journal Club
One week prior, email paper to lab members.
Presentation:
o Novel approaches that are “off the beaten track”
o Conclusions that might be challenged
o Be familiar with not only the paper and supporting material but also related work.
 Hosting Lab Meeting
o One day prior, email Eduardo your presentation and Materials and Methods/Conditions.
o For first lab meeting presentation, include all your work to that date and email Jenny
your draft presentation one week prior.
o See also PART TWO below.
Subsequent presentations:
o General background or context of your research (if you are discussing the same topic)
o Last slide of previous presentation
o Clear overall hypothesis for presentation
~10 min
o Recap all experiments leading to current hypothesis
o It may be useful to present a working model before you tell your results
o Clear hypothesis for each experiment in presentation
o Results and ideas developed since your last presentation
Slide titles should state a result or conclusion rather than an experimental method.
~30 min
~10 min
o Outline questions still unanswered and how you will answer them.
Use the group to find alternative approaches and/or to change the project’s direction.
 Daily Discussions
You will have a scheduled time to meet with Eduardo every 3-4 weeks. However, Eduardo is always
eager to learn about new, exciting findings and happy to help you sort out any difficult experiments.
Thus, you can always see him outside the scheduled time slot.
 Presentations
If you have an upcoming postdoc or other formal presentation, it is recommended that you practice
your talk in front of Jenny and/or lab members at least one week in advance or that you send Jenny
your slides for feedback. Eduardo is also happy to hear your practice talk after you have received
input from others and made revisions.
VIII. Ordering
For all lab or office products – including primers, mice, and radioactive items – see the “Ordering
Guide” on our lab website.
 Always check if anyone has recently ordered the products you want.
 When we receive items, check that shipment is correct and complete.
 Put all packing slips and receipts in BCMM lab wall folder for Jenny.
When possible, conserve lab resources: printing/two-sided/black-white, orders, reimbursements.
IX. Shipping
 Documents
To ship documents only, give your shipping details to Jenny to create a shipment or to create labels
for receiving a shipment via FedEx.
 Materials
To ship all biological or chemical materials, give your content and shipping details to our designated
lab shipping person (see Lab Duties list) to create a shipment or to create labels for receiving a
shipment via eShipGlobal: http://yalebiz.yale.edu/transactions/express-shipping.
Give our lab shipping person:
• Sender name, address, phone and e-mail
• Recipient name, address, phone and e-mail
• Description of materials to be sent or received, approximate package size and weight.
X. Travel
Always let Eduardo know (cc: Jenny) your vacation and travel plans as well in advance as possible.
For lab-related travel expense reimbursements:
 Book flight/hotel as soon as possible to get a reasonable price
 Make sure length of stay corresponds to lab business
 Share expenses (hotel, transportation, etc.) with other lab members when possible
 Give Jenny original detailed receipts (plane ticket/boarding passes to and from destination,
itemized meal receipts, hotel charges itemized by date, etc.)
XI. Lab Departure
Please inform Eduardo as soon as possible if considering leaving the lab. Even the possibility of
departure has implications for the research of other lab members. Then, complete the Lab Departure
Checklist from Jenny.
XII. Lab Duties
DUTY
Prepare bench, whole lab for inspections:
EHS, State Health Dept., et al.
Order items routinely used by lab:
tubes, pipet tips, cuvettes, etc.
Radioactivity: waste disposal, room
1
maintenance, Quarterly inventory,
Yearly training, Safety officer
Biological Safety: contact person for
2
EHS, call for waste pick-up,
requesting sufficient supplies
Chemical Safety: Maintaining a clean
3
chemical storage bay, chemicals in
desiccators
*Real-time PCR machine, PCR
4
machines: maintenance, contact
person for first-time users
5
6
7
8
9
10
11
*Phosphoimager: maintenance
*Water baths: water levels,
Incubators: maintenance
Shipping/Receiving strains, plasmids,
non-documents
Clean gel electrophoresis room or
bench
*Organizing and maintaining -80
freezers: scrape ice off doors, freezers
maintenance, samples accessible
*Synergy/ Victor 3: maintenance,
contact person for first-time users
*Microplate reader and
spectrophotometer: maintenance,
contact person for first-time users
WEST
BCMM
EVERYBODY 
Anyone who takes item near end of box
(Eunjin/Kerry)
(…Jinki?/Varsha)
KERRY
GUY/ANASTASIA
SUN-YANG
JOHN/ANASTASIA
MAURICIO
VARSHA/NATHAN
EUNJIN
VARSHA
KERRY
GUY
MICHELLE
Temp / …Jinki?
MAURICIO
NATHAN
MICHELLE
VARSHA
KERRY
JEONGJOON
EUNJIN
Temp / …Jinki?
SUN-YANG
KYLE
12
*Centrifuge and microfuge
MICHELLE
NATHAN
13
*Printers: check/replace/order toner
SUN-YANG
JEONGJOON
14
Balances: maintaining clean balances,
calibration
EUNJIN
JOHN
15
*Millipore water purifier: maintenance
MAURICIO
KYLE
* Duties for machine maintenance include contacting companies for service, repairs, quotes, etc.
See Jenny re: service agreements, company contacts, quotes (include “HHMI/Yale”).
XIII. The Basics
Basic Microbiological Practices and Procedures
The following practices, corresponding to Biosafety Level 2, are important for the prevention of
laboratory infection and disease and reduce contamination of experimental material. These practices
provide the foundation for the more restrictive containment of RG3 organisms.
Personal Hygiene
 DO not eat, drink, chew gum, use tobacco, apply cosmetics or handle contact lenses in
the laboratory.
 Do not store food for human consumption in laboratory refrigerators.
 Wash hands frequently after handling infectious materials, after removing rubber
gloves and protective clothing, and always before leaving the laboratory.
 Keep hands away from mouth, nose, eyes, face and hair.
 Do not store personal items such as coats, boots, bags and books in the laboratory.
Laboratory Procedures for Handling Infectious Microorganisms
 Wear a fully fastened laboratory coat when working with infectious agents.
 Wear protective gloves whenever handling potentially hazardous materials, including human
blood and body fluids.
 Remove all protective clothing, including gloves, and leave within the
laboratory before exiting.
 Never mouth-pipette; use mechanical pipetting devices.
 When practical, perform all aerosol-producing procedures such as shaking,
grinding, sonicating, mixing, and blending in a properly operating biological safety cabinet. Note that
some equipment may compromise cabinet function by disturbing the air curtain.
 Centrifuge materials containing infectious agents in unbreakable, closable
tubes. Use a centrifuge with sealed heads or screw-capped safety cups. After centrifugation, open
the tubes in a biological safety cabinet.
 Avoid using needles and syringes whenever possible. If it is necessary to
use them, discard used syringe-needle units in a sharps container without removing or re-capping the
needles.
 Cover counter tops where hazardous materials are used with plastic-backed
disposable paper to absorb spills.
 Wipe work surfaces with an appropriate disinfectant after experiments
and immediately after spills.
 Decontaminate all infected materials by appropriate methods before disposal.
 Report all accidents and spills to the laboratory supervisor. All laboratory
personnel should be familiar with the emergency spill protocol and the location of clean-up
equipment.
 Good housekeeping practices are essential in laboratories engaged in work
with infectious microorganisms. Establish the habit of weekly cleaning.
 Be sure to advise custodial staff of hazardous areas and places they are not to
enter. Use appropriate warning signs.
 All chemical containers are to be dated upon opening.
Bench Basics - A
 All bottles kept at benches and in coolers are to be labeled (formula included). Bottles with
formulas listed at the end of benches may be labeled in an abbreviated form.
 All chemical bottle containers must be intact. Dispose of any chemical bottle if the lid breaks
or does not secure completely.
 All hazardous chemicals must be stored in isolation boxes. One chemical per box.
 Chemical bottles may not be left in the hood area or on the floor.
 All chemical bottles need to be dated at the time they are received into the lab.
 Hazardous chemicals may not be taken to benches or left on individuals’ shelves (acids and
alcohol included).
 Pipettes must be stored on benches not on shelves.
 Burners must be turned off and not left unattended.
 Sharps may not be left loose on any bench or counter. Place in a Petri dish and dispose of in
sharps container.
 Lab coats must be worn when working at a bench.
 All food and beverages must be kept in the breakroom. Door to the breakroom must be kept
closed. No eating or drinking in the lab or in the hallway. Please do not dispose of any cups or
wrappers in lab trashcans, as it will be viewed as evidence of eating in the lab.
Bench Basics - B
 Lab coats are to be worn at all times.
 Goggles are to be worn when working with chemicals, preparing solutions, etc.
 Rubber gloves, sterile surgical or disposable latex are to be used for all procedures involving
animals or chemicals, depending on whether sterile precautions are required.
 Fume hoods are to be used with any appreciably volatile substance with a Threshold Limit
value (TL) of less than 50ppm.
 Do not use mouth suction for pipeting or starting a siphon.
 Do not work alone if the procedures being conducted are hazardous.
 There are presently no procedures in use involving electrical hazards.
 Acids and bases are to be stored separately.
 Flammable agents are to be stored in a “flammable cabinet”.
 Deposit chemical waste in closed, suitably labeled containers.
 Sharps are to be placed in a sharps container.
 Follow YSM policies in case of accidents or spills: www.yale.edu/ehs/emergency.htm
 Standard operating procedures are described in: I. Binding interactions of convulsant and
anticonvulsant γ-thiobutyrolcatones with the picrotoxin receptor. J. Pharmacology & Experimental
Therapeutics, 254(2), 578-583, 1990. II. Comparison of the anticonvulsant activities of Ethosuximide,
Valproate, and a new anticonvulsant, thiobutyrolactone. Epilepsia, 30(5): 617-622, 1989.
PART TWO:
I. Posters
You can e-mail posters to Jenny for printing. In your e-mail, please include:
- attached pdf of poster
- type and version of software used to create poster
- output size (larger than 24”x36” ok but much higher price bracket).
- date and time needed (delivery to BCMM)
Yale Printing (ypps.yale.edu) can handle 1-2 day requests, but submit orders to Jenny at least 3 days
in advance to ensure proof approval before final printing.
Optional: Yale/HHMI-approved logos are on our lab website.
II. Figures and Graphics
These guidelines can help an audience understand your data.
Be as consistent as possible with respect to:
- Alignment: align figures with each other, center images.
- Font: Helvetica
- Format: colors, lines, shapes, arrows, size, direction, boxes, glow, highlight, bold, shading…
- Copy and paste the same objects as you create and revise figures
Use these details only to the extent that they clarify the meaning of your data.
- Labels: use direct labeling instead of keys when possible.
- Logos: avoid logos or use HHMI/Yale-approved logos only.
- Resolution: use the highest resolution possible, e.g., use a table created from original data
rather than a copied image of the table.
- Sparklines: consider using sparklines for time series or other data to show obvious differences.
- Supergraphics: consider creating a single-panel graphical abstract to represent only the main
message of your presentation or manuscript.
- Words: use consistent phrasing in titles and legends.
Slide titles should state a result or conclusion rather than an experimental method.
III. Manuscript Guidelines
 Outline the exact scope with Eduardo before writing: working title, main message, results to
be included, discussion.
 All manuscripts should start in the correct submission format of the journal you have in mind:
font, capitalization, indentation, section titles, references, etc.
 Ask Jenny, lab members to review your manuscript at any stage before submitting to Eduardo.
 Be consistent:
o Follow a similar paragraph structure throughout manuscript
o Check that each sentence and figure directly relates to your title
o Introduction and Discussion should be clear to a general audience
o Use language consistent with previously published Groisman lab manuscripts, including
in the Materials and Methods section
 See Eduardo’s “On Writing Manuscripts” and the “Guidelines for Manuscript Reviewers” below.
IV. Abstract Outline
It is suggested that you write an abstract at the outset to choose the best take-home message and
scope for your manuscript.
First sentence:
General statement of known biological or chemical process as it usually or normally functions.
Field level (general biology, general chemistry, general medicine).
You are talking to an undergraduate student.
Second sentence:
Continuance of general statement or statement of alternative process.
Field level.
Third sentence:
What is the main question that the research shown in the manuscript will address?
Lab level.
You are talking to a visiting graduate student.
Have in mind a direct connection between your question and the overall goals of the Groisman lab.
This may be the first sentence you write.
Two-three sentences:
Main results of research in the manuscript only, including key terms and processes.
Lab level.
First to last sentence:
Answer to question in third sentence.
Lab level.
Dictates title.
Last sentence:
Significance of results to everyone.
Global level.
You are talking to a movie audience.
Place your single most important result within the context of global applications or understandings
(e.g., evolution, medicine).
V. Guidelines for Manuscript Reviewers
General considerations:
o Is the paper important?
o Is the work original? Does the work add enough to what is already in the literature?
o Is there a clear message?
o Does the paper read well and make sense?
o Is this journal the right place for this paper?
Scientific reliability:
o Abstract/summary — does it reflect accurately what the paper says?
o Research question — is it clearly defined and appropriately answered?
o Overall design of study — is it adequate?
o Participants studied — are they adequately described and their conditions defined?
o Methods — are they adequately described? For randomized trials: CONSORT Ethical?
o Results — does it answer the research question? Credible? Well presented?
o Usefulness of tables and figures? Is the quality good enough? Can some eliminated? Is
the data correct in the tables?
o Interpretation and conclusions — are they warranted by and sufficiently derived
from/focused on the data? Message clear?
o References — are they up to date and relevant? Any glaring omissions?
http://www.journals.asm.org/misc/reviewguide.dtl
Please consider the following aspects when reviewing a manuscript:
 Significance to the target scientific community
 Originality
 Appropriateness of the approach or experimental design
 Appropriateness of the statistical analyses
 Adherence to correct scientific nomenclature
 Appropriate literature citations
 Adequacy of experimental techniques
 Soundness of conclusions and interpretation
 Relevance of discussion
 Organization
 Adherence to the Instructions to Authors
 Adequacy of title and abstract
 Appropriateness of figures and tables
 Appropriateness of supplemental material intended for posting (if applicable)
 Length
 Whether it describes misuse of microbial systems or the information derived therefrom
http://www.plosbiology.org/static/reviewerGuidelines.action
The manuscript must be exceptional in the following ways:
 Originality
 Importance to researchers in its field
 Interest to scientists outside the field
 Rigorous methodology and substantial evidence for its conclusions
http://www.ejssm.org/ReviewGuidelines.html#content
A. Scientific content
Although there can be no simple formula for what is acceptable scientific content, there are some
basic principles that generally apply. The standards for a manuscript depend somewhat on the
category of submission, but there are some general guidelines.
1. References in support of an assertion. Generally, references are used to provide support for
assertions within a paper. There is no simple way to determine what assertions do or do not
require substantiation. It is within the purview of a reviewer to request references if the
reviewer believes a reference is needed where none was provided. The use of "principal
source" references (e.g., the original source of information) is encouraged whenever possible.
Generally, refereed publications are more acceptable for this purpose than unrefereed
material. Thus, if the author uses an unrefereed reference, this may not be considered
acceptable support. The availability of unrefereed manuscripts is a major issue with their use in
support of an assertion within the manuscript, and the author can be asked to provide a copy
of such to the reviewer.
2. Speculation. For the most part, speculation in a scientific manuscript is not acceptable.
Speculation is defined as an unsubstantiated assertion or hypothesis. Very limited speculation
is possible but it should be confined to the end of a manuscript, within a "discussion" of the
paper’s content or areas of future research, and it should be identified clearly as speculation.
3. Significance of results. Whenever possible, authors are expected to analyze the statistical
significance of their calculations. The use of statistical analysis to assess the confidence that
can be placed on a calculation based on real data is essential to any scientific paper.
Generally, failure to provide statistical analysis of results is not acceptable. Sample size is an
important aspect of statistical confidence limits and small samples need to be identified as
such. Verification of forecasting schemes should be as extensive as possible and any
limitations to the credibility of a verification analysis, such as failing to consider false alarms, or
correct predictions of nonevents, need to be identified.
4. Reproducibility. It should be possible for anyone reading the manuscript to reproduce the
results. The manuscript, therefore, should provide any and all information necessary for a
reader to repeat any analysis contained therein. Any withholding of needed information is
unacceptable. However, it is acceptable to use references to accomplish this. To the maximum
extent possible consistent with a concise presentation, a manuscript should be self-contained.
Extensive mathematical derivations can be moved to an Appendix. Large datasets and
detailed software information need not be provided, although it is encouraged to make
software and data available whenever possible, perhaps by the World Wide Web or in an
unrefereed technical paper.
5. Proof. Reviewers should recognize that in a formal sense, "proof" of scientific ideas is never
possible. Proof is feasible in pure mathematics, but it not possible in science that uses
experimental data or observations in support of ideas. Thus, it is not appropriate for a reviewer
to ask for proof, unless it refers to mathematical issues. Rather, it is appropriate to review how
convincing the supporting analysis is in terms of accepting some hypothesis. The rigor of the
test is the primary means of judging how convincing the evidence is. Data sample size,
accuracy and precision of the data, and the degree to which the data permit an unambiguous
interpretation all are part of a convincing argument. Thus, these are all fair issues for a
reviewer to consider when reviewing the scientific content. Of course, for mathematical
content, the logic must follow the appropriate rules without error, including such issues as the
existence and uniqueness of solutions.
6. Relevance. The only issue of the relevance of a paper that is appropriate for a reviewer to
consider is whether or not the content of the presentation fit within the guidelines of what is
acceptable content for the EJSSM. Otherwise, it is not up to the reviewer to assess the
relevance of a manuscript for publication in EJSSM.
7. Originality. It is our belief that papers reproducing already published work may or may not be
acceptable. If the manuscript simply reproduces the results of an already published work with
no change and adds nothing else, this is probably not acceptable. In some cases, it is valuable
to the community if a particular piece of work can be confirmed (see item d). In particular, if the
analysis methods of an already published work are reproduced, but with a different set of data,
or an expanded data set, this is quite likely to be acceptable.
8. Comparisons with existing work. To the maximum extent possible, comparisons within a
manuscript with already published work should be as unambiguous as possible. If a
comparison with previous work is made, the same definitions should be used, as well as the
same data. If it is felt that the definitions and/or data of an existing work have problems, then a
comparison with that existing work should be done both with the original definitions and/or
data, as well as with the changed definitions and/or data.
9. Negative results. The EJSSM Editorial Board has determined that papers reporting negative
results may or may not be acceptable for publication. Based on the reviews, the Editor decides
whether to accept any manuscript reporting negative results for an experiment or analysis. We
believe that negative results can be useful to the scientific community.
B. Quality of presentation
Again, there is no simple formula to follow for a successful presentation. The Editorial Board is quite
agreeable to accepting a variety of stylistic choices, permitting authors to express themselves in their
own unique way. The EJSSM will generally follow the American Meteorological Society’s guidelines
for basic style issues, since those formats are familiar to most of our authors, but the EJSSM will
allow extra flexibility, including allowing the use of first person within the text, references within an
abstract, etc. Reviewers can find the American Meteorological Society’s Author’s Guide online at .
Here are some basic recommendations for authors to follow and reviewers to consider.
1. Quality of figures. Figures should be legible as well as easy to read and understand.
Generally, figures provide supporting documentation and illustrate some important point within
the paper. Thus, reviewers should pay close attention to the figures and offer specific
suggestions for changing them, if need be, to help the authors improve the presentation.
2. Quality of the English. For nonnative English speakers, and perhaps even for some native
English speakers, the grammar, spelling, usage, and punctuation of the text are very important
for an effective presentation. EJSSM Editor(s) will not put a paper into review if the English
presentation is inadequate. Furthermore, if the reviewer feels the paper is not readable, the
reviewer may reject such a paper on those grounds alone.
3. Organization. The quality of presentation includes the issue of how the paper is organized. To
some extent, the organization of the content is a style issue and the author should be allowed
to do whatever s/he wishes, provided the resulting content can be followed reasonably easily.
However, it is appropriate for a reviewer to make recommendations for reorganizing a paper’s
content in an effort to improve the presentation. Again, there is no magic formula for a proper
organization, but this is fair game for a reviewer.
4. Completeness. An important issue is whether or not everything that needs to be in the
manuscript is actually there. Of particular significance is that all the literature citations should
be included in the reference list, and all the items in the reference list should actually be cited
somewhere in the text. All figures and tables should have captions that describe their content
sufficiently well that interpretation of their content is straightforward. Equations in the text need
not all be numbered, but all equations cited in the text should have numbers.
C. Manuscript length
Although electronic publishing is inherently less concerned with space limitations than printed
journals, the Editorial Board wishes to keep manuscripts within some bounds. Hence, any manuscript
that exceeds 32 pages in length (title page, abstract, text of manuscript, and acknowledgments),
double-spaced and using 12-point font, will need to receive special permission from the Editor. Thus,
it is in the author’s interest to avoid deadwood in the text, such as extensive description of the figures,
using figures of dubious relevance to the material, or repeating the content of figure captions in the
text, which are common problems with submitted manuscripts. Reviewers should be prepared to offer
specific suggestions for shortening long manuscripts.
When reviewers offer suggestions, it is common to ask for more supporting evidence and additional
analysis. Please keep in mind that when the paper is at or near the length limit, asking for more
material will put the author in the position of having to remove other content to stay within the length
limit. Please be considerate of the author when asking for additional material and offer suggestions
where the manuscript can be trimmed to make room for the requested content.
D. Unreviewed content
Sometimes, reviewers choose to not review some parts of the content, for any of a number of
reasons. If, for any reason, a review does not consider some part of the manuscript’s content, that
should be specifically noted by the reviewer. Examples might include the details of a mathematical
derivation, or some aspect of the paper upon which the reviewer is not qualified to comment. There
can be many good reasons for this, but it is important for the reviewer to inform the Editor about any
such omission.
http://www.embomolmed.org/view/0/reviewerInstruction.html
Criteria for Publication
1. Technical quality (including statistical analysis)
2. Strong evidence for the conclusions that are drawn
3. Novelty
4. Medical impact
5. Adequacy of model system
6. Clarity and interest for the non-specialist
All material for the reviews section is critically evaluated for compliance with the following criteria:
7. General interest and medical relevance
8. Novelty/timeliness
9. Clarity for the non-specialist
10. Balance
11. Use of figures and tables
12. Depth of analysis: integration and analysis of the literature cited
http://www.nature.com/authors/policies/peer_review.html
Nature journals receive many more submissions than they can publish. Therefore, we ask peerreviewers to keep in mind that every paper that is accepted means that another good paper must be
rejected. To be published in a Nature journal, a paper should meet four general criteria:
 Provides strong evidence for its conclusions.
 Novel (we do not consider meeting report abstracts and preprints on community servers to
compromise novelty).
 Of extreme importance to scientists in the specific field.
 Ideally, interesting to researchers in other related disciplines.
In general, to be acceptable, a paper should represent an advance in understanding likely to
influence thinking in the field. There should be a discernible reason why the work deserves the
visibility of publication in a Nature journal rather than the best of the specialist journals.
http://www.sciencemag.org/site/feature/contribinfo/refinstr.xhtml
Research Articles should report a major breakthrough in a particular field. They should be in the top
20% of the papers that Science publishes and be of strong interdisciplinary interest or unusual
interest to the specialist.
Technical Rigor: Evaluate whether, or to what extent, the data and methods substantiate the
conclusions and interpretations. If appropriate, indicate what additional data and information are
needed to validate the conclusions or support the interpretations.
Novelty: Indicate in your review if the conclusions are novel or are too similar to work already
published.
Supporting Online Material. Supporting online material includes methods, text or data that is of
interest only to the specialist, but that is still necessary for the integrity and excellence of the paper. It
must be directly related to the conclusions of the print paper. We welcome suggestions for deletions
of supporting online material or items that should be moved to supporting online material.
http://www.springer.com/biomed/pharmaceutical+science/journal/12248
• Is the information presented of significant interest to the readership of the AAPS e-journals?
• Is the title of the manuscript accurate, and does it sufficiently describe the content of the
manuscript?
• Is the purpose or objective of the manuscript clearly stated?
• Are the methods appropriate and scientifically sound?
• If the manuscript is based on data, do the data represent an adequate population? Is a valid
statistical justification included to support the conclusions?
• Are appropriate statistical tests used?
• Are the tables and figures well designed? Do they add to the understanding of the text? Is the
information presented in the tables and figures redundant?
• Are the references cited the most appropriate to support the manuscript?
www.jyi.org
Writing a Scientific Manuscript
Writing Style
Void of anecdotes or stories
Reports facts not outlandish conclusions
No misspellings
Grammatical accuracy
Meets formatting guidelines
Avoids using the first person
Write for your target audience
Word Choice
Examine vs. Analyze
Activity to gain knowledge vs. Describing the analysis of that knowledge
Bloom’s Taxonomy & Word Choice
Knowledge: Recitation of fact
Found, identified, labeled
Comprehension: State a problem or interpret fact
Discuss, predict, compare
Application: Apply old information to solve new problems
Solve, show, examine, classify
Analysis: Used to explain patterns or meaning
Analyze, investigate, compare, contrast
Synthesis: Making predictions or discussing possibilities
Predict, plan, devise, propose
Evaluation: Drawing conclusions, making recommendations
Justify, verify, argue, recommend, determine
Manuscript Structure
Abstract
Summary of Manuscript (200-300 Words)
Problem investigated
Purpose of Research
Methods
Results
Conclusion
Abstract
Common Mistakes
Too much background or methods information
Figures or images
References to other literature, figures or images
Abbreviations or acronyms
Introduction
Broad information on topic
Previous research
Narrower background information
Need for study
Focus of paper
Hypothesis
Summary of problem (selling point)
Overall 300-500 words
Introduction: Common Mistakes
Too much or not enough information
Unclear purpose
Lists
Confusing structure
First-Person anecdotes
Methods and Materials
Provides instruction on exactly how to repeat experiment
Subjects
Sample preparation techniques
Sample origins
Field site description
Data collection protocol
Data analysis techniques
Any computer programs used
Description of equipment and its use
Methods and Materials: Common Mistakes
Too little information
Information from Introduction
Verbosity
Results/ sources of error reported
Results
Objective presentation of experiment results
Summary of data
NOT a Discussion!
Results: Common mistakes
Raw data
Redundancy
Discussion and interpretation of data
No figures or tables
Methods/materials reported
Discussion
Interpret results
Did the study confirm/deny the hypothesis?
If not, did the results provide an alternative hypothesis? What interpretation can be made?
Do results agree with other research? Sources of error/anomalous data?
Implications of study for field
Suggestions for improvement and future research?
Relate to previous research
Discussion: Common Mistakes
Combined with Results
New results discussed
Broad statements
Incorrectly discussing inconclusive results
Ambiguous data sources
Missing information
Figures and Tables
Tables
Presents lists of numbers/ text in columns
Figures
Visual representation of results or illustration of concepts/methods
Captions
Must be stand-alone
Guidelines for Figures and Tables
High resolution
Neat, legible labels
Simple
Clearly formatted
Indicate error
Detailed captions
References
Check specific referencing style of journal
Should reference:
Peer-reviewed journal articles, abstracts, books
Should not reference:
Non-peer-reviewed works, textbooks, personal communications
References: Common Mistakes
Format, Format, Format
(Figures & Tables, Equations, and References)
Redundant Information
Text, Figures, Tables, and Captions
Type of Reference
VI.
Our introduction is
typically two pages.