Writing a Manuscript for the Journal of Biological Chemistry

1. Writing a Manuscript for the Journal of Biological Chemistry PHSC 327L Molecular Biology Lab: The Long Lab Report

2. PHSC 327L Molecular Biology Lab:The Long Lab Report • The purpose of this is to: • Demonstrate that you have a clear understanding of what was done in the experiments and why. • Have you draw together all the lab experiments into it’s actual cohesive whole. • Show that you can clearly, concisely, and carefully organize and communicate scientifically the major project of this course.

3. PHSC 327L Molecular Biology Lab:The Long Lab Report • The report will include all the experiment from the beginning up through PCR. • Do not leave writing this until the end. • Sections of the Experimental Procedures and Results can be written up before and then carefully and logically blended together in the final long report. • You will have figures and table on your data. Use Excel or similar graphing programs.

4. A Regular Paper A Regular paper is the normal medium of publication. Although there is no fixed length, Regular papers should be as concise as possible, while providing sufficient information for the work to be repeated and for the claims of the authors to be judged by the readers.

5. Organization of the Manuscript I (a) title, author(s), and complete name(s) of institution(s)   (b) running title   (c) summary   (d) introduction   (e) experimental procedures   (f) results

6. Organization of the Manuscript II (g) discussion   (h) references   (i) footnotes   (j) figure legends   (k) tables   (l) figures

7. Manuscript Title • Should be as short and informative as possible •   Should not contain non-standard acronyms or abbreviations •   Should not exceed two printed lines

8. Manuscript Title Page The title page should contain the names of all authors and their complete institutional mailing addresses   Corresponding author: the author to whom all correspondence about the manuscript, including proofs, will be sent:   a) name   b) telephone and fax numbers   c) email address Running Title

9. The Running Title • The running title is indicated on the title page; • Running title: This is the Running Title • will be at the top of each printed page • cannot exceed 60 characters and spaces

10. The Summary • Should succinctly and clearly describe the major findings reported in the manuscript. • Should indicate the major techniques and methods used. • Must not exceed 200 words nor contain abbreviations or specialized terms. • Should be understandable in itself, since it is frequently used as an abstract. • should be self-explanatory and intelligible without reference to the body of the paper.

11. Experimental Procedures I • Bebrief, but sufficiently complete to permit a qualified reader to repeat the experiments reported • Describe your procedures in detail in contrast to actual submitted manuscripts where they have different requirements (In an actual submitted manuscript only truly new procedures would be described in detail) •   Cite previously published procedures in References •   Modifications of previously published procedures not given in detail except when necessary to repeat the work

12. Experimental Procedures II • Procedures should be logically organized. • Different Procedures should have an italic subheading at the beginning of the paragraph. • Agarose Electrophoresis - Procedures for agarose … • Experimental Procedures are written in the past tense! • Electrophoresis was performed • If you refer to a buffer or medium for the first time indicate its composition. • Lysis buffer ( 200 mM NaOH, 1% w/v sodium dodecyl sulfate) was used to lyse bacterial cells.

13. Experimental Procedures III • The Experimental Procedures should be written in paragraphs using clear English sentences. • Your results are NOT described in the Procedures. • You can indicate what a positive or negative result WOULD or SHOULD BE if it determines how the rest of the procedures are followed.

14. Experimental Procedures IV • Materials and Equipment • You should have a paragraph indicating where your chemicals and special reagents, etc., came from. • EcoR I (lot XXXX) was purchased from Promega (Madison, WI). • See JBC example.

15. Results I • The results section should be written in paragraph form with clear concise sentences. • Use paragraph subheadings to logically organize your results section. • Present your results do not discuss or explain them. • The results section is typically written in the past tense. This is, in part, because the results are not validated as accepted fact. The result of a calculation may be written in the present tense.

16. Results II • Most of the data is best presented in figures and tables which are referred to in the text but are placed at the end of the manuscript. You will have figures and tables in your results. • Pay attention to the instructions for figure and table legends. •  Some results not requiring documentation may be given solely in the text. Upon addition of reagent X a clear and viscous supernatant was observed. • The citation of a figure or table can be as follows: • Short, 1000 bp, restriction fragments were detected (Fig. 1).

17. Discussion • Be concise (usually less than four typed pages) • Focus on the interpretation of the results rather than a repetition of the Results section. • Authors should always refer to other work on the same subject, indicating whether or not their experimental results are in agreement with previous work. Place your work in scientific context. • The overall conclusions based on the work reported should be given in the Discussion.

18. Discussion II • Known, published facts are considered to be true and are referred to in the present tense. Bacteria contain plasmids. • Work that is submitted for publication is referred to in the past tense. We determined… We concluded • The results of calculations are typically referred to in the present tense where appropriate.

19. References • cited in text by number rather than author and date •  numbered consecutively in the order of appearance in the manuscript

20. References II References for journals and books should be in the following styles: 1. MacDonald, G. M., Steenhuis, J. J., and Barry, B. A. (1995) J. Biol. Chem. 270, 8420-8428 2. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

21. Abbreviations All abbreviations used in the text must be defined in a single footnote inserted in the text immediately after the first abbreviation is cited. The abbreviations of some important biochemical compounds, e.g. ATP, NADH, DNA, and amino acids in proteins, need not be defined. Phrases such as "central nervous system" or "red blood cells" should not be abbreviated. Names of enzymes are usually not abbreviated except in terms of the substrates for which there are accepted abbreviations, e.g. ATPase and RNase.

22. Tables • The base pair length analyses of your plasmid DNA restriction digest may be suitable as a table. • Tables should have titles and sufficient experimental detail in a legend immediately following the title to be understandable without reference to the text. • Each column in a table must have a heading, and abbreviations, when necessary, should be defined in the legend. • Each table should have a legend. • The legends can be combined on page in the manuscript called table legends.

23. Figures I • Figures are photographs and graphs. Graphs should be done with a graphing program like Excel. • This should include your gel photos (or high quality, legible copies) etc. • Figures should have titles and explanatory legends containing sufficient detail to make the figure easily understood. • All legends should be printed consecutively in a separate section of the manuscript. Appropriately sized numbers, letters, and symbols should be used. Superscript and subscript characters are not excluded from this rule. • Numbers, letters, and symbols used in multi-paneled figures must be consistent.

24. Figures II • The abscissa and ordinate should be clearly labeled with appropriately sized type, and units of measurement must be given. • Scales for plotting the data should be marked by short index lines, but every index line need not be numbered. • Use standard symbols found in MS Word with symbols and curves identified in the legend and not on the figure. Indicate the figure number on the front of each figure.

25. HAVE A GOOD SPRING BREAK!