1. Scientific Writing Getting ready for your formal writing assignments Assembled from various sources, including the BIOL 1208 lab manual (LSU), notes made by Arundhati Bakshi and Warwick Allen, and the presentation “Designing Scientific Posters” by Dr. Becky Carmichael.

2. Notes to the TAs This is meant to be more of an “exercise” for the students, and less of a lecture, despite the format. Assign students most of the slides (excluding the exercise slides) beforehand. Have them read over these notes and bring them to class. Perform the exercises with them, and engage them in the material. Maybe begin each section with, “What did you learn about how to write this section?” as a segue into talking more about it or dispelling misconceptions (encourage questions, what did you think it was vs. what it really was type of questions perhaps), maybe compare to the paper read previously in the semester, and then introduce clicker questions & exercise handouts. Feel free to use your own example abstracts, intros, methods, etc. or maybe pick one from a published paper. The examples provided hee may be freely used with proper attribution. But please feel free to replace any of that with any of your own pieces as you see fit! Some “exercise-slides” have notes on the notes panel on the bottom. ~ Arundhati Bakshi

3. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

4. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

5. Title Should concisely convey the fundamental nature of your research Keep it short and specific but include important aspects of your work Include the scientific name of any organism studied Variable factors manipulated, parameters measured, etc. may be included Sometimes, phrasing the title as a question can be powerful and effective (especially on a poster!!!) Superfluous and redundant words must be avoided

6. Pick an appropriate title for a report describing an experiment studying the effects of light intensities on the rate of photosynthesis in Elodia sprigs in the LSU lakes. A. A biology lab report B. A study of the rate of photosynthesis in Elodia C. The effects of different light intensities on the rate of photosynthesis D. A study of the effects of different light intensities on the rate of photosynthesis in water plant sprigs E. Reducing light intensity reduces photosynthesis in Elodia canadensis in the University Lake system based on water clarity A bit too long but still the most descriptive!

7. Can you make this title better? The Effects of Suburban Greenways on Neotropical Migrant and Forest- Interior Bird Habitat in North Carolina Can Suburban Greenways Provide High Quality Bird Habitat?

8. Can you make this title better? An Evaluation of Temperature-Dependent Sex Determination of Southern Flounder for Aquaculture Water Temperature Determines Sex of Southern Flounder

9. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

10. Abstract Summary of the entire paper in <250 words. One of the first sections in a paper...... That is usually written at the end! We will discuss this at the end!

11. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

12. Introduction (Background) Written in present tense Provides the background for why you did the experiments presented in the paper: relevant background information with citations to other published material (papers, websites, etc.) In-line citations: (Last name of first author, year) or (Last name of first author et al., year) Provides hypotheses for your experiment and your prediction

13. Introduction (Background) The introduction should be developed as a “funnel” – where you go from making broad general statements to getting more specific about your particular experiment. Start each paragraph with a topic sentence. Paragraphs should be cohesive and have a nice flow with good transition statements.

14. Evaluate the EXAMPLE introduction as a group. Checklist:  Does it contain background information and give a general perspective?  Is background information properly referenced?  Does it includes the hypothesis(es) to be tested?  Does it provide a rationale for the experiments performed?  Is the significance of the investigation mentioned? Consider whether or not, or how well, the above points are addressed in the introduction. Give it a score out of 10 and be able to justify why you scored it what you did!

15. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

16. Materials & Methods Written in past tense & narrative form (not step-by-step!) Explains how your experiment was done in a way that someone else, reasonably experienced in the lab, can repeat them based on this description Include experimental details (only) without talking about trivialities in a lab setting

17. Materials & Methods You need to include all relevant & important information here but not trivial things. See examples below : Example 1: Do not say how many tubes were used, but say how many replicates were made. Example 2: You need to say what volumes were used but not what pipets. DO NOT include any results here! Only describe what you did, not what you found. Can include a diagram or flowchart to in a poster!

18. What’s wrong with the Methods? As a group, take the a look at the short Methods section written by a student. Discuss and identify some mistakes made by the student. Identify how the mistakes may be corrected (if appropriate).

19. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

20. Results & Discussion Results: State your results interpreting what it means. Example: How much time the 3 types of glycols took to rupture the RBC relative to each other. Discussion: Interpret your results and state your conclusions. Example: If EG took the least time, then it must be the most permeable. TG took the most time, therefore least permeable.

21. Results & Discussion Results: State your results without interpreting what it means. Includes both tables/figures (with legends) and accompanying explanatory text Talk about what you saw without saying what all of that means Written in past tense & narrative form Discussion: Interpret your results and state your conclusions.

22. EXAMPLE 1 Figure & Figure caption Figure 1. Gel electrophoresis results from the PCR performed to isolate the unUAS that will specifically replace the endogenous RPSh81 promoter. Initials at the top of the gel indicate wells where each student loaded their PCR product. My well is marked with a red asterisk. Important ladder band sizes are indicated to the left of the gel and the expected PCR fragment size to the right of the gel. Figure caption – 1 phrase description of the figure Figure description – explains some of the symbols in the figure, axes meanings, etc.

23. EXAMPLE 2 Figure & Figure caption

24. EXAMPLE 3 Table & Table caption Table 1. Frequency of the “R” allele. Data represent frequency of the “R” allele after 1000 generations from 4 populations of 10,000 rats under high and low Vitamin K availability, and conditions with and without warfarin use. What differences do you see between how a table is presented vs. how a figure is presented in the Results section?

25. EXAMPLE 3 Table & Table caption Table 1. Frequency of the “R” allele. Data represent frequency of the “R” allele after 1000 generations from 4 populations of 10,000 rats under high and low Vitamin K availability, and conditions with and without warfarin use. Note that a Table Caption/description starts with Table 1 (NOT Figure 1) and it is on the TOP of the table (not bottom, like it is with a graph. The table description follows the table caption (the part NOT in bold). Like a figure, a table caption is a one-phrase “title” for the table. The table description goes into a bit more detail about where the numbers actually came from and what they represent. Tables should ONLY contain analyzed data, e.g. average ± stdev. NO RAW DATA tables must be presented in this section.

26. Suggest a figure/table + legend! As a group, decide on one figure or table you would want to include in your report. Draw out a rough sketch of it on the board. Give it a figure/table title and a description (figure/table legend). As a class, provide comments to each group. Keep it constructive!

27. Results & Discussion Results: State your results without interpreting what it means. Discussion: Interpret your results and state your conclusions. Acknowledge all possible explanations of your data here Discuss problems with the experiment and how to improve them How do your data relate to the bigger picture? Written in past tense & narrative form

28. Decide if the statements below belong in the Results or Discussion sections. Statement #1: At all concentrations up to 0.2 M sucrose, the potato cells gained mass. At 0.3 M sucrose, there was no change in mass. Then in 0.4 M and 0.5 M sucrose solutions, the potato lost mass. Statement #2: Since the best fit line through our percent change of mass vs. sucrose concentration data points crossed the “zero mark” at 0.35 M sucrose, we conclude that 0.35 M is the iso-osmotic concentration of our potato cells. A. #1 belongs in Discussion, #2 in Results B. #1 belongs in Results, #2 in Discussion C. Both belong in Results D. Both belong in Discussion

29. NOW let’s talk about the Abstract! (The final section of the paper is the References – we will get to it next)

30. Abstract Brief summary of the entire paper Typically 250 words or less It should include the research question/hypothesis/aim, very brief background (from Introduction), general summary of the methods (from Materials & Methods), significant results (from Results) and conclusions (from Discussion). Write this last, after writing all the other sections! Usually the hardest part to write – write, revise and rewrite!

31. Identify the critical elements from each section within this EXAMPLE abstract Fermentation is a biochemical process used by yeast to convert pyruvate to ethanol and carbon dioxide (CO2), following glycolysis, so as to regenerate NAD+ under anaerobic conditions. However, not all carbohydrate sources can be fermented by yeast. Since glycolysis must precede fermentation and its input substance in glucose, the only carbohydrates that can be fermented are the ones which can first be enzymatically converted to glucose for glycolysis. Here we tested the level of CO2 produced in an hour in water (control), glucose, sucrose, lactose, starch and lactose/lactaid solutions by yeast as a measure of fermentation so as to understand whether yeast has the ability ferment these carbohydrate sources and whether the fermentation occurs at the same rate. We found that that lactose and starch did not produce significantly more CO2 compared to water, indicating that yeast lacks the enzymes to convert these substances to glucose and thus they cannot be fermented. Glucose, sucrose and lactose/lactaid solutions produced the highest levels of CO2 in an hour, indicating that as long as yeast have the enzymes to convert a carbohydrate source to glucose (whether endogenously present or exogenously added, such as in the case of lactose/lactaid solution), it can ferment those carbohydrates.

32. Introduction: Background info, aim Fermentation is a biochemical process used by yeast to convert pyruvate to ethanol and carbon dioxide (CO2), following glycolysis, so as to regenerate NAD+ under anaerobic conditions. However, not all carbohydrate sources can be fermented by yeast. Since glycolysis must precede fermentation and its input substance in glucose, the only carbohydrates that can be fermented are the ones which can first be enzymatically converted to glucose for glycolysis. Here we tested the level of CO2 produced in an hour in water (control), glucose, sucrose, lactose, starch and lactose/lactaid solutions by yeast as a measure of fermentation so as to understand whether yeast has the ability ferment these carbohydrate sources and whether the fermentation occurs at the same rate. We found that that lactose and starch did not produce significantly more CO2 compared to water, indicating that yeast lacks the enzymes to convert these substances to glucose and thus they cannot be fermented. Glucose, sucrose and lactose/lactaid solutions produced the highest levels of CO2 in an hour, indicating that as long as yeast have the enzymes to convert a carbohydrate source to glucose (whether endogenously present or exogenously added, such as in the case of lactose/lactaid solution), it can ferment those carbohydrates.

33. Methods: Summary of what was done Fermentation is a biochemical process used by yeast to convert pyruvate to ethanol and carbon dioxide (CO2), following glycolysis, so as to regenerate NAD+ under anaerobic conditions. However, not all carbohydrate sources can be fermented by yeast. Since glycolysis must precede fermentation and its input substance in glucose, the only carbohydrates that can be fermented are the ones which can first be enzymatically converted to glucose for glycolysis. Here we tested the level of CO2 produced in an hour in water (control), glucose, sucrose, lactose, starch and lactose/lactaid solutions by yeast as a measure of fermentation so as to understand whether yeast has the ability ferment these carbohydrate sources and whether the fermentation occurs at the same rate. We found that that lactose and starch did not produce significantly more CO2 compared to water, indicating that yeast lacks the enzymes to convert these substances to glucose and thus they cannot be fermented. Glucose, sucrose and lactose/lactaid solutions produced the highest levels of CO2 in an hour, indicating that as long as yeast have the enzymes to convert a carbohydrate source to glucose (whether endogenously present or exogenously added, such as in the case of lactose/lactaid solution), it can ferment those carbohydrates.

34. Results: Summary of what you found Fermentation is a biochemical process used by yeast to convert pyruvate to ethanol and carbon dioxide (CO2), following glycolysis, so as to regenerate NAD+ under anaerobic conditions. However, not all carbohydrate sources can be fermented by yeast. Since glycolysis must precede fermentation and its input substance in glucose, the only carbohydrates that can be fermented are the ones which can first be enzymatically converted to glucose for glycolysis. Here we tested the level of CO2 produced in an hour in water (control), glucose, sucrose, lactose, starch and lactose/lactaid solutions by yeast as a measure of fermentation so as to understand whether yeast has the ability ferment these carbohydrate sources and whether the fermentation occurs at the same rate. We found that that lactose and starch did not produce significantly more CO2 compared to water, indicating that yeast lacks the enzymes to convert these substances to glucose and thus they cannot be fermented. Glucose, sucrose and lactose/lactaid solutions produced the highest levels of CO2 in an hour, indicating that as long as yeast have the enzymes to convert a carbohydrate source to glucose (whether endogenously present or exogenously added, such as in the case of lactose/lactaid solution), it can ferment those carbohydrates.

35. Discussion: What the results mean Fermentation is a biochemical process used by yeast to convert pyruvate to ethanol and carbon dioxide (CO2), following glycolysis, so as to regenerate NAD+ under anaerobic conditions. However, not all carbohydrate sources can be fermented by yeast. Since glycolysis must precede fermentation and its input substance in glucose, the only carbohydrates that can be fermented are the ones which can first be enzymatically converted to glucose for glycolysis. Here we tested the level of CO2 produced in an hour in water (control), glucose, sucrose, lactose, starch and lactose/lactaid solutions by yeast as a measure of fermentation so as to understand whether yeast has the ability ferment these carbohydrate sources and whether the fermentation occurs at the same rate. We conclude that that lactose and starch did not produce significantly more CO2 compared to water, indicating that yeast lacks the enzymes to convert these substances to glucose and thus they cannot be fermented. Glucose, sucrose and lactose/lactaid solutions produced the highest levels of CO2 in an hour, indicating that as long as yeast have the enzymes to convert a carbohydrate source to glucose (whether endogenously present or exogenously added, such as in the case of lactose/lactaid solution), it can ferment those carbohydrates.

36. And finally...... The very last section of a scientific paper...

37. Sections in a scientific paper: 1. Title 2. Abstract 3. Introduction (Background) 4. Methods (Materials & Methods) 5. Results 6. Discussion 7. References (Literature cited)

38. References Pay attention to the format! There are several types. We will follow what is below. Scientific Journal: Last name of 1 st author, first initial of 1 st author., Initials of all following authors, last names of all following authors. Year of publication. Title of the paper. Journal name (in italics), issue:page-range. Example: Mazumdar, A. and K.E. Havens. 1998. Nutrient-chlorophyll-Secchi relationships under constrasting grazer communities of temperate versus subtropical lakes. Can. J. Fish. Aquat. Sci. 55: 1652-1662.

39. References Pay attention to the format! There are several types. We will follow what is below. Book : Last name of 1 st author, first initial of 1 st author., Initials of all following authors, last names of all following authors. Year of publication. Book title (in italics). Edition number, Publisher’s name, City of publication, State of publication. Example: Raven, P.H., R.F. Evert, and S.E. Eichhorn. 1992. Biology of Plants. 5 th Ed., Worth Publishers, New York, New York.

40. References Pay attention to the format! There are several types. We will follow what is below. Webpage : Name of the author (when available), date of publication or last revision, date and time of accession. Example: Masser, M.P. 2009, <Water Lettuce, http://aquaplant.tamu.edu/database/floating_plants/http://aquaplant.tamu.edu/database/floating_plants/ water_lettuce.htmwater_lettuce.htm> May 8, 2009 4:10 pm CDT.

41. References Where to find these references for your papers/reports??  Web of Science  Google Scholar  PubMed  What else... What did you come up with??

42. General Tips Be concise. Revise, revise, revise! Read your writing aloud to yourself. Use spellcheck. Have someone else proofread. Look at the writing style of the published paper you read for this class and other suggested readings – try to emulate this in your own writing.